From c1275a09bbb1de9a20b3f4f929f0bc16278f3c4c Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 3 Jul 2024 11:16:22 +0100
Subject: [PATCH 01/71] add functions for testing remotely to init and update
 ipynb testing file

---
 SBML/test_compatibility_biosimulators.ipynb |  74 +++++
 utils/__init__.py                           | 305 ++++++++++++++++++++
 2 files changed, 379 insertions(+)

diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index 11be933..dad638a 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -46,6 +46,80 @@
     "types_dict = utils.types_dict"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'tellurium', 'simulatorVersion': '2.2.1', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': 'ucbtrin@ucl.ac.uk'}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f88f7c08f12e43bea81c13338c1cab4e\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668520e4b18d214607b8560a\n",
+      "View: https://api.biosimulations.org/runs/668520e4b18d214607b8560a\n",
+      "Downloads: https://api.biosimulations.org/results/668520e4b18d214607b8560a/download\n",
+      "Logs: https://api.biosimulations.org/logs/668520e4b18d214607b8560a?includeOutput=true\n",
+      "Downloading results...\n",
+      "Download completed.\n"
+     ]
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
+      ],
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "\u001b[3;92mTrue\u001b[0m"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "#put the sedml and sbml into a combine archive\n",
+    "omex_filepath = utils.create_omex(sedml_filepath,sbml_filepath)\n",
+    "omex_file_name = os.path.basename(omex_filepath)\n",
+    "sim_dict = {\n",
+    "              \"name\": \"test\",\n",
+    "              \"simulator\": \"tellurium\",\n",
+    "              \"simulatorVersion\": \"2.2.1\",\n",
+    "              \"cpus\": 1,\n",
+    "              \"memory\": 8,\n",
+    "              \"maxTime\": 20,\n",
+    "              \"envVars\": [],\n",
+    "              \"purpose\": \"academic\",\n",
+    "              \"email\": \"ucbtrin@ucl.ac.uk\",\n",
+    "            }\n",
+    "\n",
+    "download_link, result = utils.submit_simulation_archive(\\\n",
+    "    archive_file=omex_file_name,\\\n",
+    "    sim_dict=sim_dict)\n",
+    "\n",
+    "utils.download_file(download_link)\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,
diff --git a/utils/__init__.py b/utils/__init__.py
index d0b2fa7..7d0c4f5 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -793,3 +793,308 @@ def safe_md_string(value):
     '''
 
     return str(value).replace("\n"," ").replace("\r","").replace("\t"," ").replace("   "," ").replace("  "," ")
+
+import time
+
+def download_file_from_link(download_link, output_file='results.zip', max_wait_time=120, wait_time=2):
+    """
+    Function to download a file from a given URL.
+
+    Parameters:
+    download_link (str): The URL of the file to download.
+    output_file (str): The name of the file to save the download as. Defaults to 'results.zip'.
+    max_wait_time (int): The maximum time to wait for the file to be ready to download. Defaults to 120 seconds.
+    wait_time (int): The time to wait between checks if the file is ready to download. Defaults to 2 seconds.
+
+    Returns:
+    bool: True if the file was downloaded successfully, False otherwise.
+    """
+
+    start_time = time.time()
+
+    while True:
+        # Check status of download_link
+        response = requests.get(download_link)
+
+        # If status is not 404 or max_wait_time has passed, break the loop
+        if response.status_code != 404 or time.time() - start_time > max_wait_time:
+            break
+
+        # Wait for wait_time seconds before checking again
+        time.sleep(wait_time)
+
+    # If status == 200 then download the results
+    if response.status_code == 200:
+        print('Downloading results...')
+        with requests.get(download_link, stream=True) as r:
+            with open(output_file, 'wb') as f:
+                shutil.copyfileobj(r.raw, f)
+        print('Download completed.')
+        return True
+    else:
+        print('Failed to download the file.')
+        return False
+
+
+#!/usr/bin/env python3
+"""
+Functions related to Biosimulations.org
+
+File: pyneuroml/biosimulations.py
+
+Copyright 2024 NeuroML contributors
+"""
+
+import logging
+import typing
+from datetime import datetime
+
+import requests
+
+from pyneuroml import __version__
+from pyneuroml.annotations import create_annotation
+from pyneuroml.archive import create_combine_archive
+from pyneuroml.runners import run_jneuroml
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+
+try:
+    from pydantic import BaseModel
+    from requests_toolbelt.multipart.encoder import MultipartEncoder
+except ImportError:
+    logger.warning(
+        "Please install optional dependencies to use Biosimulation.org features:"
+    )
+    logger.warning("pip install pyneuroml[combine]")
+
+
+biosimulators_api_url = "https://api.biosimulators.org"
+biosimulations_api_url = "https://api.biosimulations.org"
+
+
+
+
+
+class _SimulationRunApiRequest(BaseModel):
+    """class for runSimulation data
+
+    Based on
+    https://github.com/biosimulations/biosimulations-runutils/blob/dev/biosimulations_runutils/biosim_pipeline/biosim_api.py
+
+    Once biosimulations-runutils is published, we will use their API instead
+    of replicating it ourselves.
+    """
+
+    name: str
+    simulator: str
+    simulatorVersion: str
+    maxTime: int
+    cpus: typing.Optional[int] = None
+    memory: typing.Optional[int] = None
+    purpose: typing.Optional[str] = "academic"
+    email: typing.Optional[str] = None
+    envVars: typing.Optional[typing.List[str]] = []
+
+
+def get_simulator_versions(
+    simulators: typing.Union[str, typing.List[str]] = [
+        "neuron",
+        "netpyne",
+        "tellurium",
+        "pyneuroml",
+        "pyneuroml",
+        "xpp",
+        "brian2",
+        "copasi",
+    ],
+) -> typing.Dict[str, typing.List[str]]:
+    """Get simulator list from biosimulators.
+
+    .. versionadded:: 1.2.10
+
+    :param simulators: a simulator or list of simulators to get versions for
+    :type simulators: str or list(str)
+    :returns: json response from API
+    :rtype: str
+    """
+    if isinstance(simulators, str):
+        simulators = [simulators]
+    all_siminfo = {}  # type: typing.Dict[str, typing.List[str]]
+    for sim in simulators:
+        resp = requests.get(f"{biosimulators_api_url}/simulators/{sim}")
+        siminfo = resp.json()
+        for s in siminfo:
+            try:
+                all_siminfo[s["id"]].append(s["version"])
+            except KeyError:
+                all_siminfo[s["id"]] = [s["version"]]
+
+    return all_siminfo
+
+
+def submit_simulation(
+    rootfile: str,
+    metadata_file: typing.Optional[str] = None,
+    sim_dict: typing.Dict[
+        str, typing.Optional[typing.Union[int, str, typing.List[typing.Any]]]
+    ] = {},
+    dry_run: bool = True,
+):
+    """Submit a simulation to Biosimulations using its REST API
+
+    .. versionadded:: 1.2.10
+
+    :param rootfile: main LEMS or SEDML simulation file
+        If it is a LEMS file, a SEDML file will be generated for it
+    :type rootfile: str
+    :param metadata_file: path to a RDF metadata file to be included in the
+        OMEX archive.  If not provided, a generic one with a title and
+        description will be generated.
+    :type metadata_file: str
+    :param sim_dict: dictionary holding parameters required to send the
+        simulation to biosimulations
+
+        .. code-block:: json
+
+            {
+              "name": "Kockout of gene A",
+              "simulator": "tellurium",
+              "simulatorVersion": "2.2.1",
+              "cpus": 1,
+              "memory": 8,
+              "maxTime": 20,
+              "envVars": [],
+              "purpose": "academic",
+              "email": "info@biosimulations.org",
+            }
+
+        Here, the "name", "simulator", and "simulatorVersion" fields are
+        required. You can use the py::func`get_simulator_versions` function to
+        query Biosimulations or visit https://biosimulators.org/simulators
+
+        See also: "SimulationRun" on this page (at the bottom)
+        https://api.biosimulations.org/#/Simulations/SimulationRunController_createRun
+
+    :type sim_dict: dict
+
+    :returns: the requests.post response object from the submission, or True if dry_run
+
+    """
+    if metadata_file is None:
+        logger.info("No metadata file given, generating one.")
+        metadata_file = "metadata.rdf"
+        with open(metadata_file, "w") as f:
+            annotation = create_annotation(
+                rootfile + ".omex",
+                title=f"Biosimulation of {rootfile} created using PyNeuroML version {__version__}",
+                description=f"Biosimulation of {rootfile} created using PyNeuroML version {__version__}",
+                creation_date=datetime.now().strftime("%Y-%m-%d"),
+            )
+            print(annotation, file=f)
+
+    if rootfile.startswith("LEMS") and rootfile.endswith(".xml"):
+        logger.info("Generating SED-ML file from LEMS file")
+        run_jneuroml("", rootfile, "-sedml")
+        rootfile = rootfile.replace(".xml", ".sedml")
+
+    create_combine_archive(
+        rootfile, zipfile_extension=".omex", extra_files=[metadata_file]
+    )
+
+    return submit_simulation_archive(f"{rootfile}.omex", sim_dict, dry_run=dry_run)
+
+
+def submit_simulation_archive(
+    archive_file: str,
+    sim_dict: typing.Dict[str, typing.Union[int, str, typing.List[str]]] = {},
+    dry_run: bool = False,
+) -> object:
+    """Submit an OMEX archive to biosimulations using the provided simulation run dictionary
+
+    .. versionadded:: 1.2.10
+
+    Note that this function does not validate either the OMEX archive nor the
+    simulation dictionary. It simply submits it to the API.
+
+    :param archive_file: OMEX archive file to submit
+    :type archive_file: str
+    :param sim_dict: dictionary holding parameters required to send the
+        simulation to biosimulations
+
+        .. code-block:: json
+
+            {
+              "name": "Kockout of gene A",
+              "simulator": "tellurium",
+              "simulatorVersion": "2.2.1",
+              "cpus": 1,
+              "memory": 8,
+              "maxTime": 20,
+              "envVars": [],
+              "purpose": "academic",
+              "email": "info@biosimulations.org",
+            }
+
+        Here, the "name", "simulator", and "simulatorVersion" fields are
+        required. You can use the py::func`get_simulator_versions` function to
+        query Biosimulations or visit https://biosimulators.org/simulators
+
+        See also: "SimulationRun" on this page (at the bottom)
+        https://api.biosimulations.org/#/Simulations/SimulationRunController_createRun
+
+    :type sim_dict: dict
+    :returns: the requests.post response object, or True if dry_run
+
+    """
+    api_url = f"{biosimulations_api_url}/runs"
+    logger.debug(f"Sim dict is: {sim_dict}")
+
+    simulation_run_request = _SimulationRunApiRequest(**sim_dict)
+    logger.debug(
+        f"simulation_run_request is {simulation_run_request.model_dump_json()}"
+    )
+
+    with open(archive_file, "rb") as archive_file_handle:
+        multipart_form_data: dict[
+            str,
+            typing.Union[typing.Tuple[str, typing.BinaryIO], typing.Tuple[None, str]],
+        ] = {
+            "file": (archive_file, archive_file_handle),
+            "simulationRun": (None, simulation_run_request.model_dump_json()),
+        }
+
+        logger.debug(f"data is:\n{multipart_form_data}")
+
+        m = MultipartEncoder(fields=multipart_form_data)
+
+        logger.info(f"multipart encoded data is {m}")
+        logger.info(f"with content type: {m.content_type}")
+
+        if dry_run is False:
+            logger.info("Submitting archive to biosimulations")
+            response = requests.post(
+                api_url, data=m, headers={"Content-Type": m.content_type}
+            )  # type: requests.Response
+            if response.status_code != requests.codes.CREATED:
+                response.raise_for_status()
+            else:
+                serv_response = response.json()
+                print(
+                    f"Submitted {archive_file} successfully with id: {serv_response['id']}"
+                )
+                print(f"View: {biosimulations_api_url}/runs/{serv_response['id']}")
+                download_link = f"{biosimulations_api_url}/results/{serv_response['id']}/download"
+                print(
+                    f"Downloads: {download_link}"
+                )
+                print(
+                    f"Logs: {biosimulations_api_url}/logs/{serv_response['id']}?includeOutput=true"
+                )
+                
+        else:
+            response = True
+            print("Dry run, not submitting")
+            print(f"Simulation dictionary: {sim_dict}")
+        
+    return download_link, response
\ No newline at end of file

From fac09896ce51c5238e771fdda08f4d5ea9c34eba Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Wed, 3 Jul 2024 13:02:41 +0100
Subject: [PATCH 02/71] Update non-omv.yml

---
 .github/workflows/non-omv.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index f821bd9..23af47e 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -45,7 +45,7 @@ jobs:
 
     - name: Test validity of files
       run: |
-        pip install pyNeuroML
+        pip install pyNeuroML pyNeuroML[annotations]
         cd SBML
         ./validateAll.sh
 

From 662b7224c2c2c61436a197967eadffbbf8b3546b Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 3 Jul 2024 13:28:46 +0100
Subject: [PATCH 03/71] add unzip_file function and update ipynb for testing

---
 SBML/test_compatibility_biosimulators.ipynb | 196 ++++++++++++++------
 utils/__init__.py                           |  38 +++-
 2 files changed, 176 insertions(+), 58 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index dad638a..097dca6 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -1,5 +1,19 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Biosimulators compatibility"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## set-up"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -32,23 +46,24 @@
     "sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml'\n",
     "sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing\n",
     "\n",
+    "engines = utils.engines\n",
+    "types_dict = utils.types_dict\n",
+    "\n",
     "cwd = os.getcwd()\n",
     "print(cwd)"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 2,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "engines = utils.engines\n",
-    "types_dict = utils.types_dict"
+    "## test compatibility biosimulators remotely\n",
+    "see https://github.com/OpenSourceBrain/SBMLShowcase/issues/32"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -60,7 +75,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f88f7c08f12e43bea81c13338c1cab4e\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a940f1c6daa04b368d7d6890e002d178\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -68,33 +83,22 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668520e4b18d214607b8560a\n",
-      "View: https://api.biosimulations.org/runs/668520e4b18d214607b8560a\n",
-      "Downloads: https://api.biosimulations.org/results/668520e4b18d214607b8560a/download\n",
-      "Logs: https://api.biosimulations.org/logs/668520e4b18d214607b8560a?includeOutput=true\n",
-      "Downloading results...\n",
-      "Download completed.\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 6685273ab18d214607b8564f\n",
+      "View: https://api.biosimulations.org/runs/6685273ab18d214607b8564f\n",
+      "Downloads: https://api.biosimulations.org/results/6685273ab18d214607b8564f/download\n",
+      "Logs: https://api.biosimulations.org/logs/6685273ab18d214607b8564f?includeOutput=true\n"
      ]
     },
     {
-     "data": {
-      "text/html": [
-       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
-      ],
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "\u001b[3;92mTrue\u001b[0m"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
+     "ename": "AttributeError",
+     "evalue": "module 'utils' has no attribute 'download_file'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
+      "Cell \u001b[1;32mIn[2], line 20\u001b[0m\n\u001b[0;32m      4\u001b[0m sim_dict \u001b[38;5;241m=\u001b[39m {\n\u001b[0;32m      5\u001b[0m               \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtest\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m      6\u001b[0m               \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msimulator\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtellurium\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m     13\u001b[0m               \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124memail\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mucbtrin@ucl.ac.uk\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m     14\u001b[0m             }\n\u001b[0;32m     16\u001b[0m download_link, result \u001b[38;5;241m=\u001b[39m utils\u001b[38;5;241m.\u001b[39msubmit_simulation_archive(\\\n\u001b[0;32m     17\u001b[0m     archive_file\u001b[38;5;241m=\u001b[39momex_file_name,\\\n\u001b[0;32m     18\u001b[0m     sim_dict\u001b[38;5;241m=\u001b[39msim_dict)\n\u001b[1;32m---> 20\u001b[0m filepath_results \u001b[38;5;241m=\u001b[39m \u001b[43mutils\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdownload_file\u001b[49m(download_link)\n",
+      "\u001b[1;31mAttributeError\u001b[0m: module 'utils' has no attribute 'download_file'"
+     ]
     }
    ],
    "source": [
@@ -117,7 +121,85 @@
     "    archive_file=omex_file_name,\\\n",
     "    sim_dict=sim_dict)\n",
     "\n",
-    "utils.download_file(download_link)\n"
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Downloading results...\n",
+      "Download completed.\n"
+     ]
+    }
+   ],
+   "source": [
+    "filepath_results = utils.download_file_from_link(download_link)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
+      ],
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "\u001b[32m'c:\\\\Users\\\\prins\\\\GitHub\\\\SBMLShowcase\\\\SBML\\\\results.zip'\u001b[0m"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "filepath_results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Downloading results...\n",
+      "Download completed.\n"
+     ]
+    }
+   ],
+   "source": [
+    "filepath_results = utils.download_file_from_link(download_link)\n",
+    "# unzip file in filepath_results and place in a folder cwd/results\n",
+    "extract_dir = os.path.join(cwd, 'results')\n",
+    "shutil.unpack_archive(filepath_results, extract_dir=extract_dir)\n",
+    "os.remove(filepath_results)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## test compatibility biosimulators locally using docker\n",
+    "see https://github.com/OpenSourceBrain/SBMLShowcase/issues/31\n"
    ]
   },
   {
@@ -190,35 +272,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/markdown": [
-       "| Engine     | pass/FAIL                                | Error                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | Compatibility                                                                                                                                                                                                                                                              | d1                                                         |\n",
-       "|:-----------|:-----------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|\n",
-       "| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       | <a href=\"d1_plots\\amici_d1.pdf\">amici_d1.pdf</a>           |\n",
-       "| brian2     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |\n",
-       "| bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp492978` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href=\"d1_plots\\bionetgen_d1.pdf\">bionetgen_d1.pdf</a>   |\n",
-       "| boolnet    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp49383` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).<br>R[write to console]: Warning message:<br><br>R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :<br>R[write to console]: <br> <br>R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages<br><br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href=\"d1_plots\\boolnet_d1.pdf\">boolnet_d1.pdf</a>       |\n",
-       "| cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><br>INFO: No xlwt module available, Excel spreadsheet creation disabled<br><br><br><br>No module named 'cplex'<br><br><br><br>CPLEX not available<br><br>*****<br>Using GLPK<br>*****<br><br><br>INFO: No xlrd module available, Excel spreadsheet reading disabled<br><br>CBMPy environment<br>******************<br>Revision: r689<br><br><br>***********************************************************************<br>* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *<br>*                http://cbmpy.sourceforge.net                         *<br>* Copyright(C) Brett G. Olivier 2014 - 2019                           *<br>* Dept. of Systems Bioinformatics                                     *<br>* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *<br>* CBMPy is developed as part of the BeBasic MetaToolKit Project       *<br>* Distributed under the GNU GPL v 3.0 licence, see                    *<br>* LICENCE (supplied with this release) for details                    *<br>***********************************************************************<br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp882022` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href=\"d1_plots\\cbmpy_d1.pdf\">cbmpy_d1.pdf</a>           |\n",
-       "| cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp968636` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href=\"d1_plots\\cobrapy_d1.pdf\">cobrapy_d1.pdf</a>       |\n",
-       "| copasi     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp380316` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <a href=\"d1_plots\\copasi_d1.pdf\">copasi_d1.pdf</a>         |\n",
-       "| gillespy2  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href=\"d1_plots\\gillespy2_d1.pdf\">gillespy2_d1.pdf</a>   |\n",
-       "| ginsim     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp48023` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000<br></details> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href=\"d1_plots\\ginsim_d1.pdf\">ginsim_d1.pdf</a>         |\n",
-       "| libsbmlsim | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href=\"d1_plots\\libsbmlsim_d1.pdf\">libsbmlsim_d1.pdf</a> |\n",
-       "| masspy     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp784349` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <a href=\"d1_plots\\masspy_d1.pdf\">masspy_d1.pdf</a>         |\n",
-       "| netpyne    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |\n",
-       "| neuron     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    |                                                            |\n",
-       "| opencor    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with opencor</details>                                                                                                                     |                                                            |\n",
-       "| pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> |                                                            |\n",
-       "| pysces     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>Could not find GLIMDA.<br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp655477` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpthlujip5/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpthlujip5/./LEMS_NML2_Ex9_FN.sbml.xml does not exist<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <a href=\"d1_plots\\pysces_d1.pdf\">pysces_d1.pdf</a>         |\n",
-       "| rbapy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp250073` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).<br></details>                | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href=\"d1_plots\\rbapy_d1.pdf\">rbapy_d1.pdf</a>           |\n",
-       "| smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>[Errno 2] No such file or directory: '/tmp/tmpfn2dvdje/model.txt'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |\n",
-       "| tellurium  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   | <a href=\"d1_plots\\tellurium_d1.pdf\">tellurium_d1.pdf</a>   |\n",
-       "| vcell      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1: b'  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SEDML(preProcessDoc)  **** Error: SED-ML processing for /tmp/vcell_temp_9e9c4770-45b0-4abf-aa17-49ffcf03bff52259667327810196674/tmp910870 failed with error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  SIMULATIONS_RUN(runSimulations)  **** Error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SIMULATION_OUTPUTS(processOutputs)  **** Error: Error processing outputs\\n'```</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |\n",
-       "| xpp        | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |"
+       "| Engine     | pass/FAIL                                | Error                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Compatibility                                                                                                                                                                                                                                                              | d1                                                         |\n",
+       "|:-----------|:-----------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|\n",
+       "| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <a href=\"d1_plots\\amici_d1.pdf\">amici_d1.pdf</a>           |\n",
+       "| brian2     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |\n",
+       "| bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp874978` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href=\"d1_plots\\bionetgen_d1.pdf\">bionetgen_d1.pdf</a>   |\n",
+       "| boolnet    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp346023` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).<br>R[write to console]: Warning message:<br><br>R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :<br>R[write to console]: <br> <br>R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages<br><br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href=\"d1_plots\\boolnet_d1.pdf\">boolnet_d1.pdf</a>       |\n",
+       "| cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><br>INFO: No xlwt module available, Excel spreadsheet creation disabled<br><br><br><br>No module named 'cplex'<br><br><br><br>CPLEX not available<br><br>*****<br>Using GLPK<br>*****<br><br><br>INFO: No xlrd module available, Excel spreadsheet reading disabled<br><br>CBMPy environment<br>******************<br>Revision: r689<br><br><br>***********************************************************************<br>* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *<br>*                http://cbmpy.sourceforge.net                         *<br>* Copyright(C) Brett G. Olivier 2014 - 2019                           *<br>* Dept. of Systems Bioinformatics                                     *<br>* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *<br>* CBMPy is developed as part of the BeBasic MetaToolKit Project       *<br>* Distributed under the GNU GPL v 3.0 licence, see                    *<br>* LICENCE (supplied with this release) for details                    *<br>***********************************************************************<br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp291004` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href=\"d1_plots\\cbmpy_d1.pdf\">cbmpy_d1.pdf</a>           |\n",
+       "| cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp657538` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href=\"d1_plots\\cobrapy_d1.pdf\">cobrapy_d1.pdf</a>       |\n",
+       "| copasi     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp381402` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[W]'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href=\"d1_plots\\copasi_d1.pdf\">copasi_d1.pdf</a>         |\n",
+       "| gillespy2  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href=\"d1_plots\\gillespy2_d1.pdf\">gillespy2_d1.pdf</a>   |\n",
+       "| ginsim     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp435528` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000<br></details> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href=\"d1_plots\\ginsim_d1.pdf\">ginsim_d1.pdf</a>         |\n",
+       "| libsbmlsim | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href=\"d1_plots\\libsbmlsim_d1.pdf\">libsbmlsim_d1.pdf</a> |\n",
+       "| masspy     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp538935` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href=\"d1_plots\\masspy_d1.pdf\">masspy_d1.pdf</a>         |\n",
+       "| netpyne    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |\n",
+       "| neuron     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    |                                                            |\n",
+       "| opencor    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with opencor</details>                                                                                                                     |                                                            |\n",
+       "| pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> |                                                            |\n",
+       "| pysces     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>Could not find GLIMDA.<br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp672905` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpppel0hvg/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpppel0hvg/./LEMS_NML2_Ex9_FN.sbml.xml does not exist<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href=\"d1_plots\\pysces_d1.pdf\">pysces_d1.pdf</a>         |\n",
+       "| rbapy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp52923` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).<br></details>                  | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href=\"d1_plots\\rbapy_d1.pdf\">rbapy_d1.pdf</a>           |\n",
+       "| smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>[Errno 2] No such file or directory: '/tmp/tmpjz7l79p3/model.txt'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |\n",
+       "| tellurium  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <a href=\"d1_plots\\tellurium_d1.pdf\">tellurium_d1.pdf</a>   |\n",
+       "| vcell      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1: b'  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SEDML(preProcessDoc)  **** Error: SED-ML processing for /tmp/vcell_temp_916701e4-ab9b-46cf-a3d3-1b27130d24697037699608403018826/tmp108713 failed with error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  SIMULATIONS_RUN(runSimulations)  **** Error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SIMULATION_OUTPUTS(processOutputs)  **** Error: Error processing outputs\\n'```</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |\n",
+       "| xpp        | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |"
       ]
      },
      "metadata": {},
@@ -257,7 +339,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/utils/__init__.py b/utils/__init__.py
index 7d0c4f5..7edded8 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -830,11 +830,47 @@ def download_file_from_link(download_link, output_file='results.zip', max_wait_t
             with open(output_file, 'wb') as f:
                 shutil.copyfileobj(r.raw, f)
         print('Download completed.')
-        return True
+        # filepath where the file is downloaded
+        filepath = os.path.abspath(output_file)
+        return filepath
     else:
         print('Failed to download the file.')
         return False
 
+# unzip the file in file_path if it is a zip file and remove the zip file, replace with the unzipped folder
+def unzip_file(file_path, output_dir=None):
+    """
+    Unzip a file if it is a zip file.
+
+    Parameters:
+    file_path (str): The path to the file to unzip.
+    output_dir (str): The directory to extract the contents of the zip file to. Defaults to None.
+
+    Returns:
+    str: The path to the unzipped folder.
+    """
+
+    # If the file is a zip file, unzip it
+    if zipfile.is_zipfile(file_path):
+        # If the output directory is not specified, use the directory of the file
+        if output_dir is None:
+            output_dir = os.path.dirname(file_path)
+
+        # Create a ZipFile object
+        with zipfile.ZipFile(file_path, 'r') as zip_ref:
+            # Extract the contents of the zip file
+            zip_ref.extractall(output_dir)
+
+        # Remove the zip file
+        os.remove(file_path)
+
+        # Get the name of the unzipped folder
+        unzipped_folder = os.path.join(output_dir, os.path.splitext(os.path.basename(file_path))[0])
+
+        return unzipped_folder
+
+    return file_path
+
 
 #!/usr/bin/env python3
 """

From bff703652a139db8a5d355f0f7b4aa45a20208a1 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 4 Jul 2024 09:49:56 +0100
Subject: [PATCH 04/71] import functions from pyneuroml biosimulators fork

---
 SBML/test_compatibility_biosimulators.ipynb | 142 ++---------
 utils/__init__.py                           | 263 --------------------
 2 files changed, 21 insertions(+), 384 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index 097dca6..c3661af 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -63,45 +63,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'tellurium', 'simulatorVersion': '2.2.1', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': 'ucbtrin@ucl.ac.uk'}\n",
-      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}\n",
-      "pyNeuroML >>> DEBUG - data is:\n",
-      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}\n",
-      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a940f1c6daa04b368d7d6890e002d178\n",
-      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 6685273ab18d214607b8564f\n",
-      "View: https://api.biosimulations.org/runs/6685273ab18d214607b8564f\n",
-      "Downloads: https://api.biosimulations.org/results/6685273ab18d214607b8564f/download\n",
-      "Logs: https://api.biosimulations.org/logs/6685273ab18d214607b8564f?includeOutput=true\n"
-     ]
-    },
-    {
-     "ename": "AttributeError",
-     "evalue": "module 'utils' has no attribute 'download_file'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
-      "Cell \u001b[1;32mIn[2], line 20\u001b[0m\n\u001b[0;32m      4\u001b[0m sim_dict \u001b[38;5;241m=\u001b[39m {\n\u001b[0;32m      5\u001b[0m               \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtest\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m      6\u001b[0m               \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msimulator\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtellurium\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m     13\u001b[0m               \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124memail\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mucbtrin@ucl.ac.uk\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m     14\u001b[0m             }\n\u001b[0;32m     16\u001b[0m download_link, result \u001b[38;5;241m=\u001b[39m utils\u001b[38;5;241m.\u001b[39msubmit_simulation_archive(\\\n\u001b[0;32m     17\u001b[0m     archive_file\u001b[38;5;241m=\u001b[39momex_file_name,\\\n\u001b[0;32m     18\u001b[0m     sim_dict\u001b[38;5;241m=\u001b[39msim_dict)\n\u001b[1;32m---> 20\u001b[0m filepath_results \u001b[38;5;241m=\u001b[39m \u001b[43mutils\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdownload_file\u001b[49m(download_link)\n",
-      "\u001b[1;31mAttributeError\u001b[0m: module 'utils' has no attribute 'download_file'"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
+    "from pyneuroml import biosimulations\n",
     "#put the sedml and sbml into a combine archive\n",
     "omex_filepath = utils.create_omex(sedml_filepath,sbml_filepath)\n",
     "omex_file_name = os.path.basename(omex_filepath)\n",
@@ -117,76 +83,10 @@
     "              \"email\": \"ucbtrin@ucl.ac.uk\",\n",
     "            }\n",
     "\n",
-    "download_link, result = utils.submit_simulation_archive(\\\n",
+    "download_link, result = biosimulations.submit_simulation_archive(\\\n",
     "    archive_file=omex_file_name,\\\n",
     "    sim_dict=sim_dict)\n",
     "\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Downloading results...\n",
-      "Download completed.\n"
-     ]
-    }
-   ],
-   "source": [
-    "filepath_results = utils.download_file_from_link(download_link)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
-      ],
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "\u001b[32m'c:\\\\Users\\\\prins\\\\GitHub\\\\SBMLShowcase\\\\SBML\\\\results.zip'\u001b[0m"
-      ]
-     },
-     "execution_count": 4,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "filepath_results"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 11,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Downloading results...\n",
-      "Download completed.\n"
-     ]
-    }
-   ],
-   "source": [
     "filepath_results = utils.download_file_from_link(download_link)\n",
     "# unzip file in filepath_results and place in a folder cwd/results\n",
     "extract_dir = os.path.join(cwd, 'results')\n",
@@ -204,7 +104,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -272,7 +172,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -282,24 +182,24 @@
        "|:-----------|:-----------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|\n",
        "| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <a href=\"d1_plots\\amici_d1.pdf\">amici_d1.pdf</a>           |\n",
        "| brian2     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |\n",
-       "| bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp874978` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href=\"d1_plots\\bionetgen_d1.pdf\">bionetgen_d1.pdf</a>   |\n",
-       "| boolnet    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp346023` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).<br>R[write to console]: Warning message:<br><br>R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :<br>R[write to console]: <br> <br>R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages<br><br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href=\"d1_plots\\boolnet_d1.pdf\">boolnet_d1.pdf</a>       |\n",
-       "| cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><br>INFO: No xlwt module available, Excel spreadsheet creation disabled<br><br><br><br>No module named 'cplex'<br><br><br><br>CPLEX not available<br><br>*****<br>Using GLPK<br>*****<br><br><br>INFO: No xlrd module available, Excel spreadsheet reading disabled<br><br>CBMPy environment<br>******************<br>Revision: r689<br><br><br>***********************************************************************<br>* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *<br>*                http://cbmpy.sourceforge.net                         *<br>* Copyright(C) Brett G. Olivier 2014 - 2019                           *<br>* Dept. of Systems Bioinformatics                                     *<br>* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *<br>* CBMPy is developed as part of the BeBasic MetaToolKit Project       *<br>* Distributed under the GNU GPL v 3.0 licence, see                    *<br>* LICENCE (supplied with this release) for details                    *<br>***********************************************************************<br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp291004` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href=\"d1_plots\\cbmpy_d1.pdf\">cbmpy_d1.pdf</a>           |\n",
-       "| cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp657538` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href=\"d1_plots\\cobrapy_d1.pdf\">cobrapy_d1.pdf</a>       |\n",
-       "| copasi     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp381402` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[W]'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href=\"d1_plots\\copasi_d1.pdf\">copasi_d1.pdf</a>         |\n",
+       "| bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp149263` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href=\"d1_plots\\bionetgen_d1.pdf\">bionetgen_d1.pdf</a>   |\n",
+       "| boolnet    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp151894` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).<br>R[write to console]: Warning message:<br><br>R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :<br>R[write to console]: <br> <br>R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages<br><br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href=\"d1_plots\\boolnet_d1.pdf\">boolnet_d1.pdf</a>       |\n",
+       "| cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><br>INFO: No xlwt module available, Excel spreadsheet creation disabled<br><br><br><br>No module named 'cplex'<br><br><br><br>CPLEX not available<br><br>*****<br>Using GLPK<br>*****<br><br><br>INFO: No xlrd module available, Excel spreadsheet reading disabled<br><br>CBMPy environment<br>******************<br>Revision: r689<br><br><br>***********************************************************************<br>* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *<br>*                http://cbmpy.sourceforge.net                         *<br>* Copyright(C) Brett G. Olivier 2014 - 2019                           *<br>* Dept. of Systems Bioinformatics                                     *<br>* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *<br>* CBMPy is developed as part of the BeBasic MetaToolKit Project       *<br>* Distributed under the GNU GPL v 3.0 licence, see                    *<br>* LICENCE (supplied with this release) for details                    *<br>***********************************************************************<br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp369389` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href=\"d1_plots\\cbmpy_d1.pdf\">cbmpy_d1.pdf</a>           |\n",
+       "| cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp31836` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href=\"d1_plots\\cobrapy_d1.pdf\">cobrapy_d1.pdf</a>       |\n",
+       "| copasi     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp987364` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href=\"d1_plots\\copasi_d1.pdf\">copasi_d1.pdf</a>         |\n",
        "| gillespy2  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href=\"d1_plots\\gillespy2_d1.pdf\">gillespy2_d1.pdf</a>   |\n",
-       "| ginsim     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp435528` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000<br></details> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href=\"d1_plots\\ginsim_d1.pdf\">ginsim_d1.pdf</a>         |\n",
+       "| ginsim     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp382733` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000<br></details> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href=\"d1_plots\\ginsim_d1.pdf\">ginsim_d1.pdf</a>         |\n",
        "| libsbmlsim | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href=\"d1_plots\\libsbmlsim_d1.pdf\">libsbmlsim_d1.pdf</a> |\n",
-       "| masspy     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp538935` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href=\"d1_plots\\masspy_d1.pdf\">masspy_d1.pdf</a>         |\n",
+       "| masspy     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp750289` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href=\"d1_plots\\masspy_d1.pdf\">masspy_d1.pdf</a>         |\n",
        "| netpyne    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |\n",
-       "| neuron     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    |                                                            |\n",
-       "| opencor    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with opencor</details>                                                                                                                     |                                                            |\n",
-       "| pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> |                                                            |\n",
-       "| pysces     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>Could not find GLIMDA.<br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp672905` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpppel0hvg/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpppel0hvg/./LEMS_NML2_Ex9_FN.sbml.xml does not exist<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href=\"d1_plots\\pysces_d1.pdf\">pysces_d1.pdf</a>         |\n",
-       "| rbapy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp52923` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).<br></details>                  | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href=\"d1_plots\\rbapy_d1.pdf\">rbapy_d1.pdf</a>           |\n",
-       "| smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>[Errno 2] No such file or directory: '/tmp/tmpjz7l79p3/model.txt'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |\n",
+       "| neuron     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'NeuroML', 'LEMS']</details></span>    |                                                            |\n",
+       "| opencor    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            |                                                            |\n",
+       "| pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'NeuroML', 'LEMS']</details></span> |                                                            |\n",
+       "| pysces     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>Could not find GLIMDA.<br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp757728` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp0b0_er9p/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp0b0_er9p/./LEMS_NML2_Ex9_FN.sbml.xml does not exist<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href=\"d1_plots\\pysces_d1.pdf\">pysces_d1.pdf</a>         |\n",
+       "| rbapy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp987912` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).<br></details>                 | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href=\"d1_plots\\rbapy_d1.pdf\">rbapy_d1.pdf</a>           |\n",
+       "| smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>[Errno 2] No such file or directory: '/tmp/tmpmu42eki7/model.txt'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |\n",
        "| tellurium  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <a href=\"d1_plots\\tellurium_d1.pdf\">tellurium_d1.pdf</a>   |\n",
-       "| vcell      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1: b'  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SEDML(preProcessDoc)  **** Error: SED-ML processing for /tmp/vcell_temp_916701e4-ab9b-46cf-a3d3-1b27130d24697037699608403018826/tmp108713 failed with error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  SIMULATIONS_RUN(runSimulations)  **** Error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SIMULATION_OUTPUTS(processOutputs)  **** Error: Error processing outputs\\n'```</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |\n",
+       "| vcell      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1: b'  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SEDML(preProcessDoc)  **** Error: SED-ML processing for /tmp/vcell_temp_4d26fa44-2457-4a00-b0d1-d8bf8a3a541412142204403474173125/tmp605892 failed with error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  SIMULATIONS_RUN(runSimulations)  **** Error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SIMULATION_OUTPUTS(processOutputs)  **** Error: Error processing outputs\\n'```</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |\n",
        "| xpp        | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |"
       ]
      },
@@ -339,7 +239,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/utils/__init__.py b/utils/__init__.py
index 8519e59..249e79c 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -881,266 +881,3 @@ def unzip_file(file_path, output_dir=None):
 
     return file_path
 
-
-#!/usr/bin/env python3
-"""
-Functions related to Biosimulations.org
-
-File: pyneuroml/biosimulations.py
-
-Copyright 2024 NeuroML contributors
-"""
-
-import logging
-import typing
-from datetime import datetime
-
-import requests
-
-from pyneuroml import __version__
-from pyneuroml.annotations import create_annotation
-from pyneuroml.archive import create_combine_archive
-from pyneuroml.runners import run_jneuroml
-
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.DEBUG)
-
-try:
-    from pydantic import BaseModel
-    from requests_toolbelt.multipart.encoder import MultipartEncoder
-except ImportError:
-    logger.warning(
-        "Please install optional dependencies to use Biosimulation.org features:"
-    )
-    logger.warning("pip install pyneuroml[combine]")
-
-
-biosimulators_api_url = "https://api.biosimulators.org"
-biosimulations_api_url = "https://api.biosimulations.org"
-
-
-
-
-
-class _SimulationRunApiRequest(BaseModel):
-    """class for runSimulation data
-
-    Based on
-    https://github.com/biosimulations/biosimulations-runutils/blob/dev/biosimulations_runutils/biosim_pipeline/biosim_api.py
-
-    Once biosimulations-runutils is published, we will use their API instead
-    of replicating it ourselves.
-    """
-
-    name: str
-    simulator: str
-    simulatorVersion: str
-    maxTime: int
-    cpus: typing.Optional[int] = None
-    memory: typing.Optional[int] = None
-    purpose: typing.Optional[str] = "academic"
-    email: typing.Optional[str] = None
-    envVars: typing.Optional[typing.List[str]] = []
-
-
-def get_simulator_versions(
-    simulators: typing.Union[str, typing.List[str]] = [
-        "neuron",
-        "netpyne",
-        "tellurium",
-        "pyneuroml",
-        "pyneuroml",
-        "xpp",
-        "brian2",
-        "copasi",
-    ],
-) -> typing.Dict[str, typing.List[str]]:
-    """Get simulator list from biosimulators.
-
-    .. versionadded:: 1.2.10
-
-    :param simulators: a simulator or list of simulators to get versions for
-    :type simulators: str or list(str)
-    :returns: json response from API
-    :rtype: str
-    """
-    if isinstance(simulators, str):
-        simulators = [simulators]
-    all_siminfo = {}  # type: typing.Dict[str, typing.List[str]]
-    for sim in simulators:
-        resp = requests.get(f"{biosimulators_api_url}/simulators/{sim}")
-        siminfo = resp.json()
-        for s in siminfo:
-            try:
-                all_siminfo[s["id"]].append(s["version"])
-            except KeyError:
-                all_siminfo[s["id"]] = [s["version"]]
-
-    return all_siminfo
-
-
-def submit_simulation(
-    rootfile: str,
-    metadata_file: typing.Optional[str] = None,
-    sim_dict: typing.Dict[
-        str, typing.Optional[typing.Union[int, str, typing.List[typing.Any]]]
-    ] = {},
-    dry_run: bool = True,
-):
-    """Submit a simulation to Biosimulations using its REST API
-
-    .. versionadded:: 1.2.10
-
-    :param rootfile: main LEMS or SEDML simulation file
-        If it is a LEMS file, a SEDML file will be generated for it
-    :type rootfile: str
-    :param metadata_file: path to a RDF metadata file to be included in the
-        OMEX archive.  If not provided, a generic one with a title and
-        description will be generated.
-    :type metadata_file: str
-    :param sim_dict: dictionary holding parameters required to send the
-        simulation to biosimulations
-
-        .. code-block:: json
-
-            {
-              "name": "Kockout of gene A",
-              "simulator": "tellurium",
-              "simulatorVersion": "2.2.1",
-              "cpus": 1,
-              "memory": 8,
-              "maxTime": 20,
-              "envVars": [],
-              "purpose": "academic",
-              "email": "info@biosimulations.org",
-            }
-
-        Here, the "name", "simulator", and "simulatorVersion" fields are
-        required. You can use the py::func`get_simulator_versions` function to
-        query Biosimulations or visit https://biosimulators.org/simulators
-
-        See also: "SimulationRun" on this page (at the bottom)
-        https://api.biosimulations.org/#/Simulations/SimulationRunController_createRun
-
-    :type sim_dict: dict
-
-    :returns: the requests.post response object from the submission, or True if dry_run
-
-    """
-    if metadata_file is None:
-        logger.info("No metadata file given, generating one.")
-        metadata_file = "metadata.rdf"
-        with open(metadata_file, "w") as f:
-            annotation = create_annotation(
-                rootfile + ".omex",
-                title=f"Biosimulation of {rootfile} created using PyNeuroML version {__version__}",
-                description=f"Biosimulation of {rootfile} created using PyNeuroML version {__version__}",
-                creation_date=datetime.now().strftime("%Y-%m-%d"),
-            )
-            print(annotation, file=f)
-
-    if rootfile.startswith("LEMS") and rootfile.endswith(".xml"):
-        logger.info("Generating SED-ML file from LEMS file")
-        run_jneuroml("", rootfile, "-sedml")
-        rootfile = rootfile.replace(".xml", ".sedml")
-
-    create_combine_archive(
-        rootfile, zipfile_extension=".omex", extra_files=[metadata_file]
-    )
-
-    return submit_simulation_archive(f"{rootfile}.omex", sim_dict, dry_run=dry_run)
-
-
-def submit_simulation_archive(
-    archive_file: str,
-    sim_dict: typing.Dict[str, typing.Union[int, str, typing.List[str]]] = {},
-    dry_run: bool = False,
-) -> object:
-    """Submit an OMEX archive to biosimulations using the provided simulation run dictionary
-
-    .. versionadded:: 1.2.10
-
-    Note that this function does not validate either the OMEX archive nor the
-    simulation dictionary. It simply submits it to the API.
-
-    :param archive_file: OMEX archive file to submit
-    :type archive_file: str
-    :param sim_dict: dictionary holding parameters required to send the
-        simulation to biosimulations
-
-        .. code-block:: json
-
-            {
-              "name": "Kockout of gene A",
-              "simulator": "tellurium",
-              "simulatorVersion": "2.2.1",
-              "cpus": 1,
-              "memory": 8,
-              "maxTime": 20,
-              "envVars": [],
-              "purpose": "academic",
-              "email": "info@biosimulations.org",
-            }
-
-        Here, the "name", "simulator", and "simulatorVersion" fields are
-        required. You can use the py::func`get_simulator_versions` function to
-        query Biosimulations or visit https://biosimulators.org/simulators
-
-        See also: "SimulationRun" on this page (at the bottom)
-        https://api.biosimulations.org/#/Simulations/SimulationRunController_createRun
-
-    :type sim_dict: dict
-    :returns: the requests.post response object, or True if dry_run
-
-    """
-    api_url = f"{biosimulations_api_url}/runs"
-    logger.debug(f"Sim dict is: {sim_dict}")
-
-    simulation_run_request = _SimulationRunApiRequest(**sim_dict)
-    logger.debug(
-        f"simulation_run_request is {simulation_run_request.model_dump_json()}"
-    )
-
-    with open(archive_file, "rb") as archive_file_handle:
-        multipart_form_data: dict[
-            str,
-            typing.Union[typing.Tuple[str, typing.BinaryIO], typing.Tuple[None, str]],
-        ] = {
-            "file": (archive_file, archive_file_handle),
-            "simulationRun": (None, simulation_run_request.model_dump_json()),
-        }
-
-        logger.debug(f"data is:\n{multipart_form_data}")
-
-        m = MultipartEncoder(fields=multipart_form_data)
-
-        logger.info(f"multipart encoded data is {m}")
-        logger.info(f"with content type: {m.content_type}")
-
-        if dry_run is False:
-            logger.info("Submitting archive to biosimulations")
-            response = requests.post(
-                api_url, data=m, headers={"Content-Type": m.content_type}
-            )  # type: requests.Response
-            if response.status_code != requests.codes.CREATED:
-                response.raise_for_status()
-            else:
-                serv_response = response.json()
-                print(
-                    f"Submitted {archive_file} successfully with id: {serv_response['id']}"
-                )
-                print(f"View: {biosimulations_api_url}/runs/{serv_response['id']}")
-                download_link = f"{biosimulations_api_url}/results/{serv_response['id']}/download"
-                print(
-                    f"Downloads: {download_link}"
-                )
-                print(
-                    f"Logs: {biosimulations_api_url}/logs/{serv_response['id']}?includeOutput=true"
-                )
-                
-        else:
-            response = True
-            print("Dry run, not submitting")
-            print(f"Simulation dictionary: {sim_dict}")
-        
-    return download_link, response
\ No newline at end of file

From bdc013288d61bd74bb29bc0f942cd997a75184aa Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 4 Jul 2024 10:36:10 +0100
Subject: [PATCH 05/71] change name function (parse_error_message to
 ansi_to_html)

---
 SBML/test_compatibility_biosimulators.ipynb | 118 +++++++++++++++++++-
 SBML/test_compatibility_biosimulators.py    |   2 +-
 utils/__init__.py                           |   3 +-
 3 files changed, 117 insertions(+), 6 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index c3661af..9fecc8d 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -63,9 +63,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'tellurium', 'simulatorVersion': '2.2.1', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': 'ucbtrin@ucl.ac.uk'}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ab2b252b438d419eafb7f0a0479a3f64\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 6686624b6b7c343121b0ac1e\n",
+      "View: https://api.biosimulations.org/runs/6686624b6b7c343121b0ac1e\n",
+      "Downloads: https://api.biosimulations.org/results/6686624b6b7c343121b0ac1e/download\n",
+      "Logs: https://api.biosimulations.org/logs/6686624b6b7c343121b0ac1e?includeOutput=true\n",
+      "Downloading results...\n",
+      "Download completed.\n"
+     ]
+    }
+   ],
    "source": [
     "from pyneuroml import biosimulations\n",
     "#put the sedml and sbml into a combine archive\n",
@@ -88,12 +114,96 @@
     "    sim_dict=sim_dict)\n",
     "\n",
     "filepath_results = utils.download_file_from_link(download_link)\n",
-    "# unzip file in filepath_results and place in a folder cwd/results\n",
     "extract_dir = os.path.join(cwd, 'results')\n",
     "shutil.unpack_archive(filepath_results, extract_dir=extract_dir)\n",
     "os.remove(filepath_results)\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'tellurium', 'simulatorVersion': '2.2.8', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': 'ucbtrin@ucl.ac.uk'}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c1fa1e3657fc41659f0f2158456e8db7\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668666cf6b7c343121b0ac70\n",
+      "View: https://api.biosimulations.org/runs/668666cf6b7c343121b0ac70\n",
+      "Downloads: https://api.biosimulations.org/results/668666cf6b7c343121b0ac70/download\n",
+      "Logs: https://api.biosimulations.org/logs/668666cf6b7c343121b0ac70?includeOutput=true\n",
+      "Downloading results...\n",
+      "Download completed.\n"
+     ]
+    }
+   ],
+   "source": [
+    "from pyneuroml import biosimulations\n",
+    "\n",
+    "# get the version of the engine\n",
+    "engine = 'tellurium'\n",
+    "engine_version = biosimulations.get_simulator_versions(engine)\n",
+    "\n",
+    "#put the sedml and sbml into a combine archive\n",
+    "omex_filepath = utils.create_omex(sedml_filepath,sbml_filepath)\n",
+    "omex_file_name = os.path.basename(omex_filepath)\n",
+    "\n",
+    "sim_dict = {\n",
+    "              \"name\": \"test\",\n",
+    "              \"simulator\": engine,\n",
+    "              \"simulatorVersion\": engine_version[engine][-1],\n",
+    "              \"cpus\": 1,\n",
+    "              \"memory\": 8,\n",
+    "              \"maxTime\": 20,\n",
+    "              \"envVars\": [],\n",
+    "              \"purpose\": \"academic\",\n",
+    "              \"email\": \"ucbtrin@ucl.ac.uk\",\n",
+    "            }\n",
+    "\n",
+    "download_link, result = biosimulations.submit_simulation_archive(\\\n",
+    "    archive_file=omex_file_name,\\\n",
+    "    sim_dict=sim_dict)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Downloading results...\n",
+      "Download completed.\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\results\\log.yml\n"
+     ]
+    }
+   ],
+   "source": [
+    "filepath_results = utils.download_file_from_link(download_link)\n",
+    "extract_dir = os.path.join(cwd, 'results')\n",
+    "# fetch yml log file from extract_dir\n",
+    "yml_log =  os.path.join(extract_dir, 'log.yml')\n",
+    "print(yml_log)\n",
+    "\n",
+    "shutil.unpack_archive(filepath_results, extract_dir=extract_dir)\n",
+    "os.remove(filepath_results)\n"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -220,7 +330,7 @@
     "\n",
     "# for non empty cells in error col print error message\n",
     "\n",
-    "results_table['Error'] = results_table['Error'].apply(lambda x: utils.parse_error_message(x))\n",
+    "results_table['Error'] = results_table['Error'].apply(lambda x: utils.ansi_to_html(x))\n",
     "results_table['Error'] = results_table['Error'].apply(lambda x: utils.collapsible_content(x))\n",
     "\n",
     "# compatibility_message\n",
diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/test_compatibility_biosimulators.py
index 84e7c98..f6391ed 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/test_compatibility_biosimulators.py
@@ -48,7 +48,7 @@
 results_table['Error'] = results_table.apply(lambda x: None if x['pass/FAIL'] == x['Error'] else x['Error'], axis=1)
 results_table['pass/FAIL'] = results_table['pass/FAIL'].replace('other', 'FAIL')
 
-results_table['Error'] = results_table['Error'].apply(lambda x: utils.parse_error_message(x))
+results_table['Error'] = results_table['Error'].apply(lambda x: utils.ansi_to_html(x))
 results_table['Error'] = results_table['Error'].apply(lambda x: utils.collapsible_content(x))
 
 results_table['Compatibility'] = results_table['Engine'].apply(lambda x: utils.check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))
diff --git a/utils/__init__.py b/utils/__init__.py
index 249e79c..ea41ea9 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -277,7 +277,7 @@ def create_hyperlink(file_path):
         return None
     
 
-def parse_error_message(text):
+def ansi_to_html(text):
     if text != None:
         text_message = re.findall(r'"([^"]*)"', text) 
         if len(text_message) > 0:
@@ -397,6 +397,7 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir=None
         # error_str = safe_md_string(e)
         error_str = str(e)
 
+    # TODO: add back functionality to get error message from log.yml
     # #try to load the cleaner error message from the log.yml file
     # log_str = read_log_yml(os.path.join(os.path.dirname(omex_filepath),"log.yml"))
 

From f85ffeb041d1f84d56ffe651c4af9ae25c81dc6e Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 4 Jul 2024 10:37:35 +0100
Subject: [PATCH 06/71] use  biosimulations.get_simulator_versions to determine
 engine_version

---
 SBML/test_compatibility_biosimulators.ipynb | 58 ---------------------
 1 file changed, 58 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index 9fecc8d..61d0f5b 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -61,64 +61,6 @@
     "see https://github.com/OpenSourceBrain/SBMLShowcase/issues/32"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'tellurium', 'simulatorVersion': '2.2.1', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': 'ucbtrin@ucl.ac.uk'}\n",
-      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}\n",
-      "pyNeuroML >>> DEBUG - data is:\n",
-      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}\n",
-      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ab2b252b438d419eafb7f0a0479a3f64\n",
-      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 6686624b6b7c343121b0ac1e\n",
-      "View: https://api.biosimulations.org/runs/6686624b6b7c343121b0ac1e\n",
-      "Downloads: https://api.biosimulations.org/results/6686624b6b7c343121b0ac1e/download\n",
-      "Logs: https://api.biosimulations.org/logs/6686624b6b7c343121b0ac1e?includeOutput=true\n",
-      "Downloading results...\n",
-      "Download completed.\n"
-     ]
-    }
-   ],
-   "source": [
-    "from pyneuroml import biosimulations\n",
-    "#put the sedml and sbml into a combine archive\n",
-    "omex_filepath = utils.create_omex(sedml_filepath,sbml_filepath)\n",
-    "omex_file_name = os.path.basename(omex_filepath)\n",
-    "sim_dict = {\n",
-    "              \"name\": \"test\",\n",
-    "              \"simulator\": \"tellurium\",\n",
-    "              \"simulatorVersion\": \"2.2.1\",\n",
-    "              \"cpus\": 1,\n",
-    "              \"memory\": 8,\n",
-    "              \"maxTime\": 20,\n",
-    "              \"envVars\": [],\n",
-    "              \"purpose\": \"academic\",\n",
-    "              \"email\": \"ucbtrin@ucl.ac.uk\",\n",
-    "            }\n",
-    "\n",
-    "download_link, result = biosimulations.submit_simulation_archive(\\\n",
-    "    archive_file=omex_file_name,\\\n",
-    "    sim_dict=sim_dict)\n",
-    "\n",
-    "filepath_results = utils.download_file_from_link(download_link)\n",
-    "extract_dir = os.path.join(cwd, 'results')\n",
-    "shutil.unpack_archive(filepath_results, extract_dir=extract_dir)\n",
-    "os.remove(filepath_results)\n"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 27,

From 218053c8f9a3b64bae704ab68e2b10dde95cfe84 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 4 Jul 2024 14:33:41 +0100
Subject: [PATCH 07/71] remove print for d1 plot filepaths in move_d1_files

---
 utils/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/utils/__init__.py b/utils/__init__.py
index ea41ea9..7ef9997 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -248,7 +248,6 @@ def move_d1_files(file_paths, plot_dir='d1_plots',engines=engines):
         engine = [key for key in engines.keys() if key in file_paths[i]]
         new_file_name = '_'.join(engine) + '_' + os.path.basename(file_paths[i])
         new_file_path = os.path.join(plot_dir, new_file_name)
-        print(new_file_path)
         if os.path.exists(new_file_path):
             os.remove(new_file_path)
         shutil.move(file_paths[i], new_file_path)

From 7ae14fd7b45855b4616f8e3b65bb9f309b3217b2 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 4 Jul 2024 14:36:47 +0100
Subject: [PATCH 08/71] add back log.yml functionality  in
 run_biosimulators_docker

---
 utils/__init__.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/utils/__init__.py b/utils/__init__.py
index 7ef9997..8a31943 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -392,14 +392,15 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir=None
         biosimulators_core(engine,omex_filepath,output_dir=output_dir)
         return "pass" #no errors
     except Exception as e:
-        #capture the error as a string which won't break markdown tables
+        #capture the error as a string which won't break markdown tables 
         # error_str = safe_md_string(e)
         error_str = str(e)
 
-    # TODO: add back functionality to get error message from log.yml
-    # #try to load the cleaner error message from the log.yml file
-    # log_str = read_log_yml(os.path.join(os.path.dirname(omex_filepath),"log.yml"))
+    #try to load the cleaner error message from the log.yml file
+    log_str = read_log_yml(os.path.join(os.path.dirname(omex_filepath),"log.yml"))
 
+    if log_str:
+        error_str = log_str
     # if log_str:
     #     error_str = safe_md_string(log_str)
 

From 8efc4019b28c85ca293b7d722a94168f51eaa940 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Fri, 5 Jul 2024 16:09:17 +0100
Subject: [PATCH 09/71] add tests and table for compatibility biosimulators
 remote

---
 ...ults_compatibility_biosimulators_remote.md |  23 +
 SBML/test_compatibility_biosimulators.ipynb   | 868 ++++++++++++++++--
 utils/__init__.py                             |  96 +-
 3 files changed, 902 insertions(+), 85 deletions(-)
 create mode 100644 SBML/results_compatibility_biosimulators_remote.md

diff --git a/SBML/results_compatibility_biosimulators_remote.md b/SBML/results_compatibility_biosimulators_remote.md
new file mode 100644
index 0000000..1f1167d
--- /dev/null
+++ b/SBML/results_compatibility_biosimulators_remote.md
@@ -0,0 +1,23 @@
+| Engine     | pass/FAIL                                | Error                                                                                                                                                                                                                                                                                                                                                                                                                                                              | Type                         | Compatibility                                                                                                                                                                                                                                                              | d1                                                         |
+|:-----------|:-----------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|
+| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <a href="d1_plots\amici_d1.pdf">amici_d1.pdf</a>           |
+| brian2     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |
+| bionetgen  | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | CombineArchiveExecutionError | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href="d1_plots\bionetgen_d1.pdf">bionetgen_d1.pdf</a>   |
+| boolnet    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | CombineArchiveExecutionError | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href="d1_plots\boolnet_d1.pdf">boolnet_d1.pdf</a>       |
+| cbmpy      | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href="d1_plots\cbmpy_d1.pdf">cbmpy_d1.pdf</a>           |
+| cobrapy    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href="d1_plots\cobrapy_d1.pdf">cobrapy_d1.pdf</a>       |
+| copasi     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href="d1_plots\copasi_d1.pdf">copasi_d1.pdf</a>         |
+| gillespy2  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href="d1_plots\gillespy2_d1.pdf">gillespy2_d1.pdf</a>   |
+| ginsim     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | CombineArchiveExecutionError | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href="d1_plots\ginsim_d1.pdf">ginsim_d1.pdf</a>         |
+| libsbmlsim | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href="d1_plots\libsbmlsim_d1.pdf">libsbmlsim_d1.pdf</a> |
+| masspy     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href="d1_plots\masspy_d1.pdf">masspy_d1.pdf</a>         |
+| netpyne    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |
+| neuron     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    |                                                            |
+| opencor    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            |                                                            |
+| pyneuroml  | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> |                                                            |
+| pysces     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpbz6s_tkd/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpbz6s_tkd/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href="d1_plots\pysces_d1.pdf">pysces_d1.pdf</a>         |
+| rbapy      | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | CombineArchiveExecutionError | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href="d1_plots\rbapy_d1.pdf">rbapy_d1.pdf</a>           |
+| smoldyn    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |
+| tellurium  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <a href="d1_plots\tellurium_d1.pdf">tellurium_d1.pdf</a>   |
+| vcell      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |
+| xpp        | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |
\ No newline at end of file
diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index 61d0f5b..ff21fc1 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [
     {
@@ -63,19 +63,387 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 22,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'tellurium', 'simulatorVersion': '2.2.8', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': 'ucbtrin@ucl.ac.uk'}\n",
-      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'amici', 'simulatorVersion': '0.18.1', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=93271286db574e49a97da9c3790cdeab\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806e4fb4b102485fe22a7\n",
+      "View: https://api.biosimulations.org/runs/668806e4fb4b102485fe22a7\n",
+      "Downloads: https://api.biosimulations.org/results/668806e4fb4b102485fe22a7/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806e4fb4b102485fe22a7?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'brian2', 'simulatorVersion': '2.5.0.3', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4134f52d1854428e8e95c30e336df32c\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806e5ececf8e28b89fca5\n",
+      "View: https://api.biosimulations.org/runs/668806e5ececf8e28b89fca5\n",
+      "Downloads: https://api.biosimulations.org/results/668806e5ececf8e28b89fca5/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806e5ececf8e28b89fca5?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'bionetgen', 'simulatorVersion': '2.8.0', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=56c9af85d0bc48a29de382f70d2d05f5\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806e7244e3c6918b311e8\n",
+      "View: https://api.biosimulations.org/runs/668806e7244e3c6918b311e8\n",
+      "Downloads: https://api.biosimulations.org/results/668806e7244e3c6918b311e8/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806e7244e3c6918b311e8?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'boolnet', 'simulatorVersion': '2.1.5', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=21a0b6bb0eff4e5cafead5064cc61a2b\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806e9244e3c6918b311ec\n",
+      "View: https://api.biosimulations.org/runs/668806e9244e3c6918b311ec\n",
+      "Downloads: https://api.biosimulations.org/results/668806e9244e3c6918b311ec/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806e9244e3c6918b311ec?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'cbmpy', 'simulatorVersion': '0.7.25', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=d19e99eb439c4d99a6b2d4bee9e0ad5c\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806ebfb4b102485fe22ab\n",
+      "View: https://api.biosimulations.org/runs/668806ebfb4b102485fe22ab\n",
+      "Downloads: https://api.biosimulations.org/results/668806ebfb4b102485fe22ab/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806ebfb4b102485fe22ab?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'cobrapy', 'simulatorVersion': '0.24.0', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ca3289a48ed94a408868820c4d1b445c\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806edfb4b102485fe22ae\n",
+      "View: https://api.biosimulations.org/runs/668806edfb4b102485fe22ae\n",
+      "Downloads: https://api.biosimulations.org/results/668806edfb4b102485fe22ae/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806edfb4b102485fe22ae?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'copasi', 'simulatorVersion': '4.42.284', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=aeb7aa318b954661aad3318985f85a6d\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806ef244e3c6918b311f0\n",
+      "View: https://api.biosimulations.org/runs/668806ef244e3c6918b311f0\n",
+      "Downloads: https://api.biosimulations.org/results/668806ef244e3c6918b311f0/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806ef244e3c6918b311f0?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'gillespy2', 'simulatorVersion': '1.6.6', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=d99c8c1bc095441682e2b194c68e8737\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806f3244e3c6918b311f7\n",
+      "View: https://api.biosimulations.org/runs/668806f3244e3c6918b311f7\n",
+      "Downloads: https://api.biosimulations.org/results/668806f3244e3c6918b311f7/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806f3244e3c6918b311f7?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'ginsim', 'simulatorVersion': '3.0.0b', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f15dd95c13e1457192012b8a5ebc218a\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806f5fb4b102485fe22b8\n",
+      "View: https://api.biosimulations.org/runs/668806f5fb4b102485fe22b8\n",
+      "Downloads: https://api.biosimulations.org/results/668806f5fb4b102485fe22b8/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806f5fb4b102485fe22b8?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'libsbmlsim', 'simulatorVersion': '1.4.0', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a9bd50ee3867471289eb032856c5d240\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806f7244e3c6918b311fe\n",
+      "View: https://api.biosimulations.org/runs/668806f7244e3c6918b311fe\n",
+      "Downloads: https://api.biosimulations.org/results/668806f7244e3c6918b311fe/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806f7244e3c6918b311fe?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'masspy', 'simulatorVersion': '0.1.6', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=03ad32d237334ab1b2733c622d2e9e36\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806f8244e3c6918b31205\n",
+      "View: https://api.biosimulations.org/runs/668806f8244e3c6918b31205\n",
+      "Downloads: https://api.biosimulations.org/results/668806f8244e3c6918b31205/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806f8244e3c6918b31205?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'netpyne', 'simulatorVersion': '1.0.0.2', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=646c6152e60440d892ae2e33c5d39ef2\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806fa244e3c6918b3120f\n",
+      "View: https://api.biosimulations.org/runs/668806fa244e3c6918b3120f\n",
+      "Downloads: https://api.biosimulations.org/results/668806fa244e3c6918b3120f/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806fa244e3c6918b3120f?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'neuron', 'simulatorVersion': '8.0.2', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5a845236cbff49b486f9878c692b5a42\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806fc244e3c6918b3121f\n",
+      "View: https://api.biosimulations.org/runs/668806fc244e3c6918b3121f\n",
+      "Downloads: https://api.biosimulations.org/results/668806fc244e3c6918b3121f/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806fc244e3c6918b3121f?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'opencor', 'simulatorVersion': '2021-10-05', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c0993445e55b4bc3a12f1f52b98b6b6a\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806fdececf8e28b89fcdd\n",
+      "View: https://api.biosimulations.org/runs/668806fdececf8e28b89fcdd\n",
+      "Downloads: https://api.biosimulations.org/results/668806fdececf8e28b89fcdd/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806fdececf8e28b89fcdd?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'pyneuroml', 'simulatorVersion': '0.5.20', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=2e5968b0640040f1aa0279c45fd92e75\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806ffececf8e28b89fce5\n",
+      "View: https://api.biosimulations.org/runs/668806ffececf8e28b89fce5\n",
+      "Downloads: https://api.biosimulations.org/results/668806ffececf8e28b89fce5/download\n",
+      "Logs: https://api.biosimulations.org/logs/668806ffececf8e28b89fce5?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'pysces', 'simulatorVersion': '1.2.1', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=dc3365a2494446c7a9e1b025984a0452\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880701fb4b102485fe22e2\n",
+      "View: https://api.biosimulations.org/runs/66880701fb4b102485fe22e2\n",
+      "Downloads: https://api.biosimulations.org/results/66880701fb4b102485fe22e2/download\n",
+      "Logs: https://api.biosimulations.org/logs/66880701fb4b102485fe22e2?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'rbapy', 'simulatorVersion': '1.0.2', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
       "pyNeuroML >>> DEBUG - data is:\n",
-      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}\n",
-      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"ucbtrin@ucl.ac.uk\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c1fa1e3657fc41659f0f2158456e8db7\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=978baa42c2314a1a8c63d8112169c7f8\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -83,67 +451,358 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668666cf6b7c343121b0ac70\n",
-      "View: https://api.biosimulations.org/runs/668666cf6b7c343121b0ac70\n",
-      "Downloads: https://api.biosimulations.org/results/668666cf6b7c343121b0ac70/download\n",
-      "Logs: https://api.biosimulations.org/logs/668666cf6b7c343121b0ac70?includeOutput=true\n",
-      "Downloading results...\n",
-      "Download completed.\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880703fb4b102485fe22ef\n",
+      "View: https://api.biosimulations.org/runs/66880703fb4b102485fe22ef\n",
+      "Downloads: https://api.biosimulations.org/results/66880703fb4b102485fe22ef/download\n",
+      "Logs: https://api.biosimulations.org/logs/66880703fb4b102485fe22ef?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'smoldyn', 'simulatorVersion': '2.72', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6294eb22392e403296800f8ed5472108\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880705ececf8e28b89fd01\n",
+      "View: https://api.biosimulations.org/runs/66880705ececf8e28b89fd01\n",
+      "Downloads: https://api.biosimulations.org/results/66880705ececf8e28b89fd01/download\n",
+      "Logs: https://api.biosimulations.org/logs/66880705ececf8e28b89fd01?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'tellurium', 'simulatorVersion': '2.2.8', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=754b851ebd654c89b4a87779de1b997b\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880707ececf8e28b89fd06\n",
+      "View: https://api.biosimulations.org/runs/66880707ececf8e28b89fd06\n",
+      "Downloads: https://api.biosimulations.org/results/66880707ececf8e28b89fd06/download\n",
+      "Logs: https://api.biosimulations.org/logs/66880707ececf8e28b89fd06?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'vcell', 'simulatorVersion': '7.5.0.99', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6218fc6f41c64866a5878c7a3c2d0721\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880709244e3c6918b31257\n",
+      "View: https://api.biosimulations.org/runs/66880709244e3c6918b31257\n",
+      "Downloads: https://api.biosimulations.org/results/66880709244e3c6918b31257/download\n",
+      "Logs: https://api.biosimulations.org/logs/66880709244e3c6918b31257?includeOutput=true\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "pyNeuroML >>> DEBUG - Sim dict is: {'name': 'test', 'simulator': 'xpp', 'simulatorVersion': '8.0', 'cpus': 1, 'memory': 8, 'maxTime': 20, 'envVars': [], 'purpose': 'academic', 'email': ''}\n",
+      "pyNeuroML >>> DEBUG - simulation_run_request is {\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}\n",
+      "pyNeuroML >>> DEBUG - data is:\n",
+      "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
+      "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=8b212524d2d54e80a29a58cb2c8efe9b\n",
+      "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 6688070b244e3c6918b31272\n",
+      "View: https://api.biosimulations.org/runs/6688070b244e3c6918b31272\n",
+      "Downloads: https://api.biosimulations.org/results/6688070b244e3c6918b31272/download\n",
+      "Logs: https://api.biosimulations.org/logs/6688070b244e3c6918b31272?includeOutput=true\n"
      ]
     }
    ],
    "source": [
-    "from pyneuroml import biosimulations\n",
-    "\n",
-    "# get the version of the engine\n",
-    "engine = 'tellurium'\n",
-    "engine_version = biosimulations.get_simulator_versions(engine)\n",
+    "output_dir = 'remote_results'\n",
     "\n",
-    "#put the sedml and sbml into a combine archive\n",
-    "omex_filepath = utils.create_omex(sedml_filepath,sbml_filepath)\n",
-    "omex_file_name = os.path.basename(omex_filepath)\n",
+    "download_links_dict = dict()\n",
+    "for e in engines.keys():\n",
+    "    download_link = utils.run_biosimulators_remote(e, sedml_filepath, sbml_filepath)\n",
+    "    download_links_dict[e] = download_link"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Downloading amici results...\n",
+      "Downloading brian2 results...\n",
+      "Downloading bionetgen results...\n",
+      "Downloading boolnet results...\n",
+      "Downloading cbmpy results...\n",
+      "Downloading cobrapy results...\n",
+      "Downloading copasi results...\n",
+      "Downloading gillespy2 results...\n",
+      "Downloading ginsim results...\n",
+      "Downloading libsbmlsim results...\n",
+      "Downloading masspy results...\n",
+      "Downloading netpyne results...\n",
+      "Downloading neuron results...\n",
+      "Downloading opencor results...\n",
+      "Downloading pyneuroml results...\n",
+      "Downloading pysces results...\n",
+      "Downloading rbapy results...\n",
+      "Downloading smoldyn results...\n",
+      "Downloading tellurium results...\n",
+      "Downloading vcell results...\n",
+      "Downloading xpp results...\n"
+     ]
+    }
+   ],
+   "source": [
+    "extract_dir_dict = dict()\n",
+    "for e, link in download_links_dict.items():\n",
+    "    extract_dir = utils.get_remote_results(e, link, output_dir)\n",
+    "    extract_dir_dict[e] = extract_dir"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import yaml\n",
+    "results = dict()\n",
     "\n",
-    "sim_dict = {\n",
-    "              \"name\": \"test\",\n",
-    "              \"simulator\": engine,\n",
-    "              \"simulatorVersion\": engine_version[engine][-1],\n",
-    "              \"cpus\": 1,\n",
-    "              \"memory\": 8,\n",
-    "              \"maxTime\": 20,\n",
-    "              \"envVars\": [],\n",
-    "              \"purpose\": \"academic\",\n",
-    "              \"email\": \"ucbtrin@ucl.ac.uk\",\n",
-    "            }\n",
+    "for e, extract_dir in extract_dir_dict.items():\n",
+    "    status = \"\"\n",
+    "    error_message = \"\"\n",
+    "    exception_type = \"\"\n",
     "\n",
-    "download_link, result = biosimulations.submit_simulation_archive(\\\n",
-    "    archive_file=omex_file_name,\\\n",
-    "    sim_dict=sim_dict)\n"
+    "    log_yml_path = utils.find_file_in_dir('log.yml', extract_dir)[0]\n",
+    "    if not log_yml_path:\n",
+    "        status = None\n",
+    "        error_message = 'log.yml not found'\n",
+    "        continue\n",
+    "    with open(log_yml_path) as f:\n",
+    "        log_yml_dict = yaml.safe_load(f)\n",
+    "        if log_yml_dict['status'] == 'SUCCEEDED':\n",
+    "            status = 'pass'\n",
+    "        elif log_yml_dict['status'] == 'FAILED':\n",
+    "            status = 'FAIL'\n",
+    "            exception = log_yml_dict['exception']\n",
+    "            error_message = exception['message']\n",
+    "            exception_type = exception['type'] \n",
+    "        else:\n",
+    "            status = None\n",
+    "        results[e] = [status, error_message, exception_type] \n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Downloading results...\n",
-      "Download completed.\n",
-      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\results\\log.yml\n"
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\remote_results\n"
      ]
+    },
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
+      ],
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "\n",
+       "\u001b[1m[\u001b[0m\n",
+       "    \u001b[32m'd1_plots_remote\\\\amici_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\bionetgen_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\boolnet_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\cbmpy_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\cobrapy_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\copasi_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\gillespy2_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\ginsim_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\libsbmlsim_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\masspy_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\pysces_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\rbapy_d1.pdf'\u001b[0m,\n",
+       "    \u001b[32m'd1_plots_remote\\\\tellurium_d1.pdf'\u001b[0m\n",
+       "\u001b[1m]\u001b[0m"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
-    "filepath_results = utils.download_file_from_link(download_link)\n",
-    "extract_dir = os.path.join(cwd, 'results')\n",
-    "# fetch yml log file from extract_dir\n",
-    "yml_log =  os.path.join(extract_dir, 'log.yml')\n",
-    "print(yml_log)\n",
+    "# make list of pdf files in all directories in values extract_dir_dict\n",
+    "# find all pdf files in cwd/ output_dir\n",
+    "directory = os.path.join(cwd, output_dir)\n",
+    "print(directory)\n",
+    "file_paths = utils.find_files(directory, 'pdf')\n",
+    "utils.move_d1_files(file_paths, 'd1_plots_remote')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/markdown": [
+       "## Remote Results"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/markdown": [
+       "| Engine     | pass/FAIL                                | Error                                                                                                                                                                                                                                                                                                                                                                                                                                                              | Type                         | Compatibility                                                                                                                                                                                                                                                              | d1                                                         |\n",
+       "|:-----------|:-----------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|\n",
+       "| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <a href=\"d1_plots\\amici_d1.pdf\">amici_d1.pdf</a>           |\n",
+       "| brian2     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |\n",
+       "| bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | CombineArchiveExecutionError | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href=\"d1_plots\\bionetgen_d1.pdf\">bionetgen_d1.pdf</a>   |\n",
+       "| boolnet    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | CombineArchiveExecutionError | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href=\"d1_plots\\boolnet_d1.pdf\">boolnet_d1.pdf</a>       |\n",
+       "| cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href=\"d1_plots\\cbmpy_d1.pdf\">cbmpy_d1.pdf</a>           |\n",
+       "| cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href=\"d1_plots\\cobrapy_d1.pdf\">cobrapy_d1.pdf</a>       |\n",
+       "| copasi     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href=\"d1_plots\\copasi_d1.pdf\">copasi_d1.pdf</a>         |\n",
+       "| gillespy2  | pass                                     | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href=\"d1_plots\\gillespy2_d1.pdf\">gillespy2_d1.pdf</a>   |\n",
+       "| ginsim     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | CombineArchiveExecutionError | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href=\"d1_plots\\ginsim_d1.pdf\">ginsim_d1.pdf</a>         |\n",
+       "| libsbmlsim | pass                                     | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href=\"d1_plots\\libsbmlsim_d1.pdf\">libsbmlsim_d1.pdf</a> |\n",
+       "| masspy     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href=\"d1_plots\\masspy_d1.pdf\">masspy_d1.pdf</a>         |\n",
+       "| netpyne    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |\n",
+       "| neuron     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    |                                                            |\n",
+       "| opencor    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            |                                                            |\n",
+       "| pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> |                                                            |\n",
+       "| pysces     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpbz6s_tkd/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpbz6s_tkd/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href=\"d1_plots\\pysces_d1.pdf\">pysces_d1.pdf</a>         |\n",
+       "| rbapy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | CombineArchiveExecutionError | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href=\"d1_plots\\rbapy_d1.pdf\">rbapy_d1.pdf</a>           |\n",
+       "| smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |\n",
+       "| tellurium  | pass                                     | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <a href=\"d1_plots\\tellurium_d1.pdf\">tellurium_d1.pdf</a>   |\n",
+       "| vcell      | pass                                     | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |\n",
+       "| xpp        | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# Create a table of the results\n",
+    "results_table = pd.DataFrame.from_dict(results).T\n",
+    "results_table.columns = ['pass/FAIL', 'Error','Type']\n",
+    "results_table.index.name = 'Engine'\n",
+    "results_table.reset_index(inplace=True)\n",
+    "\n",
+    "results_table['Error'] = results_table.apply(lambda x: None if x['pass/FAIL'] == x['Error'] else x['Error'], axis=1)\n",
+    "results_table['pass/FAIL'] = results_table['pass/FAIL'].replace('other', 'FAIL')\n",
+    "# results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: x if x == 'FAIL' else x)\n",
+    "\n",
+    "\n",
+    "results_table['Error'] = results_table['Error'].apply(lambda x: utils.ansi_to_html(x))\n",
+    "results_table['Error'] = results_table['Error'].apply(lambda x: utils.collapsible_content(x))\n",
+    "\n",
+    "# compatibility_message\n",
+    "results_table['Compatibility'] = results_table['Engine'].apply(lambda x: utils.check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))\n",
+    "results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: utils.collapsible_content(x[1], title=x[0]))\n",
+    "results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: f'<span style=\"color:darkred;\">{x}</span>' if x == 'FAIL' else x)\n",
+    "results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: f'<span style=\"color:darkred;\">{x}</span>' if 'FAIL' in x else x)\n",
+    "\n",
+    "# d1 plot clickable link\n",
+    "results_table['d1'] = results_table['Engine'].apply(lambda x: utils.d1_plots_dict(engines, 'd1_plots').get(x, None))\n",
+    "results_table['d1'] = results_table['d1'].apply(lambda x: utils.create_hyperlink(x))\n",
+    "\n",
+    "results_md_table = results_table.to_markdown(index=False)\n",
+    "\n",
+    "display_markdown('## Remote Results', raw=True)\n",
+    "display_markdown(results_md_table, raw=True)\n",
     "\n",
-    "shutil.unpack_archive(filepath_results, extract_dir=extract_dir)\n",
-    "os.remove(filepath_results)\n"
+    "# give table as a row above the table\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 31,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
+      ],
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "\u001b[1m[\u001b[0m\u001b[32m'pass'\u001b[0m, \u001b[32m\"No module named 'libsbml'\"\u001b[0m, \u001b[32m'ModuleNotFoundError'\u001b[0m\u001b[1m]\u001b[0m"
+      ]
+     },
+     "execution_count": 31,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "results['tellurium']"
    ]
   },
   {
@@ -151,12 +810,65 @@
    "metadata": {},
    "source": [
     "## test compatibility biosimulators locally using docker\n",
-    "see https://github.com/OpenSourceBrain/SBMLShowcase/issues/31\n"
+    "see https://github.com/OpenSourceBrain/SBMLShowcase/issues/31\n",
+    "\n",
+    "! Start docker before running the below script\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Running amici\n",
+      "Running brian2\n",
+      "Running bionetgen\n",
+      "Running boolnet\n",
+      "Running cbmpy\n",
+      "Running cobrapy\n",
+      "Running copasi\n",
+      "Running gillespy2\n",
+      "Running ginsim\n",
+      "Running libsbmlsim\n",
+      "Running masspy\n",
+      "Running netpyne\n",
+      "Running neuron\n",
+      "Running opencor\n",
+      "Running pyneuroml\n",
+      "Running pysces\n",
+      "Running rbapy\n",
+      "Running smoldyn\n",
+      "Running tellurium\n",
+      "Running vcell\n",
+      "Running xpp\n"
+     ]
+    }
+   ],
+   "source": [
+    "engine_dict = {}\n",
+    "\n",
+    "output_folder = 'output'\n",
+    "\n",
+    "for e in engines.keys():\n",
+    "    print('Running ' + e)\n",
+    "    output_dir = os.path.abspath(os.path.join(output_folder, e))\n",
+    "    try:\n",
+    "        record = utils.run_biosimulators_docker(e, sedml_filepath, sbml_filepath, output_dir=output_dir)\n",
+    "        engine_dict[e] = record\n",
+    "    except Exception as error:\n",
+    "        error_message = str(error)\n",
+    "        print(f\"Error occurred while running {e}\")\n",
+    "        engine_dict[e] = error_message\n",
+    "        continue"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 28,
    "metadata": {},
    "outputs": [
     {
@@ -183,20 +895,7 @@
       "Running smoldyn\n",
       "Running tellurium\n",
       "Running vcell\n",
-      "Running xpp\n",
-      "d1_plots\\amici_d1.pdf\n",
-      "d1_plots\\bionetgen_d1.pdf\n",
-      "d1_plots\\boolnet_d1.pdf\n",
-      "d1_plots\\cbmpy_d1.pdf\n",
-      "d1_plots\\cobrapy_d1.pdf\n",
-      "d1_plots\\copasi_d1.pdf\n",
-      "d1_plots\\gillespy2_d1.pdf\n",
-      "d1_plots\\ginsim_d1.pdf\n",
-      "d1_plots\\libsbmlsim_d1.pdf\n",
-      "d1_plots\\masspy_d1.pdf\n",
-      "d1_plots\\pysces_d1.pdf\n",
-      "d1_plots\\rbapy_d1.pdf\n",
-      "d1_plots\\tellurium_d1.pdf\n"
+      "Running xpp\n"
      ]
     }
    ],
@@ -219,14 +918,26 @@
     "\n",
     "file_paths = utils.find_files(output_folder, '.pdf')\n",
     "utils.move_d1_files(file_paths, 'd1_plots')\n",
-    "shutil.rmtree(output_folder)"
+    "\n",
+    "# if it exists remove the output folder\n",
+    "if os.path.exists(output_folder):\n",
+    "    shutil.rmtree(output_folder)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 29,
    "metadata": {},
    "outputs": [
+    {
+     "data": {
+      "text/markdown": [
+       "## Local via Docker Results"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
     {
      "data": {
       "text/markdown": [
@@ -234,24 +945,24 @@
        "|:-----------|:-----------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|\n",
        "| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <a href=\"d1_plots\\amici_d1.pdf\">amici_d1.pdf</a>           |\n",
        "| brian2     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |\n",
-       "| bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp149263` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href=\"d1_plots\\bionetgen_d1.pdf\">bionetgen_d1.pdf</a>   |\n",
-       "| boolnet    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp151894` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).<br>R[write to console]: Warning message:<br><br>R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :<br>R[write to console]: <br> <br>R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages<br><br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href=\"d1_plots\\boolnet_d1.pdf\">boolnet_d1.pdf</a>       |\n",
-       "| cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><br>INFO: No xlwt module available, Excel spreadsheet creation disabled<br><br><br><br>No module named 'cplex'<br><br><br><br>CPLEX not available<br><br>*****<br>Using GLPK<br>*****<br><br><br>INFO: No xlrd module available, Excel spreadsheet reading disabled<br><br>CBMPy environment<br>******************<br>Revision: r689<br><br><br>***********************************************************************<br>* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *<br>*                http://cbmpy.sourceforge.net                         *<br>* Copyright(C) Brett G. Olivier 2014 - 2019                           *<br>* Dept. of Systems Bioinformatics                                     *<br>* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *<br>* CBMPy is developed as part of the BeBasic MetaToolKit Project       *<br>* Distributed under the GNU GPL v 3.0 licence, see                    *<br>* LICENCE (supplied with this release) for details                    *<br>***********************************************************************<br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp369389` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href=\"d1_plots\\cbmpy_d1.pdf\">cbmpy_d1.pdf</a>           |\n",
-       "| cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp31836` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href=\"d1_plots\\cobrapy_d1.pdf\">cobrapy_d1.pdf</a>       |\n",
-       "| copasi     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp987364` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href=\"d1_plots\\copasi_d1.pdf\">copasi_d1.pdf</a>         |\n",
+       "| bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp683880` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href=\"d1_plots\\bionetgen_d1.pdf\">bionetgen_d1.pdf</a>   |\n",
+       "| boolnet    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp95718` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).<br>R[write to console]: Warning message:<br><br>R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :<br>R[write to console]: <br> <br>R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages<br><br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href=\"d1_plots\\boolnet_d1.pdf\">boolnet_d1.pdf</a>       |\n",
+       "| cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><br>INFO: No xlwt module available, Excel spreadsheet creation disabled<br><br><br><br>No module named 'cplex'<br><br><br><br>CPLEX not available<br><br>*****<br>Using GLPK<br>*****<br><br><br>INFO: No xlrd module available, Excel spreadsheet reading disabled<br><br>CBMPy environment<br>******************<br>Revision: r689<br><br><br>***********************************************************************<br>* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *<br>*                http://cbmpy.sourceforge.net                         *<br>* Copyright(C) Brett G. Olivier 2014 - 2019                           *<br>* Dept. of Systems Bioinformatics                                     *<br>* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *<br>* CBMPy is developed as part of the BeBasic MetaToolKit Project       *<br>* Distributed under the GNU GPL v 3.0 licence, see                    *<br>* LICENCE (supplied with this release) for details                    *<br>***********************************************************************<br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp663224` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href=\"d1_plots\\cbmpy_d1.pdf\">cbmpy_d1.pdf</a>           |\n",
+       "| cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp736148` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href=\"d1_plots\\cobrapy_d1.pdf\">cobrapy_d1.pdf</a>       |\n",
+       "| copasi     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp315353` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[W]'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href=\"d1_plots\\copasi_d1.pdf\">copasi_d1.pdf</a>         |\n",
        "| gillespy2  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href=\"d1_plots\\gillespy2_d1.pdf\">gillespy2_d1.pdf</a>   |\n",
-       "| ginsim     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp382733` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000<br></details> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href=\"d1_plots\\ginsim_d1.pdf\">ginsim_d1.pdf</a>         |\n",
+       "| ginsim     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp444220` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000<br></details> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href=\"d1_plots\\ginsim_d1.pdf\">ginsim_d1.pdf</a>         |\n",
        "| libsbmlsim | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href=\"d1_plots\\libsbmlsim_d1.pdf\">libsbmlsim_d1.pdf</a> |\n",
-       "| masspy     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp750289` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href=\"d1_plots\\masspy_d1.pdf\">masspy_d1.pdf</a>         |\n",
+       "| masspy     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp68973` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href=\"d1_plots\\masspy_d1.pdf\">masspy_d1.pdf</a>         |\n",
        "| netpyne    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |\n",
-       "| neuron     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'NeuroML', 'LEMS']</details></span>    |                                                            |\n",
+       "| neuron     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    |                                                            |\n",
        "| opencor    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            |                                                            |\n",
-       "| pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'NeuroML', 'LEMS']</details></span> |                                                            |\n",
-       "| pysces     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>Could not find GLIMDA.<br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp757728` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp0b0_er9p/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp0b0_er9p/./LEMS_NML2_Ex9_FN.sbml.xml does not exist<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href=\"d1_plots\\pysces_d1.pdf\">pysces_d1.pdf</a>         |\n",
-       "| rbapy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp987912` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).<br></details>                 | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href=\"d1_plots\\rbapy_d1.pdf\">rbapy_d1.pdf</a>           |\n",
-       "| smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>[Errno 2] No such file or directory: '/tmp/tmpmu42eki7/model.txt'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |\n",
+       "| pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> |                                                            |\n",
+       "| pysces     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>Could not find GLIMDA.<br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp568087` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpphuv4n0q/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpphuv4n0q/./LEMS_NML2_Ex9_FN.sbml.xml does not exist<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href=\"d1_plots\\pysces_d1.pdf\">pysces_d1.pdf</a>         |\n",
+       "| rbapy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp941296` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).<br></details>                 | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href=\"d1_plots\\rbapy_d1.pdf\">rbapy_d1.pdf</a>           |\n",
+       "| smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>[Errno 2] No such file or directory: '/tmp/tmpxu9n6is0/model.txt'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |\n",
        "| tellurium  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <a href=\"d1_plots\\tellurium_d1.pdf\">tellurium_d1.pdf</a>   |\n",
-       "| vcell      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1: b'  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SEDML(preProcessDoc)  **** Error: SED-ML processing for /tmp/vcell_temp_4d26fa44-2457-4a00-b0d1-d8bf8a3a541412142204403474173125/tmp605892 failed with error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  SIMULATIONS_RUN(runSimulations)  **** Error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SIMULATION_OUTPUTS(processOutputs)  **** Error: Error processing outputs\\n'```</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |\n",
+       "| vcell      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1: b'  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SEDML(preProcessDoc)  **** Error: SED-ML processing for /tmp/vcell_temp_46077126-d76f-4cd8-acf3-9a4e6e14494514203906214399449282/tmp886838 failed with error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  SIMULATIONS_RUN(runSimulations)  **** Error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SIMULATION_OUTPUTS(processOutputs)  **** Error: Error processing outputs\\n'```</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |\n",
        "| xpp        | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |"
       ]
      },
@@ -286,12 +997,13 @@
     "results_table['d1'] = results_table['d1'].apply(lambda x: utils.create_hyperlink(x))\n",
     "\n",
     "results_md_table = results_table.to_markdown(index=False)\n",
+    "display_markdown('## Local via Docker Results', raw=True)\n",
     "display_markdown(results_md_table, raw=True)\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/utils/__init__.py b/utils/__init__.py
index 8a31943..1b33ba6 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -18,6 +18,7 @@
 import libsedml
 import tempfile
 import glob
+from pyneuroml import biosimulations
 
 # 
 engines = {
@@ -240,6 +241,28 @@ def find_files(directory, extension):
     files = glob.glob(f"{directory}/**/*{extension}", recursive=True)
     return files
 
+
+def find_file_in_dir(file_name, directory):
+    """
+    Searches for a specific file in a given directory and its subdirectories.
+
+    Parameters:
+    file_name (str): The name of the file to search for.
+    directory (str): The directory to search in.
+
+    Returns:
+    str: The path of the found file. If the file is not found, returns None.
+    """
+
+    list_of_files = []
+    for root, _, files in os.walk(directory):
+        for file in files:
+            if file == file_name:
+                file_path = os.path.join(root, file)
+                list_of_files.append(file_path)
+    return list_of_files
+
+
 def move_d1_files(file_paths, plot_dir='d1_plots',engines=engines):
     if not os.path.exists(plot_dir):
         os.makedirs(plot_dir, exist_ok=True)
@@ -281,10 +304,13 @@ def ansi_to_html(text):
         text_message = re.findall(r'"([^"]*)"', text) 
         if len(text_message) > 0:
             text = text_message
+            text = bytes(text[0], "utf-8").decode("unicode_escape")
+        elif 'The COMBINE/OMEX did not execute successfully:' in text:
+            text = text # to deal with remote error message
         else:
             text = text.replace('|', '')
             return text
-        text = bytes(text[0], "utf-8").decode("unicode_escape")
+
         text = text.replace('|', '')
 
         # # for any text with "<*>" remove "<" as well as ">" but leave wildcard text *
@@ -377,8 +403,65 @@ def delete_output_folder(output_dir):
         elif os.path.isdir(file_path):
             shutil.rmtree(file_path)
 
+def run_biosimulators_remote(engine,sedml_filepath,sbml_filepath):
+    '''
+    put the sedml and sbml file into an omex archive
+    run it remotely using biosimulators
+    '''
+
+    #put the sedml and sbml into a combine archive
+    omex_filepath = create_omex(sedml_filepath,sbml_filepath)
+    omex_file_name = os.path.basename(omex_filepath)
+
+    # get the version of the engine
+    engine_version = biosimulations.get_simulator_versions(engine)
+
+    sim_dict = {
+                "name": "test",
+                "simulator": engine,
+                "simulatorVersion": engine_version[engine][-1], # get the latest version
+                "cpus": 1,
+                "memory": 8,
+                "maxTime": 20,
+                "envVars": [],
+                "purpose": "academic",
+                "email": "",
+                }
+
+    download_link, _ = biosimulations.submit_simulation_archive(\
+        archive_file=omex_file_name,\
+        sim_dict=sim_dict)
+    
+    return download_link
+
+def get_remote_results(engine, download_link, output_dir='remote_results'):
+
+    filepath_results = download_file_from_link(engine, download_link)
+    extract_dir = os.path.join(os.getcwd(), output_dir, engine)
+    shutil.unpack_archive(filepath_results, extract_dir=extract_dir)
+    os.remove(filepath_results)
+
+    return extract_dir
+
+def rename_files_in_extract_dir(extract_dir, engine):
+    
+    # find the log.yml file in the extracted directory
+    log_yml_path = find_file_in_dir('log.yml', extract_dir)[0]
+    with open(log_yml_path) as f:
+        log_yml_dict = yaml.safe_load(f)
+    
+    # rename log.yml file to '{engine}_log.yml'
+    new_file_name = f'{engine}_log.yml'
+    root = os.path.dirname(log_yml_path)
+    new_file_path = os.path.join(root, new_file_name)
+    if os.path.exists(new_file_path):
+        os.remove(new_file_path)
+    os.rename(log_yml_path, new_file_path)
+    
+    return extract_dir
+
 
-def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir=None,error_categories=error_categories):
+def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='output',error_categories=error_categories):
     '''
     put the sedml and sbml file into an omex archive
     run it locally using a biosimulators docker
@@ -400,7 +483,7 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir=None
     log_str = read_log_yml(os.path.join(os.path.dirname(omex_filepath),"log.yml"))
 
     if log_str:
-        error_str = log_str
+        error_str = str(log_str)
     # if log_str:
     #     error_str = safe_md_string(log_str)
 
@@ -807,7 +890,7 @@ def safe_md_string(value):
 
 import time
 
-def download_file_from_link(download_link, output_file='results.zip', max_wait_time=120, wait_time=2):
+def download_file_from_link(engine, download_link, output_file='results.zip', max_wait_time=120, wait_time=2):
     """
     Function to download a file from a given URL.
 
@@ -836,16 +919,15 @@ def download_file_from_link(download_link, output_file='results.zip', max_wait_t
 
     # If status == 200 then download the results
     if response.status_code == 200:
-        print('Downloading results...')
+        print(f'Downloading {engine} results...')
         with requests.get(download_link, stream=True) as r:
             with open(output_file, 'wb') as f:
                 shutil.copyfileobj(r.raw, f)
-        print('Download completed.')
         # filepath where the file is downloaded
         filepath = os.path.abspath(output_file)
         return filepath
     else:
-        print('Failed to download the file.')
+        print(f'Failed to download {engine} results.')
         return False
 
 # unzip the file in file_path if it is a zip file and remove the zip file, replace with the unzipped folder

From 09ac9753822f7242d2f1f6a48eda58cea72c52ce Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Fri, 5 Jul 2024 16:20:46 +0100
Subject: [PATCH 10/71] add command line script for testing compatability
 biosimulators remotely

---
 ...test_compatibility_biosimulators_remote.py | 102 ++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100644 SBML/test_compatibility_biosimulators_remote.py

diff --git a/SBML/test_compatibility_biosimulators_remote.py b/SBML/test_compatibility_biosimulators_remote.py
new file mode 100644
index 0000000..9e857fe
--- /dev/null
+++ b/SBML/test_compatibility_biosimulators_remote.py
@@ -0,0 +1,102 @@
+'''
+This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file.
+It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation.
+The results are then displayed in a table and saved to a markdown file.
+'''
+#!/usr/bin/env python
+
+'''
+use pymetadata module to create a minimal valid combine archive
+using LEMS_NML2_Ex9_FN.sbml and LEMS_NML2_Ex9_FN.sedml
+'''
+
+import sys
+sys.path.append("..")
+import utils
+import os
+import pandas as pd
+from IPython.display import display_markdown
+import shutil
+import yaml
+
+sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml'
+sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
+
+engines = utils.engines
+types_dict = utils.types_dict
+
+cwd = os.getcwd()
+
+output_dir = 'remote_results'
+
+download_links_dict = dict()
+for e in engines.keys():
+    download_link = utils.run_biosimulators_remote(e, sedml_filepath, sbml_filepath)
+    download_links_dict[e] = download_link
+
+extract_dir_dict = dict()
+for e, link in download_links_dict.items():
+    extract_dir = utils.get_remote_results(e, link, output_dir)
+    extract_dir_dict[e] = extract_dir
+
+
+results = dict()
+for e, extract_dir in extract_dir_dict.items():
+    status = ""
+    error_message = ""
+    exception_type = ""
+
+    log_yml_path = utils.find_file_in_dir('log.yml', extract_dir)[0]
+    if not log_yml_path:
+        status = None
+        error_message = 'log.yml not found'
+        continue
+    with open(log_yml_path) as f:
+        log_yml_dict = yaml.safe_load(f)
+        if log_yml_dict['status'] == 'SUCCEEDED':
+            status = 'pass'
+        elif log_yml_dict['status'] == 'FAILED':
+            status = 'FAIL'
+            exception = log_yml_dict['exception']
+            error_message = exception['message']
+            exception_type = exception['type'] 
+        else:
+            status = None
+        results[e] = [status, error_message, exception_type] 
+
+# make list of pdf files in all directories in values extract_dir_dict
+# find all pdf files in cwd/ output_dir
+directory = os.path.join(cwd, output_dir)
+print(directory)
+file_paths = utils.find_files(directory, 'pdf')
+utils.move_d1_files(file_paths, 'd1_plots_remote')
+
+# Create a table of the results
+results_table = pd.DataFrame.from_dict(results).T
+results_table.columns = ['pass/FAIL', 'Error','Type']
+results_table.index.name = 'Engine'
+results_table.reset_index(inplace=True)
+
+results_table['Error'] = results_table.apply(lambda x: None if x['pass/FAIL'] == x['Error'] else x['Error'], axis=1)
+results_table['pass/FAIL'] = results_table['pass/FAIL'].replace('other', 'FAIL')
+# results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: x if x == 'FAIL' else x)
+
+
+results_table['Error'] = results_table['Error'].apply(lambda x: utils.ansi_to_html(x))
+results_table['Error'] = results_table['Error'].apply(lambda x: utils.collapsible_content(x))
+
+# compatibility_message
+results_table['Compatibility'] = results_table['Engine'].apply(lambda x: utils.check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))
+results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: utils.collapsible_content(x[1], title=x[0]))
+results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if x == 'FAIL' else x)
+results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if 'FAIL' in x else x)
+
+# d1 plot clickable link
+results_table['d1'] = results_table['Engine'].apply(lambda x: utils.d1_plots_dict(engines, 'd1_plots').get(x, None))
+results_table['d1'] = results_table['d1'].apply(lambda x: utils.create_hyperlink(x))
+
+results_md_table = results_table.to_markdown(index=False)
+
+# save results_md_table
+with open('results_compatibility_biosimulators_remote.md', 'w', encoding='utf-8') as f:
+    f.write(results_md_table)
\ No newline at end of file

From 7f95aff4886bcf4d2eaa6e09e6bf3716b8a9222b Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 31 Jul 2024 16:15:18 +0100
Subject: [PATCH 11/71] adjust for changes in pyneuroml development
 biosimulators module

---
 utils/__init__.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/utils/__init__.py b/utils/__init__.py
index 1b33ba6..784b103 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -428,11 +428,13 @@ def run_biosimulators_remote(engine,sedml_filepath,sbml_filepath):
                 "email": "",
                 }
 
-    download_link, _ = biosimulations.submit_simulation_archive(\
+    res = biosimulations.submit_simulation_archive(\
         archive_file=omex_file_name,\
         sim_dict=sim_dict)
     
-    return download_link
+    download_url = res["download"]
+    
+    return download_url
 
 def get_remote_results(engine, download_link, output_dir='remote_results'):
 

From 6c7b12dfdcc5d784066aa1ce91c903ebe3ea104a Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 5 Aug 2024 13:47:19 +0100
Subject: [PATCH 12/71] read log.yml file for error messages

---
 utils/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/utils/__init__.py b/utils/__init__.py
index 9c329a8..11cc15a 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -483,7 +483,7 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='out
     if not error_str: return "pass"
 
     # #try to load the cleaner error message from the log.yml file
-    # log_str = read_log_yml(os.path.join(os.path.dirname(omex_filepath),"log.yml"))
+    log_str = read_log_yml(os.path.join(os.path.dirname(omex_filepath),"log.yml"))
 
     if log_str:
         error_str = str(log_str)

From b2fbbe05aa8354befce91b358862410c9ff45015 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 6 Aug 2024 07:37:55 +0100
Subject: [PATCH 13/71] combine local and remote biosimulators compatibility
 tables and refactoring of test_compatibility_biosimulators.py

---
 .../{d1_plots => d1_plots_local}/amici_d1.pdf | Bin 13644 -> 13644 bytes
 .../bionetgen_d1.pdf                          | Bin 5948 -> 5948 bytes
 .../boolnet_d1.pdf                            | Bin 5948 -> 5948 bytes
 .../{d1_plots => d1_plots_local}/cbmpy_d1.pdf | Bin 5948 -> 5948 bytes
 .../cobrapy_d1.pdf                            | Bin 5948 -> 5948 bytes
 .../copasi_d1.pdf                             | Bin 5948 -> 5948 bytes
 .../gillespy2_d1.pdf                          | Bin 8877 -> 8877 bytes
 .../ginsim_d1.pdf                             | Bin 5948 -> 5948 bytes
 .../libsbmlsim_d1.pdf                         | Bin 14643 -> 14643 bytes
 .../masspy_d1.pdf                             | Bin 5948 -> 5948 bytes
 .../pysces_d1.pdf                             | Bin 5948 -> 5948 bytes
 .../{d1_plots => d1_plots_local}/rbapy_d1.pdf | Bin 5948 -> 5948 bytes
 .../tellurium_d1.pdf                          | Bin 14664 -> 14664 bytes
 SBML/d1_plots_remote/amici_d1.pdf             | Bin 0 -> 13650 bytes
 SBML/d1_plots_remote/bionetgen_d1.pdf         | Bin 0 -> 5954 bytes
 SBML/d1_plots_remote/boolnet_d1.pdf           | Bin 0 -> 5954 bytes
 SBML/d1_plots_remote/cbmpy_d1.pdf             | Bin 0 -> 5954 bytes
 SBML/d1_plots_remote/cobrapy_d1.pdf           | Bin 0 -> 5954 bytes
 SBML/d1_plots_remote/copasi_d1.pdf            | Bin 0 -> 5954 bytes
 SBML/d1_plots_remote/gillespy2_d1.pdf         | Bin 0 -> 8883 bytes
 SBML/d1_plots_remote/ginsim_d1.pdf            | Bin 0 -> 5954 bytes
 SBML/d1_plots_remote/libsbmlsim_d1.pdf        | Bin 0 -> 14649 bytes
 SBML/d1_plots_remote/masspy_d1.pdf            | Bin 0 -> 5954 bytes
 SBML/d1_plots_remote/pysces_d1.pdf            | Bin 0 -> 5954 bytes
 SBML/d1_plots_remote/rbapy_d1.pdf             | Bin 0 -> 5954 bytes
 SBML/d1_plots_remote/tellurium_d1.pdf         | Bin 0 -> 14670 bytes
 SBML/results_compatibility_biosimulators.md   |  46 +++----
 SBML/test_compatibility_biosimulators.py      | 125 +++++++++++++-----
 utils/__init__.py                             |  43 +++++-
 29 files changed, 158 insertions(+), 56 deletions(-)
 rename SBML/{d1_plots => d1_plots_local}/amici_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/bionetgen_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/boolnet_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/cbmpy_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/cobrapy_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/copasi_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/gillespy2_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/ginsim_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/libsbmlsim_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/masspy_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/pysces_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/rbapy_d1.pdf (99%)
 rename SBML/{d1_plots => d1_plots_local}/tellurium_d1.pdf (99%)
 create mode 100644 SBML/d1_plots_remote/amici_d1.pdf
 create mode 100644 SBML/d1_plots_remote/bionetgen_d1.pdf
 create mode 100644 SBML/d1_plots_remote/boolnet_d1.pdf
 create mode 100644 SBML/d1_plots_remote/cbmpy_d1.pdf
 create mode 100644 SBML/d1_plots_remote/cobrapy_d1.pdf
 create mode 100644 SBML/d1_plots_remote/copasi_d1.pdf
 create mode 100644 SBML/d1_plots_remote/gillespy2_d1.pdf
 create mode 100644 SBML/d1_plots_remote/ginsim_d1.pdf
 create mode 100644 SBML/d1_plots_remote/libsbmlsim_d1.pdf
 create mode 100644 SBML/d1_plots_remote/masspy_d1.pdf
 create mode 100644 SBML/d1_plots_remote/pysces_d1.pdf
 create mode 100644 SBML/d1_plots_remote/rbapy_d1.pdf
 create mode 100644 SBML/d1_plots_remote/tellurium_d1.pdf

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similarity index 99%
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z;qU#RP{8Z>Z7dvt{Dp?Mr<J2K%Jb~IM}5beC_wK)U_CcC^bhvTAga6C0jBf2-382r
Ym$#Lt_t{SbSXMCz5f6{@MHQm|2OPve8~^|S

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HcmV?d00001

diff --git a/SBML/results_compatibility_biosimulators.md b/SBML/results_compatibility_biosimulators.md
index c5cfc5b..23f2984 100644
--- a/SBML/results_compatibility_biosimulators.md
+++ b/SBML/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| Engine     | pass/FAIL                                | Error                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Compatibility                                                                                                                                                                                                                                                              | d1                                                         |
-|:-----------|:-----------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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-| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       | <a href="d1_plots\amici_d1.pdf">amici_d1.pdf</a>           |
-| brian2     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |
-| bionetgen  | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp179064` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style="color:red;"><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href="d1_plots\bionetgen_d1.pdf">bionetgen_d1.pdf</a>   |
-| boolnet    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp515819` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style="color:red;"><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).<br>R[write to console]: Warning message:<br><br>R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :<br>R[write to console]: <br> <br>R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages<br><br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href="d1_plots\boolnet_d1.pdf">boolnet_d1.pdf</a>       |
-| cbmpy      | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><br>INFO: No xlwt module available, Excel spreadsheet creation disabled<br><br><br><br>No module named 'cplex'<br><br><br><br>CPLEX not available<br><br>*****<br>Using GLPK<br>*****<br><br><br>INFO: No xlrd module available, Excel spreadsheet reading disabled<br><br>CBMPy environment<br>******************<br>Revision: r689<br><br><br>***********************************************************************<br>* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *<br>*                http://cbmpy.sourceforge.net                         *<br>* Copyright(C) Brett G. Olivier 2014 - 2019                           *<br>* Dept. of Systems Bioinformatics                                     *<br>* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *<br>* CBMPy is developed as part of the BeBasic MetaToolKit Project       *<br>* Distributed under the GNU GPL v 3.0 licence, see                    *<br>* LICENCE (supplied with this release) for details                    *<br>***********************************************************************<br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp133820` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style="color:red;"><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href="d1_plots\cbmpy_d1.pdf">cbmpy_d1.pdf</a>           |
-| cobrapy    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp818452` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style="color:red;"><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href="d1_plots\cobrapy_d1.pdf">cobrapy_d1.pdf</a>       |
-| copasi     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp443395` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[W]'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <a href="d1_plots\copasi_d1.pdf">copasi_d1.pdf</a>         |
-| gillespy2  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href="d1_plots\gillespy2_d1.pdf">gillespy2_d1.pdf</a>   |
-| ginsim     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp737874` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style="color:red;"><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000<br></details> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href="d1_plots\ginsim_d1.pdf">ginsim_d1.pdf</a>         |
-| libsbmlsim | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href="d1_plots\libsbmlsim_d1.pdf">libsbmlsim_d1.pdf</a> |
-| masspy     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp539402` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br><span style="color:red;"><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <a href="d1_plots\masspy_d1.pdf">masspy_d1.pdf</a>         |
-| netpyne    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |
-| neuron     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    |                                                            |
-| opencor    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with opencor</details>                                                                                                                     |                                                            |
-| pyneuroml  | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> |                                                            |
-| pysces     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>Could not find GLIMDA.<br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp82785` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpd0feybh_/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpd0feybh_/./LEMS_NML2_Ex9_FN.sbml.xml does not exist<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <a href="d1_plots\pysces_d1.pdf">pysces_d1.pdf</a>         |
-| rbapy      | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style="color:darkorange;">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp129913` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style="color:red;"><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).<br></details>                 | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href="d1_plots\rbapy_d1.pdf">rbapy_d1.pdf</a>           |
-| smoldyn    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>[Errno 2] No such file or directory: '/tmp/tmpss9737_4/model.txt'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |
-| tellurium  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   | <a href="d1_plots\tellurium_d1.pdf">tellurium_d1.pdf</a>   |
-| vcell      | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1: b'  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SEDML(preProcessDoc)  **** Error: SED-ML processing for /tmp/vcell_temp_365be07b-5fd9-47bf-9fe9-8a37eb03827f17379398015478899102/tmp584011 failed with error: \n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  SIMULATIONS_RUN(runSimulations)  **** Error: \n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SIMULATION_OUTPUTS(processOutputs)  **** Error: Error processing outputs\n'```</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |
-| xpp        | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |
\ No newline at end of file
+|    | Engine     | pass/FAIL (remote)                       | pass/FAIL (local)                        | Compatibility (remote)                                                                                                                                                                                                                                                     | Compatibility (local)                                                                                                                                                                                                                                                      | Type (remote)                | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                                                                        | d1 (remote)                                                       | d1 (local)   |
+|---:|:-----------|:-----------------------------------------|:-----------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------|:-------------|
+|  0 | amici      | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\amici_d1.pdf">amici_d1.pdf</a>           |              |
+|  1 | bionetgen  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">bionetgen_d1.pdf</a>   |              |
+|  2 | boolnet    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\boolnet_d1.pdf">boolnet_d1.pdf</a>       |              |
+|  3 | brian2     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                   |              |
+|  4 | cbmpy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\cbmpy_d1.pdf">cbmpy_d1.pdf</a>           |              |
+|  5 | cobrapy    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\cobrapy_d1.pdf">cobrapy_d1.pdf</a>       |              |
+|  6 | copasi     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\copasi_d1.pdf">copasi_d1.pdf</a>         |              |
+|  7 | gillespy2  | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\gillespy2_d1.pdf">gillespy2_d1.pdf</a>   |              |
+|  8 | ginsim     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\ginsim_d1.pdf">ginsim_d1.pdf</a>         |              |
+|  9 | libsbmlsim | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\libsbmlsim_d1.pdf">libsbmlsim_d1.pdf</a> |              |
+| 10 | masspy     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\masspy_d1.pdf">masspy_d1.pdf</a>         |              |
+| 11 | netpyne    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                   |              |
+| 12 | neuron     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                   |              |
+| 13 | opencor    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                   |              |
+| 14 | pyneuroml  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                   |              |
+| 15 | pysces     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp55gzczds/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp55gzczds/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\pysces_d1.pdf">pysces_d1.pdf</a>         |              |
+| 16 | rbapy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\rbapy_d1.pdf">rbapy_d1.pdf</a>           |              |
+| 17 | smoldyn    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                   |              |
+| 18 | tellurium  | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\tellurium_d1.pdf">tellurium_d1.pdf</a>   |              |
+| 19 | vcell      | pass                                     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>No such container: e2d1490af77953d602efa84ffba63a1d9dc905f7f9dd73baa3cc8ee9161e69bd</details>                                                                     |                                                                   |              |
+| 20 | xpp        | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                   |              |
\ No newline at end of file
diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/test_compatibility_biosimulators.py
index 0d2e07d..e76eea3 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/test_compatibility_biosimulators.py
@@ -3,61 +3,122 @@
 It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation.
 The results are then displayed in a table and saved to a markdown file.
 '''
+#!/usr/bin/env python
+
+'''
+use pymetadata module to create a minimal valid combine archive
+using LEMS_NML2_Ex9_FN.sbml and LEMS_NML2_Ex9_FN.sedml
+'''
 
 import sys
 sys.path.append("..")
 import utils
 import os
 import pandas as pd
+from IPython.display import display_markdown
 import shutil
-import argparse
-
-parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines')
-parser.add_argument('--output-dir',action='store',default='d1_plots',help='Where to move the output pdf plots to')
-args = parser.parse_args()
+import yaml
 
 sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml'
-sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing (original file)
+sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
 
 engines = utils.engines
 types_dict = utils.types_dict
 
-engine_dict = {}
 
-output_folder = 'output' #initial temporary output folder
+#########################################################################################
+# Run remotely
+#########################################################################################
+
+remote_output_dir = 'remote_results'
+
+download_links_dict = dict()
+for e in engines.keys():
+    download_link = utils.run_biosimulators_remote(e, sedml_filepath, sbml_filepath)
+    download_links_dict[e] = download_link
+
+extract_dir_dict = dict()
+for e, link in download_links_dict.items():
+    extract_dir = utils.get_remote_results(e, link, remote_output_dir)
+    extract_dir_dict[e] = extract_dir
+
+results = dict()
+for e, extract_dir in extract_dir_dict.items():
+    status = ""
+    error_message = ""
+    exception_type = ""
+
+    log_yml_path = utils.find_file_in_dir('log.yml', extract_dir)[0]
+    if not log_yml_path:
+        status = None
+        error_message = 'log.yml not found'
+        continue
+    with open(log_yml_path) as f:
+        log_yml_dict = yaml.safe_load(f)
+        if log_yml_dict['status'] == 'SUCCEEDED':
+            status = 'pass'
+        elif log_yml_dict['status'] == 'FAILED':
+            status = 'FAIL'
+            exception = log_yml_dict['exception']
+            error_message = exception['message']
+            exception_type = exception['type'] 
+        else:
+            status = None
+        results[e] = [status, error_message, exception_type] 
+
+file_paths = utils.find_files(remote_output_dir, '.pdf')
+utils.move_d1_files(file_paths, 'd1_plots_remote')
+
+# remove the remote results directory
+if os.path.exists(remote_output_dir):
+    shutil.rmtree(remote_output_dir)
+    print('Removed ' + remote_output_dir + ' folder')
+
+#########################################################################################
+# Run locally
+#########################################################################################
+
+results_local = {}
+
+output_folder = 'output'
 
 for e in engines.keys():
     print('Running ' + e)
     output_dir = os.path.abspath(os.path.join(output_folder, e))
-    engine_dict[e] = utils.run_biosimulators_docker(e, sedml_filepath, sbml_filepath, output_dir=output_dir)
-    utils.move_d1_files(utils.find_files(output_dir, '.pdf'), e, args.output_dir)
+    record = utils.run_biosimulators_docker(e, sedml_filepath, sbml_filepath, output_dir=output_dir)
+    results_local[e] = record
+
+file_paths = utils.find_files(output_folder, '.pdf')
+utils.move_d1_files(file_paths, 'd1_plots_local')
 
-shutil.rmtree(output_folder)
+# if it exists remove the output folder
+if os.path.exists(output_folder):
+    shutil.rmtree(output_folder)
+    print('Removed ' + output_folder + ' folder')
 
-# TODO: move part that creates table to utils 
-# Create a table of the results
-results_table = pd.DataFrame.from_dict(engine_dict).T
-results_table.columns = ['pass/FAIL', 'Error']
-results_table.index.name = 'Engine'
-results_table.reset_index(inplace=True)
+#########################################################################################
+# process results and save markdown table
+#########################################################################################
 
-results_table['Error'] = results_table.apply(lambda x: None if x['pass/FAIL'] == x['Error'] else x['Error'], axis=1)
-results_table['pass/FAIL'] = results_table['pass/FAIL'].replace('other', 'FAIL')
+results_table = utils.create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, 'd1_plots_remote')
+results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, 'd1_plots')
 
-results_table['Error'] = results_table['Error'].apply(lambda x: utils.ansi_to_html(x))
-results_table['Error'] = results_table['Error'].apply(lambda x: utils.collapsible_content(x))
+# rename cols to distinguish between local and remote results except for Engine column
+results_table.columns = [str(col) + ' (remote)' if col != 'Engine' else str(col) for col in results_table.columns]
+results_table_local.columns = [str(col) + ' (local)' if col != 'Engine' else str(col) for col in results_table_local.columns]
 
-results_table['Compatibility'] = results_table['Engine'].apply(lambda x: utils.check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))
-results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: utils.collapsible_content(x[1], title=x[0]))
-results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if x == 'FAIL' else x)
-results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if 'FAIL' in x else x)
+# combine remote and local results
+combined_results = pd.merge(results_table, results_table_local, on='Engine', how='outer')
+combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))
 
-# d1 plot clickable link
-results_table['d1'] = results_table['Engine'].apply(lambda x: utils.d1_plots_dict(engines, args.output_dir).get(x, None))
-results_table['d1'] = results_table['d1'].apply(lambda x: utils.create_hyperlink(x))
+cols_order = ['Engine', 'pass/FAIL (remote)', 'pass/FAIL (local)',\
+               'Compatibility (remote)', 'Compatibility (local)', \
+               'Type (remote)', \
+               'Error (remote)', 'Error (local)', \
+               'd1 (remote)', 'd1 (local)']
 
-results_table = results_table.to_markdown(index=False)
+combined_results = combined_results[cols_order]
 
-# save results_md_table
-with open('results_compatibility_biosimulators.md', 'w', encoding='utf-8') as f:
-    f.write(results_table)
+# save the results to a markdown file
+with open('results_compatibility_biosimulators.md', 'w') as f:
+    f.write(combined_results.to_markdown())
diff --git a/utils/__init__.py b/utils/__init__.py
index 11cc15a..e827153 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -19,6 +19,7 @@
 import tempfile
 import glob
 from pyneuroml import biosimulations
+import pandas as pd
 
 # 
 engines = {
@@ -241,8 +242,10 @@ def find_files(directory, extension):
     files = glob.glob(f"{directory}/**/*{extension}", recursive=True)
     return files
 
-def move_d1_files(file_paths, engine, plot_dir='d1_plots'):
+def move_d1_files(file_paths, plot_dir='d1_plots'):
     for fpath in file_paths:
+        # find engine.keys() in the file path and asign to engine
+        engine = next((e for e in engines.keys() if e in fpath), None)
         new_file_path = os.path.join(plot_dir, f'{engine}_{os.path.basename(fpath)}')
         if not os.path.exists(plot_dir): os.makedirs(plot_dir, exist_ok=True)
         if os.path.exists(new_file_path): os.remove(new_file_path)
@@ -972,3 +975,41 @@ def unzip_file(file_path, output_dir=None):
 
     return file_path
 
+
+def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, output_dir):
+    """
+    Create a markdown table of the results.
+    
+    Input: results, types_dict, sbml_filepath, sedml_filepath, engines, output_dir
+    Output: results_md_table
+
+    """
+    # Create a table of the results
+    results_table = pd.DataFrame.from_dict(results).T
+    # if list is three elements 
+    if results_table.shape[1] == 3:
+        results_table.columns = ['pass/FAIL', 'Error', 'Type']
+    elif results_table.shape[1] == 2:
+        results_table.columns = ['pass/FAIL', 'Error']
+
+    results_table.index.name = 'Engine'
+    results_table.reset_index(inplace=True)
+
+    results_table['Error'] = results_table.apply(lambda x: None if x['pass/FAIL'] == x['Error'] else x['Error'], axis=1)
+    results_table['pass/FAIL'] = results_table['pass/FAIL'].replace('other', 'FAIL')
+
+    results_table['Error'] = results_table['Error'].apply(lambda x: ansi_to_html(x))
+    results_table['Error'] = results_table['Error'].apply(lambda x: collapsible_content(x))
+
+    # compatibility_message
+    results_table['Compatibility'] = results_table['Engine'].apply(lambda x: check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))
+    results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: collapsible_content(x[1], title=x[0]))
+    results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if x == 'FAIL' else x)
+    results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if 'FAIL' in x else x)
+
+    # d1 plot clickable link
+    results_table['d1'] = results_table['Engine'].apply(lambda x: d1_plots_dict(engines, output_dir).get(x, None))
+    results_table['d1'] = results_table['d1'].apply(lambda x: create_hyperlink(x))
+
+
+    return results_table

From 7aba39c45e49872108e974ccc396bbb5f2d2087e Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 6 Aug 2024 08:01:10 +0100
Subject: [PATCH 14/71] fix local d1 plots links in results table

---
 SBML/results_compatibility_biosimulators.md | 46 ++++++++++-----------
 SBML/test_compatibility_biosimulators.py    |  2 +-
 2 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/SBML/results_compatibility_biosimulators.md b/SBML/results_compatibility_biosimulators.md
index 23f2984..b8f81c7 100644
--- a/SBML/results_compatibility_biosimulators.md
+++ b/SBML/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-|    | Engine     | pass/FAIL (remote)                       | pass/FAIL (local)                        | Compatibility (remote)                                                                                                                                                                                                                                                     | Compatibility (local)                                                                                                                                                                                                                                                      | Type (remote)                | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                                                                        | d1 (remote)                                                       | d1 (local)   |
-|---:|:-----------|:-----------------------------------------|:-----------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------|:-------------|
-|  0 | amici      | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\amici_d1.pdf">amici_d1.pdf</a>           |              |
-|  1 | bionetgen  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">bionetgen_d1.pdf</a>   |              |
-|  2 | boolnet    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\boolnet_d1.pdf">boolnet_d1.pdf</a>       |              |
-|  3 | brian2     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                   |              |
-|  4 | cbmpy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\cbmpy_d1.pdf">cbmpy_d1.pdf</a>           |              |
-|  5 | cobrapy    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\cobrapy_d1.pdf">cobrapy_d1.pdf</a>       |              |
-|  6 | copasi     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\copasi_d1.pdf">copasi_d1.pdf</a>         |              |
-|  7 | gillespy2  | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\gillespy2_d1.pdf">gillespy2_d1.pdf</a>   |              |
-|  8 | ginsim     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\ginsim_d1.pdf">ginsim_d1.pdf</a>         |              |
-|  9 | libsbmlsim | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\libsbmlsim_d1.pdf">libsbmlsim_d1.pdf</a> |              |
-| 10 | masspy     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\masspy_d1.pdf">masspy_d1.pdf</a>         |              |
-| 11 | netpyne    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                   |              |
-| 12 | neuron     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                   |              |
-| 13 | opencor    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                   |              |
-| 14 | pyneuroml  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                   |              |
-| 15 | pysces     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp55gzczds/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp55gzczds/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\pysces_d1.pdf">pysces_d1.pdf</a>         |              |
-| 16 | rbapy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\rbapy_d1.pdf">rbapy_d1.pdf</a>           |              |
-| 17 | smoldyn    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                   |              |
-| 18 | tellurium  | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\tellurium_d1.pdf">tellurium_d1.pdf</a>   |              |
-| 19 | vcell      | pass                                     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>No such container: e2d1490af77953d602efa84ffba63a1d9dc905f7f9dd73baa3cc8ee9161e69bd</details>                                                                     |                                                                   |              |
-| 20 | xpp        | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                   |              |
\ No newline at end of file
+|    | Engine     | pass/FAIL (remote)                       | pass/FAIL (local)                        | Compatibility (remote)                                                                                                                                                                                                                                                     | Compatibility (local)                                                                                                                                                                                                                                                      | Type (remote)                | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                                                                        | d1 (remote)                                                       | d1 (local)                                                       |
+|---:|:-----------|:-----------------------------------------|:-----------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------|:-----------------------------------------------------------------|
+|  0 | amici      | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\amici_d1.pdf">amici_d1.pdf</a>           | <a href="d1_plots_local\amici_d1.pdf">amici_d1.pdf</a>           |
+|  1 | bionetgen  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">bionetgen_d1.pdf</a>   | <a href="d1_plots_local\bionetgen_d1.pdf">bionetgen_d1.pdf</a>   |
+|  2 | boolnet    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\boolnet_d1.pdf">boolnet_d1.pdf</a>       | <a href="d1_plots_local\boolnet_d1.pdf">boolnet_d1.pdf</a>       |
+|  3 | brian2     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                   |                                                                  |
+|  4 | cbmpy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\cbmpy_d1.pdf">cbmpy_d1.pdf</a>           | <a href="d1_plots_local\cbmpy_d1.pdf">cbmpy_d1.pdf</a>           |
+|  5 | cobrapy    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\cobrapy_d1.pdf">cobrapy_d1.pdf</a>       | <a href="d1_plots_local\cobrapy_d1.pdf">cobrapy_d1.pdf</a>       |
+|  6 | copasi     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\copasi_d1.pdf">copasi_d1.pdf</a>         | <a href="d1_plots_local\copasi_d1.pdf">copasi_d1.pdf</a>         |
+|  7 | gillespy2  | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\gillespy2_d1.pdf">gillespy2_d1.pdf</a>   | <a href="d1_plots_local\gillespy2_d1.pdf">gillespy2_d1.pdf</a>   |
+|  8 | ginsim     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\ginsim_d1.pdf">ginsim_d1.pdf</a>         | <a href="d1_plots_local\ginsim_d1.pdf">ginsim_d1.pdf</a>         |
+|  9 | libsbmlsim | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\libsbmlsim_d1.pdf">libsbmlsim_d1.pdf</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">libsbmlsim_d1.pdf</a> |
+| 10 | masspy     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\masspy_d1.pdf">masspy_d1.pdf</a>         | <a href="d1_plots_local\masspy_d1.pdf">masspy_d1.pdf</a>         |
+| 11 | netpyne    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                   |                                                                  |
+| 12 | neuron     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                   |                                                                  |
+| 13 | opencor    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                   |                                                                  |
+| 14 | pyneuroml  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                   |                                                                  |
+| 15 | pysces     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpf8vg616l/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpf8vg616l/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\pysces_d1.pdf">pysces_d1.pdf</a>         | <a href="d1_plots_local\pysces_d1.pdf">pysces_d1.pdf</a>         |
+| 16 | rbapy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\rbapy_d1.pdf">rbapy_d1.pdf</a>           | <a href="d1_plots_local\rbapy_d1.pdf">rbapy_d1.pdf</a>           |
+| 17 | smoldyn    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                   |                                                                  |
+| 18 | tellurium  | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\tellurium_d1.pdf">tellurium_d1.pdf</a>   | <a href="d1_plots_local\tellurium_d1.pdf">tellurium_d1.pdf</a>   |
+| 19 | vcell      | pass                                     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>No such container: 995fff1ff43d7138f1f6a7d4c6ad58f885e53901f2f5cdaebbb4fb608a8b9521</details>                                                                     |                                                                   |                                                                  |
+| 20 | xpp        | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                   |                                                                  |
\ No newline at end of file
diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/test_compatibility_biosimulators.py
index e76eea3..90d0319 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/test_compatibility_biosimulators.py
@@ -101,7 +101,7 @@
 #########################################################################################
 
 results_table = utils.create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, 'd1_plots_remote')
-results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, 'd1_plots')
+results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, 'd1_plots_local')
 
 # rename cols to distinguish between local and remote results except for Engine column
 results_table.columns = [str(col) + ' (remote)' if col != 'Engine' else str(col) for col in results_table.columns]

From 283fcfb0daceff53af73c212b928cfffda67009a Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 6 Aug 2024 08:29:23 +0100
Subject: [PATCH 15/71] remove seperate remote script and results table after
 integration

---
 ...ults_compatibility_biosimulators_remote.md |  23 ----
 ...test_compatibility_biosimulators_remote.py | 102 ------------------
 2 files changed, 125 deletions(-)
 delete mode 100644 SBML/results_compatibility_biosimulators_remote.md
 delete mode 100644 SBML/test_compatibility_biosimulators_remote.py

diff --git a/SBML/results_compatibility_biosimulators_remote.md b/SBML/results_compatibility_biosimulators_remote.md
deleted file mode 100644
index 1f1167d..0000000
--- a/SBML/results_compatibility_biosimulators_remote.md
+++ /dev/null
@@ -1,23 +0,0 @@
-| Engine     | pass/FAIL                                | Error                                                                                                                                                                                                                                                                                                                                                                                                                                                              | Type                         | Compatibility                                                                                                                                                                                                                                                              | d1                                                         |
-|:-----------|:-----------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|
-| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <a href="d1_plots\amici_d1.pdf">amici_d1.pdf</a>           |
-| brian2     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |
-| bionetgen  | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | CombineArchiveExecutionError | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href="d1_plots\bionetgen_d1.pdf">bionetgen_d1.pdf</a>   |
-| boolnet    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | CombineArchiveExecutionError | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href="d1_plots\boolnet_d1.pdf">boolnet_d1.pdf</a>       |
-| cbmpy      | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href="d1_plots\cbmpy_d1.pdf">cbmpy_d1.pdf</a>           |
-| cobrapy    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href="d1_plots\cobrapy_d1.pdf">cobrapy_d1.pdf</a>       |
-| copasi     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href="d1_plots\copasi_d1.pdf">copasi_d1.pdf</a>         |
-| gillespy2  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href="d1_plots\gillespy2_d1.pdf">gillespy2_d1.pdf</a>   |
-| ginsim     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | CombineArchiveExecutionError | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href="d1_plots\ginsim_d1.pdf">ginsim_d1.pdf</a>         |
-| libsbmlsim | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href="d1_plots\libsbmlsim_d1.pdf">libsbmlsim_d1.pdf</a> |
-| masspy     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href="d1_plots\masspy_d1.pdf">masspy_d1.pdf</a>         |
-| netpyne    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |
-| neuron     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    |                                                            |
-| opencor    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            |                                                            |
-| pyneuroml  | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> |                                                            |
-| pysces     | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpbz6s_tkd/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpbz6s_tkd/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href="d1_plots\pysces_d1.pdf">pysces_d1.pdf</a>         |
-| rbapy      | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | CombineArchiveExecutionError | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href="d1_plots\rbapy_d1.pdf">rbapy_d1.pdf</a>           |
-| smoldyn    | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |
-| tellurium  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <a href="d1_plots\tellurium_d1.pdf">tellurium_d1.pdf</a>   |
-| vcell      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |
-| xpp        | <span style="color:darkred;">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |
\ No newline at end of file
diff --git a/SBML/test_compatibility_biosimulators_remote.py b/SBML/test_compatibility_biosimulators_remote.py
deleted file mode 100644
index 9e857fe..0000000
--- a/SBML/test_compatibility_biosimulators_remote.py
+++ /dev/null
@@ -1,102 +0,0 @@
-'''
-This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file.
-It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation.
-The results are then displayed in a table and saved to a markdown file.
-'''
-#!/usr/bin/env python
-
-'''
-use pymetadata module to create a minimal valid combine archive
-using LEMS_NML2_Ex9_FN.sbml and LEMS_NML2_Ex9_FN.sedml
-'''
-
-import sys
-sys.path.append("..")
-import utils
-import os
-import pandas as pd
-from IPython.display import display_markdown
-import shutil
-import yaml
-
-sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml'
-sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
-
-engines = utils.engines
-types_dict = utils.types_dict
-
-cwd = os.getcwd()
-
-output_dir = 'remote_results'
-
-download_links_dict = dict()
-for e in engines.keys():
-    download_link = utils.run_biosimulators_remote(e, sedml_filepath, sbml_filepath)
-    download_links_dict[e] = download_link
-
-extract_dir_dict = dict()
-for e, link in download_links_dict.items():
-    extract_dir = utils.get_remote_results(e, link, output_dir)
-    extract_dir_dict[e] = extract_dir
-
-
-results = dict()
-for e, extract_dir in extract_dir_dict.items():
-    status = ""
-    error_message = ""
-    exception_type = ""
-
-    log_yml_path = utils.find_file_in_dir('log.yml', extract_dir)[0]
-    if not log_yml_path:
-        status = None
-        error_message = 'log.yml not found'
-        continue
-    with open(log_yml_path) as f:
-        log_yml_dict = yaml.safe_load(f)
-        if log_yml_dict['status'] == 'SUCCEEDED':
-            status = 'pass'
-        elif log_yml_dict['status'] == 'FAILED':
-            status = 'FAIL'
-            exception = log_yml_dict['exception']
-            error_message = exception['message']
-            exception_type = exception['type'] 
-        else:
-            status = None
-        results[e] = [status, error_message, exception_type] 
-
-# make list of pdf files in all directories in values extract_dir_dict
-# find all pdf files in cwd/ output_dir
-directory = os.path.join(cwd, output_dir)
-print(directory)
-file_paths = utils.find_files(directory, 'pdf')
-utils.move_d1_files(file_paths, 'd1_plots_remote')
-
-# Create a table of the results
-results_table = pd.DataFrame.from_dict(results).T
-results_table.columns = ['pass/FAIL', 'Error','Type']
-results_table.index.name = 'Engine'
-results_table.reset_index(inplace=True)
-
-results_table['Error'] = results_table.apply(lambda x: None if x['pass/FAIL'] == x['Error'] else x['Error'], axis=1)
-results_table['pass/FAIL'] = results_table['pass/FAIL'].replace('other', 'FAIL')
-# results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: x if x == 'FAIL' else x)
-
-
-results_table['Error'] = results_table['Error'].apply(lambda x: utils.ansi_to_html(x))
-results_table['Error'] = results_table['Error'].apply(lambda x: utils.collapsible_content(x))
-
-# compatibility_message
-results_table['Compatibility'] = results_table['Engine'].apply(lambda x: utils.check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))
-results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: utils.collapsible_content(x[1], title=x[0]))
-results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if x == 'FAIL' else x)
-results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if 'FAIL' in x else x)
-
-# d1 plot clickable link
-results_table['d1'] = results_table['Engine'].apply(lambda x: utils.d1_plots_dict(engines, 'd1_plots').get(x, None))
-results_table['d1'] = results_table['d1'].apply(lambda x: utils.create_hyperlink(x))
-
-results_md_table = results_table.to_markdown(index=False)
-
-# save results_md_table
-with open('results_compatibility_biosimulators_remote.md', 'w', encoding='utf-8') as f:
-    f.write(results_md_table)
\ No newline at end of file

From 9a2583bdfdd0143082d08441ce414668e0d6185e Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 7 Aug 2024 14:03:12 +0100
Subject: [PATCH 16/71] remove display_markdown since it is not being used in
 test_compatibility_biosimulators

---
 SBML/test_compatibility_biosimulators.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/test_compatibility_biosimulators.py
index 90d0319..38bab75 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/test_compatibility_biosimulators.py
@@ -15,7 +15,6 @@
 import utils
 import os
 import pandas as pd
-from IPython.display import display_markdown
 import shutil
 import yaml
 

From 9af99fccc43fa949029c27a60215f5140048c010 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 7 Aug 2024 14:06:19 +0100
Subject: [PATCH 17/71] add #!/usr/bin/env python on top of
 test_compatibility_biosimulators

---
 SBML/test_compatibility_biosimulators.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/test_compatibility_biosimulators.py
index 38bab75..6f6286f 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/test_compatibility_biosimulators.py
@@ -1,14 +1,10 @@
+#!/usr/bin/env python
+
 '''
 This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file.
 It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation.
 The results are then displayed in a table and saved to a markdown file.
 '''
-#!/usr/bin/env python
-
-'''
-use pymetadata module to create a minimal valid combine archive
-using LEMS_NML2_Ex9_FN.sbml and LEMS_NML2_Ex9_FN.sedml
-'''
 
 import sys
 sys.path.append("..")

From 890ef164f3e69d09515fe8dd65e172cc6589bec0 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 7 Aug 2024 14:13:35 +0100
Subject: [PATCH 18/71] changing None to 'unknown' for engine string if not
 found in move_d1_files filepath

---
 utils/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/utils/__init__.py b/utils/__init__.py
index e827153..bff0f2a 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -245,7 +245,7 @@ def find_files(directory, extension):
 def move_d1_files(file_paths, plot_dir='d1_plots'):
     for fpath in file_paths:
         # find engine.keys() in the file path and asign to engine
-        engine = next((e for e in engines.keys() if e in fpath), None)
+        engine = next((e for e in engines.keys() if e in fpath), 'unknown')
         new_file_path = os.path.join(plot_dir, f'{engine}_{os.path.basename(fpath)}')
         if not os.path.exists(plot_dir): os.makedirs(plot_dir, exist_ok=True)
         if os.path.exists(new_file_path): os.remove(new_file_path)

From 5a61e7471c0c3015c1f74410210be1005308b8e7 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 7 Aug 2024 14:23:58 +0100
Subject: [PATCH 19/71] added back parser for --output-dir d1_plots

---
 SBML/test_compatibility_biosimulators.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/test_compatibility_biosimulators.py
index 6f6286f..aeb7dc9 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/test_compatibility_biosimulators.py
@@ -13,6 +13,14 @@
 import pandas as pd
 import shutil
 import yaml
+import argparse
+
+parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines')
+parser.add_argument('--output-dir',action='store',default='d1_plots',help='prefix of the output directory where the d1 plots will be saved')
+args = parser.parse_args()
+
+d1_plots_remote_dir = args.output_dir + '_remote'
+d1_plots_local_dir = args.output_dir + '_local'
 
 sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml'
 sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
@@ -62,7 +70,7 @@
         results[e] = [status, error_message, exception_type] 
 
 file_paths = utils.find_files(remote_output_dir, '.pdf')
-utils.move_d1_files(file_paths, 'd1_plots_remote')
+utils.move_d1_files(file_paths, d1_plots_remote_dir)
 
 # remove the remote results directory
 if os.path.exists(remote_output_dir):
@@ -84,7 +92,7 @@
     results_local[e] = record
 
 file_paths = utils.find_files(output_folder, '.pdf')
-utils.move_d1_files(file_paths, 'd1_plots_local')
+utils.move_d1_files(file_paths, d1_plots_local_dir)
 
 # if it exists remove the output folder
 if os.path.exists(output_folder):
@@ -95,8 +103,8 @@
 # process results and save markdown table
 #########################################################################################
 
-results_table = utils.create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, 'd1_plots_remote')
-results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, 'd1_plots_local')
+results_table = utils.create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir
+results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)
 
 # rename cols to distinguish between local and remote results except for Engine column
 results_table.columns = [str(col) + ' (remote)' if col != 'Engine' else str(col) for col in results_table.columns]

From c479d677999af852f0eb30041658e8ae56dadc20 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 7 Aug 2024 14:27:56 +0100
Subject: [PATCH 20/71] add closing bracket

---
 SBML/test_compatibility_biosimulators.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/test_compatibility_biosimulators.py
index aeb7dc9..2eb3661 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/test_compatibility_biosimulators.py
@@ -103,7 +103,7 @@
 # process results and save markdown table
 #########################################################################################
 
-results_table = utils.create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir
+results_table = utils.create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)
 results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)
 
 # rename cols to distinguish between local and remote results except for Engine column

From e9feb06cadc7069296df1c4360559a7bdc73fdff Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 12 Aug 2024 09:58:47 +0100
Subject: [PATCH 21/71] deacrease table width

---
 SBML/results_compatibility_biosimulators.md | 46 ++++++++++-----------
 SBML/test_compatibility_biosimulators.py    |  4 +-
 utils/__init__.py                           | 31 ++++++++------
 3 files changed, 44 insertions(+), 37 deletions(-)

diff --git a/SBML/results_compatibility_biosimulators.md b/SBML/results_compatibility_biosimulators.md
index b8f81c7..864197b 100644
--- a/SBML/results_compatibility_biosimulators.md
+++ b/SBML/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-|    | Engine     | pass/FAIL (remote)                       | pass/FAIL (local)                        | Compatibility (remote)                                                                                                                                                                                                                                                     | Compatibility (local)                                                                                                                                                                                                                                                      | Type (remote)                | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                                                                        | d1 (remote)                                                       | d1 (local)                                                       |
-|---:|:-----------|:-----------------------------------------|:-----------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------|:-----------------------------------------------------------------|
-|  0 | amici      | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\amici_d1.pdf">amici_d1.pdf</a>           | <a href="d1_plots_local\amici_d1.pdf">amici_d1.pdf</a>           |
-|  1 | bionetgen  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">bionetgen_d1.pdf</a>   | <a href="d1_plots_local\bionetgen_d1.pdf">bionetgen_d1.pdf</a>   |
-|  2 | boolnet    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\boolnet_d1.pdf">boolnet_d1.pdf</a>       | <a href="d1_plots_local\boolnet_d1.pdf">boolnet_d1.pdf</a>       |
-|  3 | brian2     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                   |                                                                  |
-|  4 | cbmpy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\cbmpy_d1.pdf">cbmpy_d1.pdf</a>           | <a href="d1_plots_local\cbmpy_d1.pdf">cbmpy_d1.pdf</a>           |
-|  5 | cobrapy    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\cobrapy_d1.pdf">cobrapy_d1.pdf</a>       | <a href="d1_plots_local\cobrapy_d1.pdf">cobrapy_d1.pdf</a>       |
-|  6 | copasi     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\copasi_d1.pdf">copasi_d1.pdf</a>         | <a href="d1_plots_local\copasi_d1.pdf">copasi_d1.pdf</a>         |
-|  7 | gillespy2  | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\gillespy2_d1.pdf">gillespy2_d1.pdf</a>   | <a href="d1_plots_local\gillespy2_d1.pdf">gillespy2_d1.pdf</a>   |
-|  8 | ginsim     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\ginsim_d1.pdf">ginsim_d1.pdf</a>         | <a href="d1_plots_local\ginsim_d1.pdf">ginsim_d1.pdf</a>         |
-|  9 | libsbmlsim | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\libsbmlsim_d1.pdf">libsbmlsim_d1.pdf</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">libsbmlsim_d1.pdf</a> |
-| 10 | masspy     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\masspy_d1.pdf">masspy_d1.pdf</a>         | <a href="d1_plots_local\masspy_d1.pdf">masspy_d1.pdf</a>         |
-| 11 | netpyne    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                   |                                                                  |
-| 12 | neuron     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                   |                                                                  |
-| 13 | opencor    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                   |                                                                  |
-| 14 | pyneuroml  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                   |                                                                  |
-| 15 | pysces     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpf8vg616l/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpf8vg616l/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\pysces_d1.pdf">pysces_d1.pdf</a>         | <a href="d1_plots_local\pysces_d1.pdf">pysces_d1.pdf</a>         |
-| 16 | rbapy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | CombineArchiveExecutionError | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\rbapy_d1.pdf">rbapy_d1.pdf</a>           | <a href="d1_plots_local\rbapy_d1.pdf">rbapy_d1.pdf</a>           |
-| 17 | smoldyn    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                   |                                                                  |
-| 18 | tellurium  | pass                                     | pass                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\tellurium_d1.pdf">tellurium_d1.pdf</a>   | <a href="d1_plots_local\tellurium_d1.pdf">tellurium_d1.pdf</a>   |
-| 19 | vcell      | pass                                     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                              |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>No such container: 995fff1ff43d7138f1f6a7d4c6ad58f885e53901f2f5cdaebbb4fb608a8b9521</details>                                                                     |                                                                   |                                                                  |
-| 20 | xpp        | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | ModuleNotFoundError          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                   |                                                                  |
\ No newline at end of file
+|    | Engine     | pass / FAIL (remote)                     | pass / FAIL (local)                      | Compat (remote)                                                                                                                                                                                                                                                            | Compat (local)                                                                                                                                                                                                                                                             | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |
+|---:|:-----------|:-----------------------------------------|:-----------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
+|  0 | amici      | pass                                     | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="d1_plots_local\amici_d1.pdf">plot</a>      |
+|  1 | bionetgen  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="d1_plots_local\bionetgen_d1.pdf">plot</a>  |
+|  2 | boolnet    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="d1_plots_local\boolnet_d1.pdf">plot</a>    |
+|  3 | brian2     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+|  4 | cbmpy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="d1_plots_local\cbmpy_d1.pdf">plot</a>      |
+|  5 | cobrapy    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="d1_plots_local\cobrapy_d1.pdf">plot</a>    |
+|  6 | copasi     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="d1_plots_local\copasi_d1.pdf">plot</a>     |
+|  7 | gillespy2  | pass                                     | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="d1_plots_local\gillespy2_d1.pdf">plot</a>  |
+|  8 | ginsim     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="d1_plots_local\ginsim_d1.pdf">plot</a>     |
+|  9 | libsbmlsim | pass                                     | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
+| 10 | masspy     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="d1_plots_local\masspy_d1.pdf">plot</a>     |
+| 11 | netpyne    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 12 | neuron     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 13 | opencor    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 14 | pyneuroml  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 15 | pysces     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpyuxhkysi/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpyuxhkysi/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
+| 16 | rbapy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_d1.pdf">plot</a>      |
+| 17 | smoldyn    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 18 | tellurium  | pass                                     | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_d1.pdf">plot</a>  |
+| 19 | vcell      | pass                                     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 20 | xpp        | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
\ No newline at end of file
diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/test_compatibility_biosimulators.py
index 2eb3661..3d41b52 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/test_compatibility_biosimulators.py
@@ -114,8 +114,8 @@
 combined_results = pd.merge(results_table, results_table_local, on='Engine', how='outer')
 combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))
 
-cols_order = ['Engine', 'pass/FAIL (remote)', 'pass/FAIL (local)',\
-               'Compatibility (remote)', 'Compatibility (local)', \
+cols_order = ['Engine', 'pass / FAIL (remote)', 'pass / FAIL (local)',\
+               'Compat (remote)', 'Compat (local)', \
                'Type (remote)', \
                'Error (remote)', 'Error (local)', \
                'd1 (remote)', 'd1 (local)']
diff --git a/utils/__init__.py b/utils/__init__.py
index bff0f2a..86c86af 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -283,13 +283,14 @@ def d1_plots_dict(engines=engines, d1_plots_path='d1_plots'):
     return d1_plots_dict
 
 
-def create_hyperlink(file_path):
+def create_hyperlink(file_path, title=None):
     """
     Create a hyperlink to a file or folder. If the path is None, return None.
     Title is the basename of the path.
     """
     if file_path:
-        title = os.path.basename(file_path)
+        if title is None:
+            title = os.path.basename(file_path)
         return f'<a href="{file_path}">{title}</a>'
     else:
         return None
@@ -984,32 +985,38 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng
     Output: results_md_table
 
     """
+
     # Create a table of the results
     results_table = pd.DataFrame.from_dict(results).T
     # if list is three elements 
     if results_table.shape[1] == 3:
-        results_table.columns = ['pass/FAIL', 'Error', 'Type']
+        results_table.columns = ['pass / FAIL', 'Error', 'Type']
     elif results_table.shape[1] == 2:
-        results_table.columns = ['pass/FAIL', 'Error']
+        results_table.columns = ['pass / FAIL', 'Error']
 
     results_table.index.name = 'Engine'
     results_table.reset_index(inplace=True)
 
-    results_table['Error'] = results_table.apply(lambda x: None if x['pass/FAIL'] == x['Error'] else x['Error'], axis=1)
-    results_table['pass/FAIL'] = results_table['pass/FAIL'].replace('other', 'FAIL')
+    results_table['Error'] = results_table.apply(lambda x: None if x['pass / FAIL'] == x['Error'] else x['Error'], axis=1)
+    results_table['pass / FAIL'] = results_table['pass / FAIL'].replace('other', 'FAIL')
 
     results_table['Error'] = results_table['Error'].apply(lambda x: ansi_to_html(x))
     results_table['Error'] = results_table['Error'].apply(lambda x: collapsible_content(x))
 
     # compatibility_message
-    results_table['Compatibility'] = results_table['Engine'].apply(lambda x: check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))
-    results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: collapsible_content(x[1], title=x[0]))
-    results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if x == 'FAIL' else x)
-    results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if 'FAIL' in x else x)
+    results_table['Compat'] = results_table['Engine'].apply(lambda x: check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))
+    results_table['Compat'] = results_table['Compat'].apply(lambda x: collapsible_content(x[1], title=x[0]))
+    results_table['Compat'] = results_table['Compat'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if 'FAIL' in x else x)
+
+    # pass / FAIL
+    results_table['pass / FAIL'] = results_table['pass / FAIL'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if x == 'FAIL' else x)
 
     # d1 plot clickable link
     results_table['d1'] = results_table['Engine'].apply(lambda x: d1_plots_dict(engines, output_dir).get(x, None))
-    results_table['d1'] = results_table['d1'].apply(lambda x: create_hyperlink(x))
-
+    results_table['d1'] = results_table['d1'].apply(lambda x: create_hyperlink(x,title='plot'))
+    
+    # if Type is in the table add message with collapsible content
+    if 'Type' in results_table.columns:
+        results_table['Type'] = results_table['Type'].apply(lambda x: collapsible_content(x,"".join(re.findall(r'[A-Z]', x))))
 
     return results_table

From 2de8efafb5f25d4ab12f7aaaa70a14f52be25f9d Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 12 Aug 2024 15:53:38 +0100
Subject: [PATCH 22/71] update jupyter notebook for trouble shooting

---
 SBML/test_compatibility_biosimulators.ipynb | 738 +++++++-------------
 1 file changed, 240 insertions(+), 498 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index ff21fc1..e8cf99c 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
@@ -42,28 +42,25 @@
     "import pandas as pd\n",
     "from IPython.display import display_markdown\n",
     "import shutil\n",
+    "import yaml\n",
+    "\n",
+    "\n",
+    "cwd = os.getcwd()\n",
+    "print(cwd)\n",
+    "\n",
+    "d1_plots_remote_dir = 'd1_plots'+ '_remote'\n",
+    "d1_plots_local_dir = 'd1_plots' + '_local'\n",
     "\n",
     "sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml'\n",
     "sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing\n",
     "\n",
     "engines = utils.engines\n",
-    "types_dict = utils.types_dict\n",
-    "\n",
-    "cwd = os.getcwd()\n",
-    "print(cwd)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## test compatibility biosimulators remotely\n",
-    "see https://github.com/OpenSourceBrain/SBMLShowcase/issues/32"
+    "types_dict = utils.types_dict\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
@@ -75,7 +72,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=93271286db574e49a97da9c3790cdeab\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6a24ae0ee444424c8ff04d62278713c0\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -83,10 +80,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806e4fb4b102485fe22a7\n",
-      "View: https://api.biosimulations.org/runs/668806e4fb4b102485fe22a7\n",
-      "Downloads: https://api.biosimulations.org/results/668806e4fb4b102485fe22a7/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806e4fb4b102485fe22a7?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f830c4ccdd4919203e7\n",
+      "View: https://api.biosimulations.org/runs/66ba1f830c4ccdd4919203e7\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f830c4ccdd4919203e7/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f830c4ccdd4919203e7?includeOutput=true\n"
      ]
     },
     {
@@ -98,7 +95,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4134f52d1854428e8e95c30e336df32c\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=39f2f2d3326348979bfde3c5434dee52\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -106,10 +103,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806e5ececf8e28b89fca5\n",
-      "View: https://api.biosimulations.org/runs/668806e5ececf8e28b89fca5\n",
-      "Downloads: https://api.biosimulations.org/results/668806e5ececf8e28b89fca5/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806e5ececf8e28b89fca5?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f85f29e09b32cb6e3e6\n",
+      "View: https://api.biosimulations.org/runs/66ba1f85f29e09b32cb6e3e6\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f85f29e09b32cb6e3e6/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f85f29e09b32cb6e3e6?includeOutput=true\n"
      ]
     },
     {
@@ -121,7 +118,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=56c9af85d0bc48a29de382f70d2d05f5\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=e7f0bb4a16734cc2b36c1298434e76fa\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -129,10 +126,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806e7244e3c6918b311e8\n",
-      "View: https://api.biosimulations.org/runs/668806e7244e3c6918b311e8\n",
-      "Downloads: https://api.biosimulations.org/results/668806e7244e3c6918b311e8/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806e7244e3c6918b311e8?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f870c4ccdd4919203ea\n",
+      "View: https://api.biosimulations.org/runs/66ba1f870c4ccdd4919203ea\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f870c4ccdd4919203ea/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f870c4ccdd4919203ea?includeOutput=true\n"
      ]
     },
     {
@@ -144,7 +141,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=21a0b6bb0eff4e5cafead5064cc61a2b\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=122fb47d395048eca2a0817141ec00a3\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -152,10 +149,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806e9244e3c6918b311ec\n",
-      "View: https://api.biosimulations.org/runs/668806e9244e3c6918b311ec\n",
-      "Downloads: https://api.biosimulations.org/results/668806e9244e3c6918b311ec/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806e9244e3c6918b311ec?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f88a641708179acfc8e\n",
+      "View: https://api.biosimulations.org/runs/66ba1f88a641708179acfc8e\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f88a641708179acfc8e/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f88a641708179acfc8e?includeOutput=true\n"
      ]
     },
     {
@@ -167,7 +164,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=d19e99eb439c4d99a6b2d4bee9e0ad5c\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=3aafbb161ddf477e8a2301911cd284f4\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -175,10 +172,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806ebfb4b102485fe22ab\n",
-      "View: https://api.biosimulations.org/runs/668806ebfb4b102485fe22ab\n",
-      "Downloads: https://api.biosimulations.org/results/668806ebfb4b102485fe22ab/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806ebfb4b102485fe22ab?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f8af29e09b32cb6e3e9\n",
+      "View: https://api.biosimulations.org/runs/66ba1f8af29e09b32cb6e3e9\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f8af29e09b32cb6e3e9/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f8af29e09b32cb6e3e9?includeOutput=true\n"
      ]
     },
     {
@@ -190,7 +187,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ca3289a48ed94a408868820c4d1b445c\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f102a0a33b3242768c9962be48ea98ca\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -198,10 +195,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806edfb4b102485fe22ae\n",
-      "View: https://api.biosimulations.org/runs/668806edfb4b102485fe22ae\n",
-      "Downloads: https://api.biosimulations.org/results/668806edfb4b102485fe22ae/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806edfb4b102485fe22ae?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f8c0c4ccdd4919203f0\n",
+      "View: https://api.biosimulations.org/runs/66ba1f8c0c4ccdd4919203f0\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f8c0c4ccdd4919203f0/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f8c0c4ccdd4919203f0?includeOutput=true\n"
      ]
     },
     {
@@ -213,7 +210,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=aeb7aa318b954661aad3318985f85a6d\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=786c1d04b44546b8925d8ee2e7b49f73\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -221,10 +218,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806ef244e3c6918b311f0\n",
-      "View: https://api.biosimulations.org/runs/668806ef244e3c6918b311f0\n",
-      "Downloads: https://api.biosimulations.org/results/668806ef244e3c6918b311f0/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806ef244e3c6918b311f0?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f8ef29e09b32cb6e3ef\n",
+      "View: https://api.biosimulations.org/runs/66ba1f8ef29e09b32cb6e3ef\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f8ef29e09b32cb6e3ef/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f8ef29e09b32cb6e3ef?includeOutput=true\n"
      ]
     },
     {
@@ -236,7 +233,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=d99c8c1bc095441682e2b194c68e8737\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6d2e0f00f44c4acbb95f27d14413bdc8\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -244,10 +241,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806f3244e3c6918b311f7\n",
-      "View: https://api.biosimulations.org/runs/668806f3244e3c6918b311f7\n",
-      "Downloads: https://api.biosimulations.org/results/668806f3244e3c6918b311f7/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806f3244e3c6918b311f7?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f90f29e09b32cb6e3f4\n",
+      "View: https://api.biosimulations.org/runs/66ba1f90f29e09b32cb6e3f4\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f90f29e09b32cb6e3f4/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f90f29e09b32cb6e3f4?includeOutput=true\n"
      ]
     },
     {
@@ -259,7 +256,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f15dd95c13e1457192012b8a5ebc218a\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=155122bca1084350a45640fa0b3193cf\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -267,10 +264,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806f5fb4b102485fe22b8\n",
-      "View: https://api.biosimulations.org/runs/668806f5fb4b102485fe22b8\n",
-      "Downloads: https://api.biosimulations.org/results/668806f5fb4b102485fe22b8/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806f5fb4b102485fe22b8?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f92f29e09b32cb6e3f9\n",
+      "View: https://api.biosimulations.org/runs/66ba1f92f29e09b32cb6e3f9\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f92f29e09b32cb6e3f9/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f92f29e09b32cb6e3f9?includeOutput=true\n"
      ]
     },
     {
@@ -282,7 +279,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a9bd50ee3867471289eb032856c5d240\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=79d21d2ea26e4757b7e665f21f1ca8ae\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -290,10 +287,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806f7244e3c6918b311fe\n",
-      "View: https://api.biosimulations.org/runs/668806f7244e3c6918b311fe\n",
-      "Downloads: https://api.biosimulations.org/results/668806f7244e3c6918b311fe/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806f7244e3c6918b311fe?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f94a641708179acfc9c\n",
+      "View: https://api.biosimulations.org/runs/66ba1f94a641708179acfc9c\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f94a641708179acfc9c/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f94a641708179acfc9c?includeOutput=true\n"
      ]
     },
     {
@@ -305,7 +302,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=03ad32d237334ab1b2733c622d2e9e36\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=05e8fe072cd2403a8cdf454adf0d4d30\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -313,10 +310,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806f8244e3c6918b31205\n",
-      "View: https://api.biosimulations.org/runs/668806f8244e3c6918b31205\n",
-      "Downloads: https://api.biosimulations.org/results/668806f8244e3c6918b31205/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806f8244e3c6918b31205?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f96f29e09b32cb6e401\n",
+      "View: https://api.biosimulations.org/runs/66ba1f96f29e09b32cb6e401\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f96f29e09b32cb6e401/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f96f29e09b32cb6e401?includeOutput=true\n"
      ]
     },
     {
@@ -328,7 +325,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=646c6152e60440d892ae2e33c5d39ef2\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=37a1033536674c2dbc3ef1a250724728\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -336,10 +333,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806fa244e3c6918b3120f\n",
-      "View: https://api.biosimulations.org/runs/668806fa244e3c6918b3120f\n",
-      "Downloads: https://api.biosimulations.org/results/668806fa244e3c6918b3120f/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806fa244e3c6918b3120f?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f980c4ccdd491920407\n",
+      "View: https://api.biosimulations.org/runs/66ba1f980c4ccdd491920407\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f980c4ccdd491920407/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f980c4ccdd491920407?includeOutput=true\n"
      ]
     },
     {
@@ -351,7 +348,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5a845236cbff49b486f9878c692b5a42\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=948b1d17fd964943983a456b847b9611\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -359,10 +356,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806fc244e3c6918b3121f\n",
-      "View: https://api.biosimulations.org/runs/668806fc244e3c6918b3121f\n",
-      "Downloads: https://api.biosimulations.org/results/668806fc244e3c6918b3121f/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806fc244e3c6918b3121f?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f9aa641708179acfcb6\n",
+      "View: https://api.biosimulations.org/runs/66ba1f9aa641708179acfcb6\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f9aa641708179acfcb6/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f9aa641708179acfcb6?includeOutput=true\n"
      ]
     },
     {
@@ -374,7 +371,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c0993445e55b4bc3a12f1f52b98b6b6a\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=d5e5d42c0d9c4f958b4a568e71fc7227\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -382,10 +379,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806fdececf8e28b89fcdd\n",
-      "View: https://api.biosimulations.org/runs/668806fdececf8e28b89fcdd\n",
-      "Downloads: https://api.biosimulations.org/results/668806fdececf8e28b89fcdd/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806fdececf8e28b89fcdd?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f9cf29e09b32cb6e426\n",
+      "View: https://api.biosimulations.org/runs/66ba1f9cf29e09b32cb6e426\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f9cf29e09b32cb6e426/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f9cf29e09b32cb6e426?includeOutput=true\n"
      ]
     },
     {
@@ -397,7 +394,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=2e5968b0640040f1aa0279c45fd92e75\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5f82c6a945f3472cbdde1c27ca8ae0eb\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -405,10 +402,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 668806ffececf8e28b89fce5\n",
-      "View: https://api.biosimulations.org/runs/668806ffececf8e28b89fce5\n",
-      "Downloads: https://api.biosimulations.org/results/668806ffececf8e28b89fce5/download\n",
-      "Logs: https://api.biosimulations.org/logs/668806ffececf8e28b89fce5?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f9ef29e09b32cb6e432\n",
+      "View: https://api.biosimulations.org/runs/66ba1f9ef29e09b32cb6e432\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f9ef29e09b32cb6e432/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f9ef29e09b32cb6e432?includeOutput=true\n"
      ]
     },
     {
@@ -420,7 +417,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=dc3365a2494446c7a9e1b025984a0452\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=cf52c47341294a89b525b5da176a9c6b\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -428,10 +425,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880701fb4b102485fe22e2\n",
-      "View: https://api.biosimulations.org/runs/66880701fb4b102485fe22e2\n",
-      "Downloads: https://api.biosimulations.org/results/66880701fb4b102485fe22e2/download\n",
-      "Logs: https://api.biosimulations.org/logs/66880701fb4b102485fe22e2?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f9f0c4ccdd491920434\n",
+      "View: https://api.biosimulations.org/runs/66ba1f9f0c4ccdd491920434\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1f9f0c4ccdd491920434/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1f9f0c4ccdd491920434?includeOutput=true\n"
      ]
     },
     {
@@ -443,7 +440,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=978baa42c2314a1a8c63d8112169c7f8\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=0f306f40d80d4a8886a4cda37daba825\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -451,10 +448,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880703fb4b102485fe22ef\n",
-      "View: https://api.biosimulations.org/runs/66880703fb4b102485fe22ef\n",
-      "Downloads: https://api.biosimulations.org/results/66880703fb4b102485fe22ef/download\n",
-      "Logs: https://api.biosimulations.org/logs/66880703fb4b102485fe22ef?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1fa10c4ccdd491920438\n",
+      "View: https://api.biosimulations.org/runs/66ba1fa10c4ccdd491920438\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1fa10c4ccdd491920438/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1fa10c4ccdd491920438?includeOutput=true\n"
      ]
     },
     {
@@ -466,7 +463,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6294eb22392e403296800f8ed5472108\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b7710c48585b4c50ace4a4b6d435a980\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -474,10 +471,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880705ececf8e28b89fd01\n",
-      "View: https://api.biosimulations.org/runs/66880705ececf8e28b89fd01\n",
-      "Downloads: https://api.biosimulations.org/results/66880705ececf8e28b89fd01/download\n",
-      "Logs: https://api.biosimulations.org/logs/66880705ececf8e28b89fd01?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1fa3a641708179acfce3\n",
+      "View: https://api.biosimulations.org/runs/66ba1fa3a641708179acfce3\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1fa3a641708179acfce3/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1fa3a641708179acfce3?includeOutput=true\n"
      ]
     },
     {
@@ -489,7 +486,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=754b851ebd654c89b4a87779de1b997b\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=adcbd4850763439085c40bb60b360d2e\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -497,10 +494,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880707ececf8e28b89fd06\n",
-      "View: https://api.biosimulations.org/runs/66880707ececf8e28b89fd06\n",
-      "Downloads: https://api.biosimulations.org/results/66880707ececf8e28b89fd06/download\n",
-      "Logs: https://api.biosimulations.org/logs/66880707ececf8e28b89fd06?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1fa5a641708179acfcea\n",
+      "View: https://api.biosimulations.org/runs/66ba1fa5a641708179acfcea\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1fa5a641708179acfcea/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1fa5a641708179acfcea?includeOutput=true\n"
      ]
     },
     {
@@ -512,7 +509,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6218fc6f41c64866a5878c7a3c2d0721\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ea1629cce1a541b09538f45dd0f5a897\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -520,10 +517,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66880709244e3c6918b31257\n",
-      "View: https://api.biosimulations.org/runs/66880709244e3c6918b31257\n",
-      "Downloads: https://api.biosimulations.org/results/66880709244e3c6918b31257/download\n",
-      "Logs: https://api.biosimulations.org/logs/66880709244e3c6918b31257?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1faaf29e09b32cb6e477\n",
+      "View: https://api.biosimulations.org/runs/66ba1faaf29e09b32cb6e477\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1faaf29e09b32cb6e477/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1faaf29e09b32cb6e477?includeOutput=true\n"
      ]
     },
     {
@@ -535,7 +532,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=8b212524d2d54e80a29a58cb2c8efe9b\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=18f5610ecb314a9693116e68d038e7a6\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -543,31 +540,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 6688070b244e3c6918b31272\n",
-      "View: https://api.biosimulations.org/runs/6688070b244e3c6918b31272\n",
-      "Downloads: https://api.biosimulations.org/results/6688070b244e3c6918b31272/download\n",
-      "Logs: https://api.biosimulations.org/logs/6688070b244e3c6918b31272?includeOutput=true\n"
-     ]
-    }
-   ],
-   "source": [
-    "output_dir = 'remote_results'\n",
-    "\n",
-    "download_links_dict = dict()\n",
-    "for e in engines.keys():\n",
-    "    download_link = utils.run_biosimulators_remote(e, sedml_filepath, sbml_filepath)\n",
-    "    download_links_dict[e] = download_link"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 23,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1facf29e09b32cb6e480\n",
+      "View: https://api.biosimulations.org/runs/66ba1facf29e09b32cb6e480\n",
+      "Downloads: https://api.biosimulations.org/results/66ba1facf29e09b32cb6e480/download\n",
+      "Logs: https://api.biosimulations.org/logs/66ba1facf29e09b32cb6e480?includeOutput=true\n",
       "Downloading amici results...\n",
       "Downloading brian2 results...\n",
       "Downloading bionetgen results...\n",
@@ -588,26 +564,79 @@
       "Downloading smoldyn results...\n",
       "Downloading tellurium results...\n",
       "Downloading vcell results...\n",
-      "Downloading xpp results...\n"
+      "Downloading xpp results...\n",
+      "Moving remote_results\\amici\\outputs\\tmp802597\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
+      "Moving remote_results\\amici\\outputs\\tmp987077\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
+      "Moving remote_results\\bionetgen\\outputs\\tmp337013\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
+      "Moving remote_results\\bionetgen\\outputs\\tmp950095\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
+      "Moving remote_results\\boolnet\\outputs\\tmp644487\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
+      "Moving remote_results\\boolnet\\outputs\\tmp649837\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
+      "Moving remote_results\\cbmpy\\outputs\\tmp516152\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
+      "Moving remote_results\\cbmpy\\outputs\\tmp591632\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
+      "Moving remote_results\\cobrapy\\outputs\\tmp220956\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
+      "Moving remote_results\\cobrapy\\outputs\\tmp589941\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
+      "Moving remote_results\\copasi\\outputs\\tmp69930\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
+      "Moving remote_results\\copasi\\outputs\\tmp820744\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
+      "Moving remote_results\\gillespy2\\outputs\\tmp334450\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
+      "Moving remote_results\\gillespy2\\outputs\\tmp952245\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
+      "Moving remote_results\\ginsim\\outputs\\tmp267937\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
+      "Moving remote_results\\ginsim\\outputs\\tmp936909\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
+      "Moving remote_results\\libsbmlsim\\outputs\\tmp282735\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
+      "Moving remote_results\\libsbmlsim\\outputs\\tmp3602\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
+      "Moving remote_results\\masspy\\outputs\\tmp648987\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
+      "Moving remote_results\\masspy\\outputs\\tmp907144\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
+      "Moving remote_results\\pysces\\outputs\\tmp312749\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
+      "Moving remote_results\\pysces\\outputs\\tmp415792\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
+      "Moving remote_results\\rbapy\\outputs\\tmp496636\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
+      "Moving remote_results\\rbapy\\outputs\\tmp499456\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
+      "Moving remote_results\\tellurium\\outputs\\tmp402952\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
+      "Moving remote_results\\tellurium\\outputs\\tmp916390\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
+      "Removed remote_results folder\n",
+      "Running amici\n",
+      "Running brian2\n",
+      "Running bionetgen\n",
+      "Running boolnet\n",
+      "Running cbmpy\n",
+      "Running cobrapy\n",
+      "Running copasi\n",
+      "Running gillespy2\n",
+      "Running ginsim\n",
+      "Running libsbmlsim\n",
+      "Running masspy\n",
+      "Running netpyne\n",
+      "Running neuron\n",
+      "Running opencor\n",
+      "Running pyneuroml\n",
+      "Running pysces\n",
+      "Running rbapy\n",
+      "Running smoldyn\n",
+      "Running tellurium\n",
+      "Running vcell\n",
+      "Running xpp\n",
+      "Removed output folder\n"
      ]
     }
    ],
    "source": [
+    "\n",
+    "\n",
+    "#########################################################################################\n",
+    "# Run remotely\n",
+    "#########################################################################################\n",
+    "\n",
+    "remote_output_dir = 'remote_results'\n",
+    "\n",
+    "download_links_dict = dict()\n",
+    "for e in engines.keys():\n",
+    "    download_link = utils.run_biosimulators_remote(e, sedml_filepath, sbml_filepath)\n",
+    "    download_links_dict[e] = download_link\n",
+    "\n",
     "extract_dir_dict = dict()\n",
     "for e, link in download_links_dict.items():\n",
-    "    extract_dir = utils.get_remote_results(e, link, output_dir)\n",
-    "    extract_dir_dict[e] = extract_dir"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 24,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import yaml\n",
-    "results = dict()\n",
+    "    extract_dir = utils.get_remote_results(e, link, remote_output_dir)\n",
+    "    extract_dir_dict[e] = extract_dir\n",
     "\n",
+    "results = dict()\n",
     "for e, extract_dir in extract_dir_dict.items():\n",
     "    status = \"\"\n",
     "    error_message = \"\"\n",
@@ -629,341 +658,70 @@
     "            exception_type = exception['type'] \n",
     "        else:\n",
     "            status = None\n",
-    "        results[e] = [status, error_message, exception_type] \n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 25,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\remote_results\n"
-     ]
-    },
-    {
-     "data": {
-      "text/html": [
-       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
-      ],
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "\n",
-       "\u001b[1m[\u001b[0m\n",
-       "    \u001b[32m'd1_plots_remote\\\\amici_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\bionetgen_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\boolnet_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\cbmpy_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\cobrapy_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\copasi_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\gillespy2_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\ginsim_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\libsbmlsim_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\masspy_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\pysces_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\rbapy_d1.pdf'\u001b[0m,\n",
-       "    \u001b[32m'd1_plots_remote\\\\tellurium_d1.pdf'\u001b[0m\n",
-       "\u001b[1m]\u001b[0m"
-      ]
-     },
-     "execution_count": 25,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "# make list of pdf files in all directories in values extract_dir_dict\n",
-    "# find all pdf files in cwd/ output_dir\n",
-    "directory = os.path.join(cwd, output_dir)\n",
-    "print(directory)\n",
-    "file_paths = utils.find_files(directory, 'pdf')\n",
-    "utils.move_d1_files(file_paths, 'd1_plots_remote')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 26,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/markdown": [
-       "## Remote Results"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/markdown": [
-       "| Engine     | pass/FAIL                                | Error                                                                                                                                                                                                                                                                                                                                                                                                                                                              | Type                         | Compatibility                                                                                                                                                                                                                                                              | d1                                                         |\n",
-       "|:-----------|:-----------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|\n",
-       "| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                              | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <a href=\"d1_plots\\amici_d1.pdf\">amici_d1.pdf</a>           |\n",
-       "| brian2     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |\n",
-       "| bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | CombineArchiveExecutionError | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href=\"d1_plots\\bionetgen_d1.pdf\">bionetgen_d1.pdf</a>   |\n",
-       "| boolnet    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | CombineArchiveExecutionError | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href=\"d1_plots\\boolnet_d1.pdf\">boolnet_d1.pdf</a>       |\n",
-       "| cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href=\"d1_plots\\cbmpy_d1.pdf\">cbmpy_d1.pdf</a>           |\n",
-       "| cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href=\"d1_plots\\cobrapy_d1.pdf\">cobrapy_d1.pdf</a>       |\n",
-       "| copasi     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href=\"d1_plots\\copasi_d1.pdf\">copasi_d1.pdf</a>         |\n",
-       "| gillespy2  | pass                                     | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href=\"d1_plots\\gillespy2_d1.pdf\">gillespy2_d1.pdf</a>   |\n",
-       "| ginsim     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | CombineArchiveExecutionError | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href=\"d1_plots\\ginsim_d1.pdf\">ginsim_d1.pdf</a>         |\n",
-       "| libsbmlsim | pass                                     | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href=\"d1_plots\\libsbmlsim_d1.pdf\">libsbmlsim_d1.pdf</a> |\n",
-       "| masspy     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href=\"d1_plots\\masspy_d1.pdf\">masspy_d1.pdf</a>         |\n",
-       "| netpyne    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |\n",
-       "| neuron     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    |                                                            |\n",
-       "| opencor    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            |                                                            |\n",
-       "| pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> |                                                            |\n",
-       "| pysces     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpbz6s_tkd/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpbz6s_tkd/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | CombineArchiveExecutionError | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href=\"d1_plots\\pysces_d1.pdf\">pysces_d1.pdf</a>         |\n",
-       "| rbapy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | CombineArchiveExecutionError | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href=\"d1_plots\\rbapy_d1.pdf\">rbapy_d1.pdf</a>           |\n",
-       "| smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |\n",
-       "| tellurium  | pass                                     | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <a href=\"d1_plots\\tellurium_d1.pdf\">tellurium_d1.pdf</a>   |\n",
-       "| vcell      | pass                                     | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |\n",
-       "| xpp        | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | ModuleNotFoundError          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "# Create a table of the results\n",
-    "results_table = pd.DataFrame.from_dict(results).T\n",
-    "results_table.columns = ['pass/FAIL', 'Error','Type']\n",
-    "results_table.index.name = 'Engine'\n",
-    "results_table.reset_index(inplace=True)\n",
+    "        results[e] = [status, error_message, exception_type] \n",
     "\n",
-    "results_table['Error'] = results_table.apply(lambda x: None if x['pass/FAIL'] == x['Error'] else x['Error'], axis=1)\n",
-    "results_table['pass/FAIL'] = results_table['pass/FAIL'].replace('other', 'FAIL')\n",
-    "# results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: x if x == 'FAIL' else x)\n",
+    "file_paths = utils.find_files(remote_output_dir, '.pdf')\n",
+    "utils.move_d1_files(file_paths, d1_plots_remote_dir)\n",
     "\n",
+    "# remove the remote results directory\n",
+    "if os.path.exists(remote_output_dir):\n",
+    "    shutil.rmtree(remote_output_dir)\n",
+    "    print('Removed ' + remote_output_dir + ' folder')\n",
     "\n",
-    "results_table['Error'] = results_table['Error'].apply(lambda x: utils.ansi_to_html(x))\n",
-    "results_table['Error'] = results_table['Error'].apply(lambda x: utils.collapsible_content(x))\n",
+    "#########################################################################################\n",
+    "# Run locally\n",
+    "#########################################################################################\n",
     "\n",
-    "# compatibility_message\n",
-    "results_table['Compatibility'] = results_table['Engine'].apply(lambda x: utils.check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))\n",
-    "results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: utils.collapsible_content(x[1], title=x[0]))\n",
-    "results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: f'<span style=\"color:darkred;\">{x}</span>' if x == 'FAIL' else x)\n",
-    "results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: f'<span style=\"color:darkred;\">{x}</span>' if 'FAIL' in x else x)\n",
-    "\n",
-    "# d1 plot clickable link\n",
-    "results_table['d1'] = results_table['Engine'].apply(lambda x: utils.d1_plots_dict(engines, 'd1_plots').get(x, None))\n",
-    "results_table['d1'] = results_table['d1'].apply(lambda x: utils.create_hyperlink(x))\n",
-    "\n",
-    "results_md_table = results_table.to_markdown(index=False)\n",
-    "\n",
-    "display_markdown('## Remote Results', raw=True)\n",
-    "display_markdown(results_md_table, raw=True)\n",
-    "\n",
-    "# give table as a row above the table\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 31,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
-      ],
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "\u001b[1m[\u001b[0m\u001b[32m'pass'\u001b[0m, \u001b[32m\"No module named 'libsbml'\"\u001b[0m, \u001b[32m'ModuleNotFoundError'\u001b[0m\u001b[1m]\u001b[0m"
-      ]
-     },
-     "execution_count": 31,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "results['tellurium']"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## test compatibility biosimulators locally using docker\n",
-    "see https://github.com/OpenSourceBrain/SBMLShowcase/issues/31\n",
-    "\n",
-    "! Start docker before running the below script\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 27,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Running amici\n",
-      "Running brian2\n",
-      "Running bionetgen\n",
-      "Running boolnet\n",
-      "Running cbmpy\n",
-      "Running cobrapy\n",
-      "Running copasi\n",
-      "Running gillespy2\n",
-      "Running ginsim\n",
-      "Running libsbmlsim\n",
-      "Running masspy\n",
-      "Running netpyne\n",
-      "Running neuron\n",
-      "Running opencor\n",
-      "Running pyneuroml\n",
-      "Running pysces\n",
-      "Running rbapy\n",
-      "Running smoldyn\n",
-      "Running tellurium\n",
-      "Running vcell\n",
-      "Running xpp\n"
-     ]
-    }
-   ],
-   "source": [
-    "engine_dict = {}\n",
-    "\n",
-    "output_folder = 'output'\n",
-    "\n",
-    "for e in engines.keys():\n",
-    "    print('Running ' + e)\n",
-    "    output_dir = os.path.abspath(os.path.join(output_folder, e))\n",
-    "    try:\n",
-    "        record = utils.run_biosimulators_docker(e, sedml_filepath, sbml_filepath, output_dir=output_dir)\n",
-    "        engine_dict[e] = record\n",
-    "    except Exception as error:\n",
-    "        error_message = str(error)\n",
-    "        print(f\"Error occurred while running {e}\")\n",
-    "        engine_dict[e] = error_message\n",
-    "        continue"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 28,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Running amici\n",
-      "Running brian2\n",
-      "Running bionetgen\n",
-      "Running boolnet\n",
-      "Running cbmpy\n",
-      "Running cobrapy\n",
-      "Running copasi\n",
-      "Running gillespy2\n",
-      "Running ginsim\n",
-      "Running libsbmlsim\n",
-      "Running masspy\n",
-      "Running netpyne\n",
-      "Running neuron\n",
-      "Running opencor\n",
-      "Running pyneuroml\n",
-      "Running pysces\n",
-      "Running rbapy\n",
-      "Running smoldyn\n",
-      "Running tellurium\n",
-      "Running vcell\n",
-      "Running xpp\n"
-     ]
-    }
-   ],
-   "source": [
-    "engine_dict = {}\n",
+    "results_local = {}\n",
     "\n",
     "output_folder = 'output'\n",
     "\n",
     "for e in engines.keys():\n",
     "    print('Running ' + e)\n",
     "    output_dir = os.path.abspath(os.path.join(output_folder, e))\n",
-    "    try:\n",
-    "        record = utils.run_biosimulators_docker(e, sedml_filepath, sbml_filepath, output_dir=output_dir)\n",
-    "        engine_dict[e] = record\n",
-    "    except Exception as error:\n",
-    "        error_message = str(error)\n",
-    "        print(f\"Error occurred while running {e}\")\n",
-    "        engine_dict[e] = error_message\n",
-    "        continue\n",
+    "    record = utils.run_biosimulators_docker(e, sedml_filepath, sbml_filepath, output_dir=output_dir)\n",
+    "    results_local[e] = record\n",
     "\n",
     "file_paths = utils.find_files(output_folder, '.pdf')\n",
-    "utils.move_d1_files(file_paths, 'd1_plots')\n",
+    "utils.move_d1_files(file_paths, d1_plots_local_dir)\n",
     "\n",
     "# if it exists remove the output folder\n",
     "if os.path.exists(output_folder):\n",
-    "    shutil.rmtree(output_folder)"
+    "    shutil.rmtree(output_folder)\n",
+    "    print('Removed ' + output_folder + ' folder')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/markdown": [
-       "## Local via Docker Results"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/markdown": [
-       "| Engine     | pass/FAIL                                | Error                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Compatibility                                                                                                                                                                                                                                                              | d1                                                         |\n",
-       "|:-----------|:-----------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|\n",
-       "| amici      | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <a href=\"d1_plots\\amici_d1.pdf\">amici_d1.pdf</a>           |\n",
-       "| brian2     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      |                                                            |\n",
-       "| bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp683880` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <a href=\"d1_plots\\bionetgen_d1.pdf\">bionetgen_d1.pdf</a>   |\n",
-       "| boolnet    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp95718` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).<br>R[write to console]: Warning message:<br><br>R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :<br>R[write to console]: <br> <br>R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages<br><br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <a href=\"d1_plots\\boolnet_d1.pdf\">boolnet_d1.pdf</a>       |\n",
-       "| cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><br>INFO: No xlwt module available, Excel spreadsheet creation disabled<br><br><br><br>No module named 'cplex'<br><br><br><br>CPLEX not available<br><br>*****<br>Using GLPK<br>*****<br><br><br>INFO: No xlrd module available, Excel spreadsheet reading disabled<br><br>CBMPy environment<br>******************<br>Revision: r689<br><br><br>***********************************************************************<br>* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *<br>*                http://cbmpy.sourceforge.net                         *<br>* Copyright(C) Brett G. Olivier 2014 - 2019                           *<br>* Dept. of Systems Bioinformatics                                     *<br>* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *<br>* CBMPy is developed as part of the BeBasic MetaToolKit Project       *<br>* Distributed under the GNU GPL v 3.0 licence, see                    *<br>* LICENCE (supplied with this release) for details                    *<br>***********************************************************************<br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp663224` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <a href=\"d1_plots\\cbmpy_d1.pdf\">cbmpy_d1.pdf</a>           |\n",
-       "| cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp736148` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <a href=\"d1_plots\\cobrapy_d1.pdf\">cobrapy_d1.pdf</a>       |\n",
-       "| copasi     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp315353` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[W]'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <a href=\"d1_plots\\copasi_d1.pdf\">copasi_d1.pdf</a>         |\n",
-       "| gillespy2  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <a href=\"d1_plots\\gillespy2_d1.pdf\">gillespy2_d1.pdf</a>   |\n",
-       "| ginsim     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp444220` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000<br></details> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <a href=\"d1_plots\\ginsim_d1.pdf\">ginsim_d1.pdf</a>         |\n",
-       "| libsbmlsim | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <a href=\"d1_plots\\libsbmlsim_d1.pdf\">libsbmlsim_d1.pdf</a> |\n",
-       "| masspy     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31m<br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp68973` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <a href=\"d1_plots\\masspy_d1.pdf\">masspy_d1.pdf</a>         |\n",
-       "| netpyne    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     |                                                            |\n",
-       "| neuron     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    |                                                            |\n",
-       "| opencor    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            |                                                            |\n",
-       "| pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> |                                                            |\n",
-       "| pysces     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>Could not find GLIMDA.<br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` has warnings.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>      - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>      - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br>/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive has warnings.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp568087` has warnings.<br>    - Model `net1` has warnings.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.<br>        - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:<br>          - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>             The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:<br>          - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>             The parameter with the id 'I' does not have a 'units' attribute.<br>  <br><br><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpphuv4n0q/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpphuv4n0q/./LEMS_NML2_Ex9_FN.sbml.xml does not exist<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <a href=\"d1_plots\\pysces_d1.pdf\">pysces_d1.pdf</a>         |\n",
-       "| rbapy      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The SED document is potentially incorrect.</span></li><li>Model `net1` may be invalid.<br>    - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>         The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'I' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'SEC' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'V' does not have a 'units' attribute.<br>        <br>      - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>         The parameter with the id 'W' does not have a 'units' attribute.<br>        <br>  <br><br>/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: <br><br>BioSimulatorsWarning:<br><br> <span style=\"color:darkorange;\">The COMBINE/OMEX archive may be invalid.</li><li>OMEX manifests should not contain content entries for themselves.</li><li>The SED-ML file at location `./tmp941296` may be invalid.<br>    - Model `net1` may be invalid.<br>      - The model file `LEMS_NML2_Ex9_FN.sbml` may be invalid.<br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. <br>           The units of the rateRule math expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'I' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'SEC' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'V' does not have a 'units' attribute.<br>          <br>        - As a principle of best modeling practice, the units of a parameter should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.<br>           The parameter with the id 'W' does not have a 'units' attribute.<br>          <br>  <br><br><span style=\"color:red;\"><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).<br></details>                 | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <a href=\"d1_plots\\rbapy_d1.pdf\">rbapy_d1.pdf</a>           |\n",
-       "| smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>[Errno 2] No such file or directory: '/tmp/tmpxu9n6is0/model.txt'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       |                                                            |\n",
-       "| tellurium  | pass                                     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <a href=\"d1_plots\\tellurium_d1.pdf\">tellurium_d1.pdf</a>   |\n",
-       "| vcell      | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1: b'  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SEDML(preProcessDoc)  **** Error: SED-ML processing for /tmp/vcell_temp_46077126-d76f-4cd8-acf3-9a4e6e14494514203906214399449282/tmp886838 failed with error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  SIMULATIONS_RUN(runSimulations)  **** Error: \\n  Root(root)  OMEX_EXECUTE(LEMS_NML2_Ex9_FN_missing_xmlns.omex)  PROCESSING_SIMULATION_OUTPUTS(processOutputs)  **** Error: Error processing outputs\\n'```</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                            |\n",
-       "| xpp        | <span style=\"color:darkred;\">FAIL</span> | <details><summary>Details</summary><span style=\"color:red;\">No module named 'libsbml'<br></details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   |                                                            |"
+       "|    | Engine     | pass / FAIL (remote)                     | pass / FAIL (local)                      | Compat (remote)                                                                                                                                                                                                                                                            | Compat (local)                                                                                                                                                                                                                                                             | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |\n",
+       "|---:|:-----------|:-----------------------------------------|:-----------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|\n",
+       "|  0 | amici      | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
+       "|  1 | bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
+       "|  2 | boolnet    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
+       "|  3 | brian2     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "|  4 | cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
+       "|  5 | cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
+       "|  6 | copasi     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
+       "|  7 | gillespy2  | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
+       "|  8 | ginsim     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
+       "|  9 | libsbmlsim | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
+       "| 10 | masspy     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
+       "| 11 | netpyne    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 12 | neuron     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 13 | opencor    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 14 | pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 15 | pysces     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpkpz53wsp/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpkpz53wsp/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
+       "| 16 | rbapy      | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
+       "| 17 | smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 18 | tellurium  | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
+       "| 19 | vcell      | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 20 | xpp        | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
       ]
      },
      "metadata": {},
@@ -971,45 +729,29 @@
     }
    ],
    "source": [
-    "# Create a table of the results\n",
-    "results_table = pd.DataFrame.from_dict(engine_dict).T\n",
-    "results_table.columns = ['pass/FAIL', 'Error']\n",
-    "results_table.index.name = 'Engine'\n",
-    "results_table.reset_index(inplace=True)\n",
+    "#########################################################################################\n",
+    "# process results and save markdown table\n",
+    "#########################################################################################\n",
     "\n",
-    "results_table['Error'] = results_table.apply(lambda x: None if x['pass/FAIL'] == x['Error'] else x['Error'], axis=1)\n",
-    "results_table['pass/FAIL'] = results_table['pass/FAIL'].replace('other', 'FAIL')\n",
-    "# # results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: x if x == 'FAIL' else x)\n",
+    "results_table = utils.create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)\n",
+    "results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)\n",
     "\n",
-    "# for non empty cells in error col print error message\n",
+    "# rename cols to distinguish between local and remote results except for Engine column\n",
+    "results_table.columns = [str(col) + ' (remote)' if col != 'Engine' else str(col) for col in results_table.columns]\n",
+    "results_table_local.columns = [str(col) + ' (local)' if col != 'Engine' else str(col) for col in results_table_local.columns]\n",
     "\n",
-    "results_table['Error'] = results_table['Error'].apply(lambda x: utils.ansi_to_html(x))\n",
-    "results_table['Error'] = results_table['Error'].apply(lambda x: utils.collapsible_content(x))\n",
+    "# combine remote and local results\n",
+    "combined_results = pd.merge(results_table, results_table_local, on='Engine', how='outer')\n",
+    "combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))\n",
     "\n",
-    "# compatibility_message\n",
-    "results_table['Compatibility'] = results_table['Engine'].apply(lambda x: utils.check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))\n",
-    "results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: utils.collapsible_content(x[1], title=x[0]))\n",
-    "results_table['pass/FAIL'] = results_table['pass/FAIL'].apply(lambda x: f'<span style=\"color:darkred;\">{x}</span>' if x == 'FAIL' else x)\n",
-    "results_table['Compatibility'] = results_table['Compatibility'].apply(lambda x: f'<span style=\"color:darkred;\">{x}</span>' if 'FAIL' in x else x)\n",
+    "cols_order = ['Engine', 'pass / FAIL (remote)', 'pass / FAIL (local)',\\\n",
+    "               'Compat (remote)', 'Compat (local)', \\\n",
+    "               'Type (remote)', \\\n",
+    "               'Error (remote)', 'Error (local)', \\\n",
+    "               'd1 (remote)', 'd1 (local)']\n",
     "\n",
-    "# d1 plot clickable link\n",
-    "results_table['d1'] = results_table['Engine'].apply(lambda x: utils.d1_plots_dict(engines, 'd1_plots').get(x, None))\n",
-    "results_table['d1'] = results_table['d1'].apply(lambda x: utils.create_hyperlink(x))\n",
-    "\n",
-    "results_md_table = results_table.to_markdown(index=False)\n",
-    "display_markdown('## Local via Docker Results', raw=True)\n",
-    "display_markdown(results_md_table, raw=True)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 30,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# save results_md_table\n",
-    "with open('results_compatibility_biosimulators.md', 'w', encoding='utf-8') as f:\n",
-    "    f.write(results_md_table)"
+    "combined_results = combined_results[cols_order]\n",
+    "display_markdown(combined_results.to_markdown(), raw=True)"
    ]
   }
  ],

From 74ac1095800549f5fdb8137fc129463189dca0a5 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 13 Aug 2024 08:45:23 +0100
Subject: [PATCH 23/71] display colored icons for pass and FAIL in
 create_results_table

---
 SBML/test_compatibility_biosimulators.ipynb | 305 ++++++++++----------
 utils/__init__.py                           |  12 +-
 2 files changed, 155 insertions(+), 162 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index e8cf99c..b85b7c9 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -60,7 +60,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -72,7 +72,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6a24ae0ee444424c8ff04d62278713c0\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a8ff030c0c124f29a696807cb5acd123\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -80,10 +80,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f830c4ccdd4919203e7\n",
-      "View: https://api.biosimulations.org/runs/66ba1f830c4ccdd4919203e7\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f830c4ccdd4919203e7/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f830c4ccdd4919203e7?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d95f29e09b32cb6f010\n",
+      "View: https://api.biosimulations.org/runs/66bb0d95f29e09b32cb6f010\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0d95f29e09b32cb6f010/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0d95f29e09b32cb6f010?includeOutput=true\n"
      ]
     },
     {
@@ -95,7 +95,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=39f2f2d3326348979bfde3c5434dee52\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4620f85b7dd0417b85317f5621d7c3cf\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -103,10 +103,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f85f29e09b32cb6e3e6\n",
-      "View: https://api.biosimulations.org/runs/66ba1f85f29e09b32cb6e3e6\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f85f29e09b32cb6e3e6/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f85f29e09b32cb6e3e6?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d97f29e09b32cb6f013\n",
+      "View: https://api.biosimulations.org/runs/66bb0d97f29e09b32cb6f013\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0d97f29e09b32cb6f013/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0d97f29e09b32cb6f013?includeOutput=true\n"
      ]
     },
     {
@@ -118,7 +118,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=e7f0bb4a16734cc2b36c1298434e76fa\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=61d678f6a20e46b69b09ef7dc6591887\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -126,10 +126,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f870c4ccdd4919203ea\n",
-      "View: https://api.biosimulations.org/runs/66ba1f870c4ccdd4919203ea\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f870c4ccdd4919203ea/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f870c4ccdd4919203ea?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d99f29e09b32cb6f016\n",
+      "View: https://api.biosimulations.org/runs/66bb0d99f29e09b32cb6f016\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0d99f29e09b32cb6f016/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0d99f29e09b32cb6f016?includeOutput=true\n"
      ]
     },
     {
@@ -141,7 +141,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=122fb47d395048eca2a0817141ec00a3\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c87fb6f5525a4d788a7e600ff2b0532e\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -149,10 +149,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f88a641708179acfc8e\n",
-      "View: https://api.biosimulations.org/runs/66ba1f88a641708179acfc8e\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f88a641708179acfc8e/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f88a641708179acfc8e?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d9bf29e09b32cb6f019\n",
+      "View: https://api.biosimulations.org/runs/66bb0d9bf29e09b32cb6f019\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0d9bf29e09b32cb6f019/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0d9bf29e09b32cb6f019?includeOutput=true\n"
      ]
     },
     {
@@ -164,7 +164,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=3aafbb161ddf477e8a2301911cd284f4\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=732fc163662445de936069cbcb4f5ca7\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -172,10 +172,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f8af29e09b32cb6e3e9\n",
-      "View: https://api.biosimulations.org/runs/66ba1f8af29e09b32cb6e3e9\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f8af29e09b32cb6e3e9/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f8af29e09b32cb6e3e9?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d9d0c4ccdd491920fff\n",
+      "View: https://api.biosimulations.org/runs/66bb0d9d0c4ccdd491920fff\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0d9d0c4ccdd491920fff/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0d9d0c4ccdd491920fff?includeOutput=true\n"
      ]
     },
     {
@@ -187,7 +187,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f102a0a33b3242768c9962be48ea98ca\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4bc1f45f8bd349d08cdacef4f74d5125\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -195,10 +195,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f8c0c4ccdd4919203f0\n",
-      "View: https://api.biosimulations.org/runs/66ba1f8c0c4ccdd4919203f0\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f8c0c4ccdd4919203f0/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f8c0c4ccdd4919203f0?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d9ff29e09b32cb6f01e\n",
+      "View: https://api.biosimulations.org/runs/66bb0d9ff29e09b32cb6f01e\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0d9ff29e09b32cb6f01e/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0d9ff29e09b32cb6f01e?includeOutput=true\n"
      ]
     },
     {
@@ -210,7 +210,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=786c1d04b44546b8925d8ee2e7b49f73\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=37d4c123616b4cd28623b6f2cee3ec7b\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -218,10 +218,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f8ef29e09b32cb6e3ef\n",
-      "View: https://api.biosimulations.org/runs/66ba1f8ef29e09b32cb6e3ef\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f8ef29e09b32cb6e3ef/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f8ef29e09b32cb6e3ef?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0da1f29e09b32cb6f021\n",
+      "View: https://api.biosimulations.org/runs/66bb0da1f29e09b32cb6f021\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0da1f29e09b32cb6f021/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0da1f29e09b32cb6f021?includeOutput=true\n"
      ]
     },
     {
@@ -233,7 +233,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6d2e0f00f44c4acbb95f27d14413bdc8\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=83a857a3f4bd4771822cb5844fc9bd89\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -241,10 +241,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f90f29e09b32cb6e3f4\n",
-      "View: https://api.biosimulations.org/runs/66ba1f90f29e09b32cb6e3f4\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f90f29e09b32cb6e3f4/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f90f29e09b32cb6e3f4?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0da4f29e09b32cb6f025\n",
+      "View: https://api.biosimulations.org/runs/66bb0da4f29e09b32cb6f025\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0da4f29e09b32cb6f025/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0da4f29e09b32cb6f025?includeOutput=true\n"
      ]
     },
     {
@@ -256,7 +256,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=155122bca1084350a45640fa0b3193cf\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=1b2aebc955de48049c8b7a7a986b1ae3\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -264,10 +264,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f92f29e09b32cb6e3f9\n",
-      "View: https://api.biosimulations.org/runs/66ba1f92f29e09b32cb6e3f9\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f92f29e09b32cb6e3f9/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f92f29e09b32cb6e3f9?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0da50c4ccdd49192100e\n",
+      "View: https://api.biosimulations.org/runs/66bb0da50c4ccdd49192100e\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0da50c4ccdd49192100e/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0da50c4ccdd49192100e?includeOutput=true\n"
      ]
     },
     {
@@ -279,7 +279,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=79d21d2ea26e4757b7e665f21f1ca8ae\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=744ab4d816eb41debf2ced82c7812d91\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -287,10 +287,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f94a641708179acfc9c\n",
-      "View: https://api.biosimulations.org/runs/66ba1f94a641708179acfc9c\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f94a641708179acfc9c/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f94a641708179acfc9c?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0da7f29e09b32cb6f028\n",
+      "View: https://api.biosimulations.org/runs/66bb0da7f29e09b32cb6f028\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0da7f29e09b32cb6f028/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0da7f29e09b32cb6f028?includeOutput=true\n"
      ]
     },
     {
@@ -302,7 +302,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=05e8fe072cd2403a8cdf454adf0d4d30\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c46e82397967401885ceb729037b15bf\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -310,10 +310,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f96f29e09b32cb6e401\n",
-      "View: https://api.biosimulations.org/runs/66ba1f96f29e09b32cb6e401\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f96f29e09b32cb6e401/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f96f29e09b32cb6e401?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0daaf29e09b32cb6f03a\n",
+      "View: https://api.biosimulations.org/runs/66bb0daaf29e09b32cb6f03a\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0daaf29e09b32cb6f03a/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0daaf29e09b32cb6f03a?includeOutput=true\n"
      ]
     },
     {
@@ -325,7 +325,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=37a1033536674c2dbc3ef1a250724728\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=0f0e828ec4354ec8a9c49a92d3b215e9\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -333,10 +333,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f980c4ccdd491920407\n",
-      "View: https://api.biosimulations.org/runs/66ba1f980c4ccdd491920407\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f980c4ccdd491920407/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f980c4ccdd491920407?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dabf29e09b32cb6f03f\n",
+      "View: https://api.biosimulations.org/runs/66bb0dabf29e09b32cb6f03f\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0dabf29e09b32cb6f03f/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0dabf29e09b32cb6f03f?includeOutput=true\n"
      ]
     },
     {
@@ -348,7 +348,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=948b1d17fd964943983a456b847b9611\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=feff0e8a568545b3b03d3ebf20c88279\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -356,10 +356,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f9aa641708179acfcb6\n",
-      "View: https://api.biosimulations.org/runs/66ba1f9aa641708179acfcb6\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f9aa641708179acfcb6/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f9aa641708179acfcb6?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dad0c4ccdd491921026\n",
+      "View: https://api.biosimulations.org/runs/66bb0dad0c4ccdd491921026\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0dad0c4ccdd491921026/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0dad0c4ccdd491921026?includeOutput=true\n"
      ]
     },
     {
@@ -371,7 +371,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=d5e5d42c0d9c4f958b4a568e71fc7227\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=42ab240770f246cea5a3f39d92e664c4\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -379,10 +379,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f9cf29e09b32cb6e426\n",
-      "View: https://api.biosimulations.org/runs/66ba1f9cf29e09b32cb6e426\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f9cf29e09b32cb6e426/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f9cf29e09b32cb6e426?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dafa641708179ad09b4\n",
+      "View: https://api.biosimulations.org/runs/66bb0dafa641708179ad09b4\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0dafa641708179ad09b4/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0dafa641708179ad09b4?includeOutput=true\n"
      ]
     },
     {
@@ -394,7 +394,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5f82c6a945f3472cbdde1c27ca8ae0eb\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=71923463315242aebf628de5b3403d14\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -402,10 +402,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f9ef29e09b32cb6e432\n",
-      "View: https://api.biosimulations.org/runs/66ba1f9ef29e09b32cb6e432\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f9ef29e09b32cb6e432/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f9ef29e09b32cb6e432?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db1a641708179ad09b9\n",
+      "View: https://api.biosimulations.org/runs/66bb0db1a641708179ad09b9\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0db1a641708179ad09b9/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0db1a641708179ad09b9?includeOutput=true\n"
      ]
     },
     {
@@ -417,7 +417,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=cf52c47341294a89b525b5da176a9c6b\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=636d048054da4d75b875f20be0d27fab\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -425,10 +425,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1f9f0c4ccdd491920434\n",
-      "View: https://api.biosimulations.org/runs/66ba1f9f0c4ccdd491920434\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1f9f0c4ccdd491920434/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1f9f0c4ccdd491920434?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db3f29e09b32cb6f05c\n",
+      "View: https://api.biosimulations.org/runs/66bb0db3f29e09b32cb6f05c\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0db3f29e09b32cb6f05c/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0db3f29e09b32cb6f05c?includeOutput=true\n"
      ]
     },
     {
@@ -440,7 +440,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=0f306f40d80d4a8886a4cda37daba825\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ee56ed4eae384139a33f79c48483a64e\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -448,10 +448,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1fa10c4ccdd491920438\n",
-      "View: https://api.biosimulations.org/runs/66ba1fa10c4ccdd491920438\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1fa10c4ccdd491920438/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1fa10c4ccdd491920438?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db4f29e09b32cb6f068\n",
+      "View: https://api.biosimulations.org/runs/66bb0db4f29e09b32cb6f068\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0db4f29e09b32cb6f068/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0db4f29e09b32cb6f068?includeOutput=true\n"
      ]
     },
     {
@@ -463,7 +463,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b7710c48585b4c50ace4a4b6d435a980\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=e30a79b61c384f51b07784970991adee\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -471,10 +471,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1fa3a641708179acfce3\n",
-      "View: https://api.biosimulations.org/runs/66ba1fa3a641708179acfce3\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1fa3a641708179acfce3/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1fa3a641708179acfce3?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db60c4ccdd49192104d\n",
+      "View: https://api.biosimulations.org/runs/66bb0db60c4ccdd49192104d\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0db60c4ccdd49192104d/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0db60c4ccdd49192104d?includeOutput=true\n"
      ]
     },
     {
@@ -486,7 +486,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=adcbd4850763439085c40bb60b360d2e\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=aaf1a7cb3be9403c91bce297e56351cd\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -494,10 +494,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1fa5a641708179acfcea\n",
-      "View: https://api.biosimulations.org/runs/66ba1fa5a641708179acfcea\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1fa5a641708179acfcea/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1fa5a641708179acfcea?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db8f29e09b32cb6f076\n",
+      "View: https://api.biosimulations.org/runs/66bb0db8f29e09b32cb6f076\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0db8f29e09b32cb6f076/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0db8f29e09b32cb6f076?includeOutput=true\n"
      ]
     },
     {
@@ -509,7 +509,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ea1629cce1a541b09538f45dd0f5a897\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=03a7aeedbb3f4180b4177a34266dbc75\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -517,10 +517,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1faaf29e09b32cb6e477\n",
-      "View: https://api.biosimulations.org/runs/66ba1faaf29e09b32cb6e477\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1faaf29e09b32cb6e477/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1faaf29e09b32cb6e477?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dbba641708179ad09fa\n",
+      "View: https://api.biosimulations.org/runs/66bb0dbba641708179ad09fa\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0dbba641708179ad09fa/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0dbba641708179ad09fa?includeOutput=true\n"
      ]
     },
     {
@@ -532,7 +532,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=18f5610ecb314a9693116e68d038e7a6\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ee5ee7567d144c60b5698e158621e5ce\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -540,10 +540,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66ba1facf29e09b32cb6e480\n",
-      "View: https://api.biosimulations.org/runs/66ba1facf29e09b32cb6e480\n",
-      "Downloads: https://api.biosimulations.org/results/66ba1facf29e09b32cb6e480/download\n",
-      "Logs: https://api.biosimulations.org/logs/66ba1facf29e09b32cb6e480?includeOutput=true\n",
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dbd0c4ccdd491921074\n",
+      "View: https://api.biosimulations.org/runs/66bb0dbd0c4ccdd491921074\n",
+      "Downloads: https://api.biosimulations.org/results/66bb0dbd0c4ccdd491921074/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb0dbd0c4ccdd491921074?includeOutput=true\n",
       "Downloading amici results...\n",
       "Downloading brian2 results...\n",
       "Downloading bionetgen results...\n",
@@ -565,32 +565,19 @@
       "Downloading tellurium results...\n",
       "Downloading vcell results...\n",
       "Downloading xpp results...\n",
-      "Moving remote_results\\amici\\outputs\\tmp802597\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
-      "Moving remote_results\\amici\\outputs\\tmp987077\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
-      "Moving remote_results\\bionetgen\\outputs\\tmp337013\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
-      "Moving remote_results\\bionetgen\\outputs\\tmp950095\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
-      "Moving remote_results\\boolnet\\outputs\\tmp644487\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
-      "Moving remote_results\\boolnet\\outputs\\tmp649837\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
-      "Moving remote_results\\cbmpy\\outputs\\tmp516152\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
-      "Moving remote_results\\cbmpy\\outputs\\tmp591632\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
-      "Moving remote_results\\cobrapy\\outputs\\tmp220956\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
-      "Moving remote_results\\cobrapy\\outputs\\tmp589941\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
-      "Moving remote_results\\copasi\\outputs\\tmp69930\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
-      "Moving remote_results\\copasi\\outputs\\tmp820744\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
-      "Moving remote_results\\gillespy2\\outputs\\tmp334450\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
-      "Moving remote_results\\gillespy2\\outputs\\tmp952245\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
-      "Moving remote_results\\ginsim\\outputs\\tmp267937\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
-      "Moving remote_results\\ginsim\\outputs\\tmp936909\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
-      "Moving remote_results\\libsbmlsim\\outputs\\tmp282735\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
-      "Moving remote_results\\libsbmlsim\\outputs\\tmp3602\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
-      "Moving remote_results\\masspy\\outputs\\tmp648987\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
-      "Moving remote_results\\masspy\\outputs\\tmp907144\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
-      "Moving remote_results\\pysces\\outputs\\tmp312749\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
-      "Moving remote_results\\pysces\\outputs\\tmp415792\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
-      "Moving remote_results\\rbapy\\outputs\\tmp496636\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
-      "Moving remote_results\\rbapy\\outputs\\tmp499456\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
-      "Moving remote_results\\tellurium\\outputs\\tmp402952\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
-      "Moving remote_results\\tellurium\\outputs\\tmp916390\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
+      "Moving remote_results\\amici\\outputs\\tmp835455\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
+      "Moving remote_results\\bionetgen\\outputs\\tmp671390\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
+      "Moving remote_results\\boolnet\\outputs\\tmp657556\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
+      "Moving remote_results\\cbmpy\\outputs\\tmp988681\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
+      "Moving remote_results\\cobrapy\\outputs\\tmp108287\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
+      "Moving remote_results\\copasi\\outputs\\tmp548282\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
+      "Moving remote_results\\gillespy2\\outputs\\tmp739285\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
+      "Moving remote_results\\ginsim\\outputs\\tmp535823\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
+      "Moving remote_results\\libsbmlsim\\outputs\\tmp54867\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
+      "Moving remote_results\\masspy\\outputs\\tmp115739\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
+      "Moving remote_results\\pysces\\outputs\\tmp900850\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
+      "Moving remote_results\\rbapy\\outputs\\tmp433704\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
+      "Moving remote_results\\tellurium\\outputs\\tmp576362\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
       "Removed remote_results folder\n",
       "Running amici\n",
       "Running brian2\n",
@@ -636,7 +623,7 @@
     "    extract_dir = utils.get_remote_results(e, link, remote_output_dir)\n",
     "    extract_dir_dict[e] = extract_dir\n",
     "\n",
-    "results = dict()\n",
+    "results_remote = dict()\n",
     "for e, extract_dir in extract_dir_dict.items():\n",
     "    status = \"\"\n",
     "    error_message = \"\"\n",
@@ -658,7 +645,7 @@
     "            exception_type = exception['type'] \n",
     "        else:\n",
     "            status = None\n",
-    "        results[e] = [status, error_message, exception_type] \n",
+    "        results_remote[e] = [status, error_message, exception_type] \n",
     "\n",
     "file_paths = utils.find_files(remote_output_dir, '.pdf')\n",
     "utils.move_d1_files(file_paths, d1_plots_remote_dir)\n",
@@ -693,35 +680,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/markdown": [
-       "|    | Engine     | pass / FAIL (remote)                     | pass / FAIL (local)                      | Compat (remote)                                                                                                                                                                                                                                                            | Compat (local)                                                                                                                                                                                                                                                             | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |\n",
-       "|---:|:-----------|:-----------------------------------------|:-----------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|\n",
-       "|  0 | amici      | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                       |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
-       "|  1 | bionetgen  | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
-       "|  2 | boolnet    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
-       "|  3 | brian2     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "|  4 | cbmpy      | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
-       "|  5 | cobrapy    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
-       "|  6 | copasi     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
-       "|  7 | gillespy2  | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
-       "|  8 | ginsim     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
-       "|  9 | libsbmlsim | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
-       "| 10 | masspy     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
-       "| 11 | netpyne    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 12 | neuron     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 13 | opencor    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 14 | pyneuroml  | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 15 | pysces     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpkpz53wsp/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpkpz53wsp/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
-       "| 16 | rbapy      | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
-       "| 17 | smoldyn    | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style=\"color:darkred;\"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 18 | tellurium  | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
-       "| 19 | vcell      | pass                                     | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style=\"color:darkred;\"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 20 | xpp        | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\">FAIL</span> | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
+       "|    | Engine     | pass / FAIL (remote)                                                                                                                                                       | pass / FAIL (local)                                                                                                                                                        | Compat (remote)                                                                                                                                                                                                                                                                                                                        | Compat (local)                                                                                                                                                                                                                                                                                                                         | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |\n",
+       "|---:|:-----------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|\n",
+       "|  0 | amici      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
+       "|  1 | bionetgen  | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
+       "|  2 | boolnet    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
+       "|  3 | brian2     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "|  4 | cbmpy      | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
+       "|  5 | cobrapy    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
+       "|  6 | copasi     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
+       "|  7 | gillespy2  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
+       "|  8 | ginsim     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
+       "|  9 | libsbmlsim | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
+       "| 10 | masspy     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
+       "| 11 | netpyne    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 12 | neuron     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 13 | opencor    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 14 | pyneuroml  | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 15 | pysces     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp8ak6qa9f/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp8ak6qa9f/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
+       "| 16 | rbapy      | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
+       "| 17 | smoldyn    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 18 | tellurium  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
+       "| 19 | vcell      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 20 | xpp        | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
       ]
      },
      "metadata": {},
@@ -733,7 +720,7 @@
     "# process results and save markdown table\n",
     "#########################################################################################\n",
     "\n",
-    "results_table = utils.create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)\n",
+    "results_table = utils.create_results_table(results_remote, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)\n",
     "results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)\n",
     "\n",
     "# rename cols to distinguish between local and remote results except for Engine column\n",
diff --git a/utils/__init__.py b/utils/__init__.py
index 86c86af..39f4fb2 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -976,7 +976,6 @@ def unzip_file(file_path, output_dir=None):
 
     return file_path
 
-
 def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, output_dir):
     """
     Create a markdown table of the results.
@@ -985,6 +984,10 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng
     Output: results_md_table
 
     """
+    
+    link_green_square = "https://via.placeholder.com/15/00dd00/00dd00.png"
+    link_orange_square = "https://via.placeholder.com/15/ec9706/ec9706.png"
+    link_red_square = "https://via.placeholder.com/15/dd0000/dd0000.png"
 
     # Create a table of the results
     results_table = pd.DataFrame.from_dict(results).T
@@ -1006,10 +1009,13 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng
     # compatibility_message
     results_table['Compat'] = results_table['Engine'].apply(lambda x: check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))
     results_table['Compat'] = results_table['Compat'].apply(lambda x: collapsible_content(x[1], title=x[0]))
-    results_table['Compat'] = results_table['Compat'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if 'FAIL' in x else x)
+    results_table['Compat'] = results_table['Compat'].apply(lambda x: f'<span style="color:darkred;"><img src={link_red_square}/> {x}</span>'\
+                                                             if 'FAIL' in x else f'<img src={link_green_square}/>{x}')
 
     # pass / FAIL
-    results_table['pass / FAIL'] = results_table['pass / FAIL'].apply(lambda x: f'<span style="color:darkred;">{x}</span>' if x == 'FAIL' else x)
+    results_table['pass / FAIL'] = results_table['pass / FAIL'].apply(lambda x: f'<span style="color:darkred;">\
+                                                                      <img src={link_red_square}/> {x}</span>' if x == 'FAIL' \
+                                                                        else f'<img src={link_green_square}/> {x}')
 
     # d1 plot clickable link
     results_table['d1'] = results_table['Engine'].apply(lambda x: d1_plots_dict(engines, output_dir).get(x, None))

From 8f4e2541407fa1269dfc81a6863379d13f0a90ac Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 13 Aug 2024 10:03:34 +0100
Subject: [PATCH 24/71] Update engines dict with biosimulator URLs and status
 and add URL hyperlink to table

---
 SBML/test_compatibility_biosimulators.ipynb | 284 ++++++++++----------
 utils/__init__.py                           | 119 +++++++-
 2 files changed, 260 insertions(+), 143 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index b85b7c9..9c8ad8d 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -72,7 +72,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a8ff030c0c124f29a696807cb5acd123\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=247184b0654243cba4dc148572be4227\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -80,10 +80,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d95f29e09b32cb6f010\n",
-      "View: https://api.biosimulations.org/runs/66bb0d95f29e09b32cb6f010\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0d95f29e09b32cb6f010/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0d95f29e09b32cb6f010?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eb40c4ccdd4919214fc\n",
+      "View: https://api.biosimulations.org/runs/66bb1eb40c4ccdd4919214fc\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1eb40c4ccdd4919214fc/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1eb40c4ccdd4919214fc?includeOutput=true\n"
      ]
     },
     {
@@ -95,7 +95,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4620f85b7dd0417b85317f5621d7c3cf\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b924b87f571d4d3ab0815e07db1d1c68\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -103,10 +103,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d97f29e09b32cb6f013\n",
-      "View: https://api.biosimulations.org/runs/66bb0d97f29e09b32cb6f013\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0d97f29e09b32cb6f013/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0d97f29e09b32cb6f013?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eb60c4ccdd4919214ff\n",
+      "View: https://api.biosimulations.org/runs/66bb1eb60c4ccdd4919214ff\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1eb60c4ccdd4919214ff/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1eb60c4ccdd4919214ff?includeOutput=true\n"
      ]
     },
     {
@@ -118,7 +118,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=61d678f6a20e46b69b09ef7dc6591887\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6f4ca7b4f22c4cd29b54f1f09f3504e7\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -126,10 +126,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d99f29e09b32cb6f016\n",
-      "View: https://api.biosimulations.org/runs/66bb0d99f29e09b32cb6f016\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0d99f29e09b32cb6f016/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0d99f29e09b32cb6f016?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eb8a641708179ad0e9b\n",
+      "View: https://api.biosimulations.org/runs/66bb1eb8a641708179ad0e9b\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1eb8a641708179ad0e9b/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1eb8a641708179ad0e9b?includeOutput=true\n"
      ]
     },
     {
@@ -141,7 +141,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c87fb6f5525a4d788a7e600ff2b0532e\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=dc48b39407844f869294f21488b21484\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -149,10 +149,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d9bf29e09b32cb6f019\n",
-      "View: https://api.biosimulations.org/runs/66bb0d9bf29e09b32cb6f019\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0d9bf29e09b32cb6f019/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0d9bf29e09b32cb6f019?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eba0c4ccdd491921502\n",
+      "View: https://api.biosimulations.org/runs/66bb1eba0c4ccdd491921502\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1eba0c4ccdd491921502/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1eba0c4ccdd491921502?includeOutput=true\n"
      ]
     },
     {
@@ -164,7 +164,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=732fc163662445de936069cbcb4f5ca7\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=fe00670b96934c8c8194595a424f7329\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -172,10 +172,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d9d0c4ccdd491920fff\n",
-      "View: https://api.biosimulations.org/runs/66bb0d9d0c4ccdd491920fff\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0d9d0c4ccdd491920fff/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0d9d0c4ccdd491920fff?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ebcf29e09b32cb6f52c\n",
+      "View: https://api.biosimulations.org/runs/66bb1ebcf29e09b32cb6f52c\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ebcf29e09b32cb6f52c/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ebcf29e09b32cb6f52c?includeOutput=true\n"
      ]
     },
     {
@@ -187,7 +187,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4bc1f45f8bd349d08cdacef4f74d5125\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=970ebf139ad34bb99d29a34cecf95601\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -195,10 +195,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0d9ff29e09b32cb6f01e\n",
-      "View: https://api.biosimulations.org/runs/66bb0d9ff29e09b32cb6f01e\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0d9ff29e09b32cb6f01e/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0d9ff29e09b32cb6f01e?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ebea641708179ad0e9e\n",
+      "View: https://api.biosimulations.org/runs/66bb1ebea641708179ad0e9e\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ebea641708179ad0e9e/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ebea641708179ad0e9e?includeOutput=true\n"
      ]
     },
     {
@@ -210,7 +210,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=37d4c123616b4cd28623b6f2cee3ec7b\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5ce0e4f76267429299ec6ae1716c6c8c\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -218,10 +218,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0da1f29e09b32cb6f021\n",
-      "View: https://api.biosimulations.org/runs/66bb0da1f29e09b32cb6f021\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0da1f29e09b32cb6f021/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0da1f29e09b32cb6f021?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec0a641708179ad0ea3\n",
+      "View: https://api.biosimulations.org/runs/66bb1ec0a641708179ad0ea3\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ec0a641708179ad0ea3/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ec0a641708179ad0ea3?includeOutput=true\n"
      ]
     },
     {
@@ -233,7 +233,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=83a857a3f4bd4771822cb5844fc9bd89\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=8b90c1b4b7b1499a8dae09a03adf23c7\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -241,10 +241,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0da4f29e09b32cb6f025\n",
-      "View: https://api.biosimulations.org/runs/66bb0da4f29e09b32cb6f025\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0da4f29e09b32cb6f025/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0da4f29e09b32cb6f025?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec20c4ccdd491921506\n",
+      "View: https://api.biosimulations.org/runs/66bb1ec20c4ccdd491921506\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ec20c4ccdd491921506/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ec20c4ccdd491921506?includeOutput=true\n"
      ]
     },
     {
@@ -256,7 +256,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=1b2aebc955de48049c8b7a7a986b1ae3\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=774ff499104a46bd9870b755062b136a\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -264,10 +264,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0da50c4ccdd49192100e\n",
-      "View: https://api.biosimulations.org/runs/66bb0da50c4ccdd49192100e\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0da50c4ccdd49192100e/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0da50c4ccdd49192100e?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec4f29e09b32cb6f536\n",
+      "View: https://api.biosimulations.org/runs/66bb1ec4f29e09b32cb6f536\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ec4f29e09b32cb6f536/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ec4f29e09b32cb6f536?includeOutput=true\n"
      ]
     },
     {
@@ -279,7 +279,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=744ab4d816eb41debf2ced82c7812d91\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ec0e7ae509274148adf3c88bd16b6e38\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -287,10 +287,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0da7f29e09b32cb6f028\n",
-      "View: https://api.biosimulations.org/runs/66bb0da7f29e09b32cb6f028\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0da7f29e09b32cb6f028/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0da7f29e09b32cb6f028?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec6a641708179ad0eaa\n",
+      "View: https://api.biosimulations.org/runs/66bb1ec6a641708179ad0eaa\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ec6a641708179ad0eaa/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ec6a641708179ad0eaa?includeOutput=true\n"
      ]
     },
     {
@@ -302,7 +302,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c46e82397967401885ceb729037b15bf\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=2a7a32dd648f410ca5774405d10d7029\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -310,10 +310,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0daaf29e09b32cb6f03a\n",
-      "View: https://api.biosimulations.org/runs/66bb0daaf29e09b32cb6f03a\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0daaf29e09b32cb6f03a/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0daaf29e09b32cb6f03a?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec80c4ccdd491921511\n",
+      "View: https://api.biosimulations.org/runs/66bb1ec80c4ccdd491921511\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ec80c4ccdd491921511/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ec80c4ccdd491921511?includeOutput=true\n"
      ]
     },
     {
@@ -325,7 +325,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=0f0e828ec4354ec8a9c49a92d3b215e9\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=8e2c7805085f4d25b40f0a7d4206a530\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -333,10 +333,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dabf29e09b32cb6f03f\n",
-      "View: https://api.biosimulations.org/runs/66bb0dabf29e09b32cb6f03f\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0dabf29e09b32cb6f03f/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0dabf29e09b32cb6f03f?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eca0c4ccdd491921514\n",
+      "View: https://api.biosimulations.org/runs/66bb1eca0c4ccdd491921514\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1eca0c4ccdd491921514/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1eca0c4ccdd491921514?includeOutput=true\n"
      ]
     },
     {
@@ -348,7 +348,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=feff0e8a568545b3b03d3ebf20c88279\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=1cf8970faf3643ea8d17adc021047a43\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -356,10 +356,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dad0c4ccdd491921026\n",
-      "View: https://api.biosimulations.org/runs/66bb0dad0c4ccdd491921026\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0dad0c4ccdd491921026/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0dad0c4ccdd491921026?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ecba641708179ad0eba\n",
+      "View: https://api.biosimulations.org/runs/66bb1ecba641708179ad0eba\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ecba641708179ad0eba/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ecba641708179ad0eba?includeOutput=true\n"
      ]
     },
     {
@@ -371,7 +371,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=42ab240770f246cea5a3f39d92e664c4\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=63f9f78ddeae4a02b00b525a31eeafd7\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -379,10 +379,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dafa641708179ad09b4\n",
-      "View: https://api.biosimulations.org/runs/66bb0dafa641708179ad09b4\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0dafa641708179ad09b4/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0dafa641708179ad09b4?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ecd0c4ccdd49192153c\n",
+      "View: https://api.biosimulations.org/runs/66bb1ecd0c4ccdd49192153c\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ecd0c4ccdd49192153c/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ecd0c4ccdd49192153c?includeOutput=true\n"
      ]
     },
     {
@@ -394,7 +394,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=71923463315242aebf628de5b3403d14\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=999bbaa17e9a4781acc6deb3ac4f0fe8\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -402,10 +402,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db1a641708179ad09b9\n",
-      "View: https://api.biosimulations.org/runs/66bb0db1a641708179ad09b9\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0db1a641708179ad09b9/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0db1a641708179ad09b9?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ecea641708179ad0ec4\n",
+      "View: https://api.biosimulations.org/runs/66bb1ecea641708179ad0ec4\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ecea641708179ad0ec4/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ecea641708179ad0ec4?includeOutput=true\n"
      ]
     },
     {
@@ -417,7 +417,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=636d048054da4d75b875f20be0d27fab\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=bedad17524724f85b49fd5d7507208ab\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -425,10 +425,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db3f29e09b32cb6f05c\n",
-      "View: https://api.biosimulations.org/runs/66bb0db3f29e09b32cb6f05c\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0db3f29e09b32cb6f05c/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0db3f29e09b32cb6f05c?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ed0f29e09b32cb6f55f\n",
+      "View: https://api.biosimulations.org/runs/66bb1ed0f29e09b32cb6f55f\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ed0f29e09b32cb6f55f/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ed0f29e09b32cb6f55f?includeOutput=true\n"
      ]
     },
     {
@@ -440,7 +440,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ee56ed4eae384139a33f79c48483a64e\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=07eacaf016564cd991943f763e90ff30\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -448,10 +448,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db4f29e09b32cb6f068\n",
-      "View: https://api.biosimulations.org/runs/66bb0db4f29e09b32cb6f068\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0db4f29e09b32cb6f068/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0db4f29e09b32cb6f068?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ed2f29e09b32cb6f569\n",
+      "View: https://api.biosimulations.org/runs/66bb1ed2f29e09b32cb6f569\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ed2f29e09b32cb6f569/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ed2f29e09b32cb6f569?includeOutput=true\n"
      ]
     },
     {
@@ -463,7 +463,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=e30a79b61c384f51b07784970991adee\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=28a10abf17534f26bf5e0e92a677bd49\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -471,10 +471,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db60c4ccdd49192104d\n",
-      "View: https://api.biosimulations.org/runs/66bb0db60c4ccdd49192104d\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0db60c4ccdd49192104d/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0db60c4ccdd49192104d?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ed4f29e09b32cb6f585\n",
+      "View: https://api.biosimulations.org/runs/66bb1ed4f29e09b32cb6f585\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ed4f29e09b32cb6f585/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ed4f29e09b32cb6f585?includeOutput=true\n"
      ]
     },
     {
@@ -486,7 +486,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=aaf1a7cb3be9403c91bce297e56351cd\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=555fe9cb8c14494ba1a20573b70f8866\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -494,10 +494,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0db8f29e09b32cb6f076\n",
-      "View: https://api.biosimulations.org/runs/66bb0db8f29e09b32cb6f076\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0db8f29e09b32cb6f076/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0db8f29e09b32cb6f076?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ed6a641708179ad0ee9\n",
+      "View: https://api.biosimulations.org/runs/66bb1ed6a641708179ad0ee9\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1ed6a641708179ad0ee9/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1ed6a641708179ad0ee9?includeOutput=true\n"
      ]
     },
     {
@@ -509,7 +509,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=03a7aeedbb3f4180b4177a34266dbc75\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f58ee5d4ad6a441a9c8a6bf68eb55b70\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -517,10 +517,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dbba641708179ad09fa\n",
-      "View: https://api.biosimulations.org/runs/66bb0dbba641708179ad09fa\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0dbba641708179ad09fa/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0dbba641708179ad09fa?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eda0c4ccdd491921592\n",
+      "View: https://api.biosimulations.org/runs/66bb1eda0c4ccdd491921592\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1eda0c4ccdd491921592/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1eda0c4ccdd491921592?includeOutput=true\n"
      ]
     },
     {
@@ -532,7 +532,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ee5ee7567d144c60b5698e158621e5ce\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=aeeb96cd32ae426fa80173e3317ffc45\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -540,10 +540,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb0dbd0c4ccdd491921074\n",
-      "View: https://api.biosimulations.org/runs/66bb0dbd0c4ccdd491921074\n",
-      "Downloads: https://api.biosimulations.org/results/66bb0dbd0c4ccdd491921074/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb0dbd0c4ccdd491921074?includeOutput=true\n",
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1edca641708179ad0f0d\n",
+      "View: https://api.biosimulations.org/runs/66bb1edca641708179ad0f0d\n",
+      "Downloads: https://api.biosimulations.org/results/66bb1edca641708179ad0f0d/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb1edca641708179ad0f0d?includeOutput=true\n",
       "Downloading amici results...\n",
       "Downloading brian2 results...\n",
       "Downloading bionetgen results...\n",
@@ -565,19 +565,19 @@
       "Downloading tellurium results...\n",
       "Downloading vcell results...\n",
       "Downloading xpp results...\n",
-      "Moving remote_results\\amici\\outputs\\tmp835455\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
-      "Moving remote_results\\bionetgen\\outputs\\tmp671390\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
-      "Moving remote_results\\boolnet\\outputs\\tmp657556\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
-      "Moving remote_results\\cbmpy\\outputs\\tmp988681\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
-      "Moving remote_results\\cobrapy\\outputs\\tmp108287\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
-      "Moving remote_results\\copasi\\outputs\\tmp548282\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
-      "Moving remote_results\\gillespy2\\outputs\\tmp739285\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
-      "Moving remote_results\\ginsim\\outputs\\tmp535823\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
-      "Moving remote_results\\libsbmlsim\\outputs\\tmp54867\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
-      "Moving remote_results\\masspy\\outputs\\tmp115739\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
-      "Moving remote_results\\pysces\\outputs\\tmp900850\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
-      "Moving remote_results\\rbapy\\outputs\\tmp433704\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
-      "Moving remote_results\\tellurium\\outputs\\tmp576362\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
+      "Moving remote_results\\amici\\outputs\\tmp262364\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
+      "Moving remote_results\\bionetgen\\outputs\\tmp98719\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
+      "Moving remote_results\\boolnet\\outputs\\tmp813849\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
+      "Moving remote_results\\cbmpy\\outputs\\tmp979743\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
+      "Moving remote_results\\cobrapy\\outputs\\tmp981863\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
+      "Moving remote_results\\copasi\\outputs\\tmp423266\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
+      "Moving remote_results\\gillespy2\\outputs\\tmp146730\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
+      "Moving remote_results\\ginsim\\outputs\\tmp968356\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
+      "Moving remote_results\\libsbmlsim\\outputs\\tmp247930\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
+      "Moving remote_results\\masspy\\outputs\\tmp905203\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
+      "Moving remote_results\\pysces\\outputs\\tmp260212\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
+      "Moving remote_results\\rbapy\\outputs\\tmp516019\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
+      "Moving remote_results\\tellurium\\outputs\\tmp540535\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
       "Removed remote_results folder\n",
       "Running amici\n",
       "Running brian2\n",
@@ -680,35 +680,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/markdown": [
-       "|    | Engine     | pass / FAIL (remote)                                                                                                                                                       | pass / FAIL (local)                                                                                                                                                        | Compat (remote)                                                                                                                                                                                                                                                                                                                        | Compat (local)                                                                                                                                                                                                                                                                                                                         | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |\n",
-       "|---:|:-----------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|\n",
-       "|  0 | amici      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
-       "|  1 | bionetgen  | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
-       "|  2 | boolnet    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
-       "|  3 | brian2     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "|  4 | cbmpy      | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
-       "|  5 | cobrapy    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
-       "|  6 | copasi     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
-       "|  7 | gillespy2  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
-       "|  8 | ginsim     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
-       "|  9 | libsbmlsim | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
-       "| 10 | masspy     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
-       "| 11 | netpyne    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 12 | neuron     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 13 | opencor    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 14 | pyneuroml  | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 15 | pysces     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp8ak6qa9f/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp8ak6qa9f/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
-       "| 16 | rbapy      | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
-       "| 17 | smoldyn    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 18 | tellurium  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
-       "| 19 | vcell      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 20 | xpp        | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
+       "|    | Engine                                                                                                          | pass / FAIL (remote)                                                                                                                                                       | pass / FAIL (local)                                                                                                                                                        | Compat (remote)                                                                                                                                                                                                                                                                                                                        | Compat (local)                                                                                                                                                                                                                                                                                                                         | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |\n",
+       "|---:|:----------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|\n",
+       "|  0 | <a href=\"https://docs.biosimulators.org/Biosimulators_AMICI/\">amici</a>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
+       "|  1 | <a href=\"https://docs.biosimulators.org/Biosimulators_BioNetGen/\">bionetgen</a>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
+       "|  2 | <a href=\"https://docs.biosimulators.org/Biosimulators_BoolNet/\">boolnet</a>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
+       "|  3 | <a href=\"https://docs.biosimulators.org/Biosimulators_CBMPy/\">cbmpy</a>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
+       "|  4 | <a href=\"https://docs.biosimulators.org/Biosimulators_COBRApy/\">cobrapy</a>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
+       "|  5 | <a href=\"https://docs.biosimulators.org/Biosimulators_COPASI/\">copasi</a>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
+       "|  6 | <a href=\"https://docs.biosimulators.org/Biosimulators_GINsim/\">ginsim</a>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
+       "|  7 | <a href=\"https://docs.biosimulators.org/Biosimulators_GillesPy2/\">gillespy2</a>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
+       "|  8 | <a href=\"https://docs.biosimulators.org/Biosimulators_LibSBMLSim/\">libsbmlsim</a>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
+       "|  9 | <a href=\"https://docs.biosimulators.org/Biosimulators_MASSpy/\">masspy</a>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
+       "| 10 | <a href=\"https://docs.biosimulators.org/Biosimulators_OpenCOR/\">opencor</a>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 11 | <a href=\"https://docs.biosimulators.org/Biosimulators_PySCeS/\">pysces</a>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpi0f2z0io/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpi0f2z0io/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
+       "| 12 | <a href=\"https://docs.biosimulators.org/Biosimulators_RBApy/\">rbapy</a>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
+       "| 13 | <a href=\"https://docs.biosimulators.org/Biosimulators_XPP/\">xpp</a>                                             | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 14 | <a href=\"https://docs.biosimulators.org/Biosimulators_pyNeuroML/\">brian2</a>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 15 | <a href=\"https://docs.biosimulators.org/Biosimulators_pyNeuroML/\">netpyne</a>                                   | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 16 | <a href=\"https://docs.biosimulators.org/Biosimulators_pyNeuroML/\">neuron</a>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 17 | <a href=\"https://docs.biosimulators.org/Biosimulators_pyNeuroML/\">pyneuroml</a>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 18 | <a href=\"https://docs.biosimulators.org/Biosimulators_tellurium/\">tellurium</a>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
+       "| 19 | <a href=\"https://github.com/virtualcell/vcell\">vcell</a>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 20 | <a href=\"https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api\">smoldyn</a> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
       ]
      },
      "metadata": {},
diff --git a/utils/__init__.py b/utils/__init__.py
index 39f4fb2..69ad87f 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -46,6 +46,116 @@
                         'xpp': ('xpp', 'sedml')               
             }
 
+engines = {
+    'amici': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_AMICI/',
+        'status': ''
+    },
+    'brian2': {
+        'formats': [('nml', 'sedml'), ('lems', 'sedml'), ('sbml', 'sedml')],
+        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
+        'status': ''
+    },
+    'bionetgen': {
+        'formats': ('bngl', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_BioNetGen/',
+        'status': ''
+    },
+    'boolnet': {
+        'formats': ('sbmlqual', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_BoolNet/',
+        'status': ''
+    },
+    'cbmpy': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_CBMPy/',
+        'status': ''
+    },
+    'cobrapy': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_COBRApy/',
+        'status': 'Only allows steady state simulations'
+    },
+    'copasi': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_COPASI/',
+        'status': ''
+    },
+    'gillespy2': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_GillesPy2/',
+        'status': ''
+    },
+    'ginsim': {
+        'formats': ('sbmlqual', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_GINsim/',
+        'status': ''
+    },
+    'libsbmlsim': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_LibSBMLSim/',
+        'status': ''
+    },
+    'masspy': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_MASSpy/',
+        'status': ''
+    },
+    'netpyne': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
+        'status': ''
+    },
+    'neuron': {
+        'formats': [('nml', 'sedml'), ('lems', 'sedml')],
+        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
+        'status': ''
+    },
+    'opencor': {
+        'formats': ('cellml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_OpenCOR/',
+        'status': ''
+    },
+    'pyneuroml': {
+        'formats': [('nml', 'sedml'), ('lems', 'sedml')],
+        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
+        'status': ''
+    },
+    'pysces': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_PySCeS/',
+        'status': ''
+    },
+    'rbapy': {
+        'formats': ('rbapy', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_RBApy/',
+        'status': ''
+    },
+    'smoldyn': {
+        'formats': None,
+        'url': 'https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api',
+        'status': 'inactive'
+    },
+    'tellurium': {
+        'formats': ('sbml', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_tellurium/',
+        'status': ''
+    },
+    'vcell': {
+        'formats': [('sbml', 'sedml'),('bngl', 'sedml')],
+        'url': 'https://github.com/virtualcell/vcell',
+        'status': ''
+    },
+    'xpp': {
+        'formats': ('xpp', 'sedml'),
+        'url': 'https://docs.biosimulators.org/Biosimulators_XPP/',
+        'status': ''
+    }
+}
+
+
+
 types_dict = {
                 'sbml':'SBML',\
                 'sedml':'SED-ML',\
@@ -59,6 +169,9 @@
                 'cellml':'CellML'\
              }
 
+
+
+
 #define error categories for detailed error counting per engine
 # (currently only tellurium)
 # key is the tag/category used to report the category, value is a regex matching the error message
@@ -351,7 +464,7 @@ def check_file_compatibility_test(engine, types_dict, model_filepath, experiment
     input_file_types_text = [types_dict[i] for i in input_filetypes]
 
 
-    engine_filetypes = engines[engine]
+    engine_filetypes = engines[engine]['formats']
     if engine_filetypes is not None:
         # Flatten the list if the engine_filetypes is a list of tuples
         if all(isinstance(i, tuple) for i in engine_filetypes):
@@ -1000,6 +1113,7 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng
     results_table.index.name = 'Engine'
     results_table.reset_index(inplace=True)
 
+    # Error
     results_table['Error'] = results_table.apply(lambda x: None if x['pass / FAIL'] == x['Error'] else x['Error'], axis=1)
     results_table['pass / FAIL'] = results_table['pass / FAIL'].replace('other', 'FAIL')
 
@@ -1025,4 +1139,7 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng
     if 'Type' in results_table.columns:
         results_table['Type'] = results_table['Type'].apply(lambda x: collapsible_content(x,"".join(re.findall(r'[A-Z]', x))))
 
+    # Engine add hyperlink
+    results_table['Engine'] = results_table['Engine'].apply(lambda x: create_hyperlink(engines[x]['url'], title=x))
+
     return results_table

From 03526d99d707bba2b9e0765a482e7101a3a0fd08 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 13 Aug 2024 12:53:31 +0100
Subject: [PATCH 25/71] Add biosimulator URLs and status to table

---
 SBML/results_compatibility_biosimulators.md |  46 +-
 SBML/test_compatibility_biosimulators.ipynb | 488 ++++++++++++++------
 utils/__init__.py                           |  74 +--
 3 files changed, 382 insertions(+), 226 deletions(-)

diff --git a/SBML/results_compatibility_biosimulators.md b/SBML/results_compatibility_biosimulators.md
index 864197b..019e5c9 100644
--- a/SBML/results_compatibility_biosimulators.md
+++ b/SBML/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-|    | Engine     | pass / FAIL (remote)                     | pass / FAIL (local)                      | Compat (remote)                                                                                                                                                                                                                                                            | Compat (local)                                                                                                                                                                                                                                                             | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |
-|---:|:-----------|:-----------------------------------------|:-----------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-|  0 | amici      | pass                                     | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                       |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="d1_plots_local\amici_d1.pdf">plot</a>      |
-|  1 | bionetgen  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="d1_plots_local\bionetgen_d1.pdf">plot</a>  |
-|  2 | boolnet    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="d1_plots_local\boolnet_d1.pdf">plot</a>    |
-|  3 | brian2     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-|  4 | cbmpy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="d1_plots_local\cbmpy_d1.pdf">plot</a>      |
-|  5 | cobrapy    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="d1_plots_local\cobrapy_d1.pdf">plot</a>    |
-|  6 | copasi     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="d1_plots_local\copasi_d1.pdf">plot</a>     |
-|  7 | gillespy2  | pass                                     | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="d1_plots_local\gillespy2_d1.pdf">plot</a>  |
-|  8 | ginsim     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="d1_plots_local\ginsim_d1.pdf">plot</a>     |
-|  9 | libsbmlsim | pass                                     | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
-| 10 | masspy     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="d1_plots_local\masspy_d1.pdf">plot</a>     |
-| 11 | netpyne    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                     | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 12 | neuron     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 13 | opencor    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 14 | pyneuroml  | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 15 | pysces     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpyuxhkysi/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpyuxhkysi/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
-| 16 | rbapy      | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_d1.pdf">plot</a>      |
-| 17 | smoldyn    | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style="color:darkred;"><details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 18 | tellurium  | pass                                     | <span style="color:darkred;">FAIL</span> | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   | <details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_d1.pdf">plot</a>  |
-| 19 | vcell      | pass                                     | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         | <span style="color:darkred;"><details><summary>FAIL</summary>vcell compatible file types unknown.</details></span>                                                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 20 | xpp        | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;">FAIL</span> | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
\ No newline at end of file
+|    | Engine                                                                                                                                     | pass / FAIL (remote)                                                                                                                                                       | pass / FAIL (local)                                                                                                                                                        | Compat (remote)                                                                                                                                                                                                                                                                                                                        | Compat (local)                                                                                                                                                                                                                                                                                                                         | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
+|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="d1_plots_local\amici_d1.pdf">plot</a>      |
+|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="d1_plots_local\bionetgen_d1.pdf">plot</a>  |
+|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="d1_plots_local\boolnet_d1.pdf">plot</a>    |
+|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="d1_plots_local\cbmpy_d1.pdf">plot</a>      |
+|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="d1_plots_local\cobrapy_d1.pdf">plot</a>    |
+|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="d1_plots_local\copasi_d1.pdf">plot</a>     |
+|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="d1_plots_local\gillespy2_d1.pdf">plot</a>  |
+|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="d1_plots_local\ginsim_d1.pdf">plot</a>     |
+|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
+| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="d1_plots_local\masspy_d1.pdf">plot</a>     |
+| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp0ouw2n9o/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp0ouw2n9o/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
+| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_d1.pdf">plot</a>      |
+| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_d1.pdf">plot</a>  |
+| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
\ No newline at end of file
diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index 9c8ad8d..f0abcdd 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -72,7 +72,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=247184b0654243cba4dc148572be4227\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=98aa4f1cb44c4f11a059359d7d9be91a\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -80,10 +80,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eb40c4ccdd4919214fc\n",
-      "View: https://api.biosimulations.org/runs/66bb1eb40c4ccdd4919214fc\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1eb40c4ccdd4919214fc/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1eb40c4ccdd4919214fc?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb47fcf29e09b32cb6fcdb\n",
+      "View: https://api.biosimulations.org/runs/66bb47fcf29e09b32cb6fcdb\n",
+      "Downloads: https://api.biosimulations.org/results/66bb47fcf29e09b32cb6fcdb/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb47fcf29e09b32cb6fcdb?includeOutput=true\n"
      ]
     },
     {
@@ -95,7 +95,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b924b87f571d4d3ab0815e07db1d1c68\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=8ac4ce046ceb4ce99c059ecefd0159ed\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -103,10 +103,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eb60c4ccdd4919214ff\n",
-      "View: https://api.biosimulations.org/runs/66bb1eb60c4ccdd4919214ff\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1eb60c4ccdd4919214ff/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1eb60c4ccdd4919214ff?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb47fea641708179ad15f5\n",
+      "View: https://api.biosimulations.org/runs/66bb47fea641708179ad15f5\n",
+      "Downloads: https://api.biosimulations.org/results/66bb47fea641708179ad15f5/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb47fea641708179ad15f5?includeOutput=true\n"
      ]
     },
     {
@@ -118,7 +118,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=6f4ca7b4f22c4cd29b54f1f09f3504e7\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c730000074a24c25a7cd35d979b1f0df\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -126,10 +126,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eb8a641708179ad0e9b\n",
-      "View: https://api.biosimulations.org/runs/66bb1eb8a641708179ad0e9b\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1eb8a641708179ad0e9b/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1eb8a641708179ad0e9b?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4800f29e09b32cb6fce2\n",
+      "View: https://api.biosimulations.org/runs/66bb4800f29e09b32cb6fce2\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4800f29e09b32cb6fce2/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4800f29e09b32cb6fce2?includeOutput=true\n"
      ]
     },
     {
@@ -141,7 +141,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=dc48b39407844f869294f21488b21484\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5e83dbb3cee2421ea87a09d4a5ee6160\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -149,10 +149,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eba0c4ccdd491921502\n",
-      "View: https://api.biosimulations.org/runs/66bb1eba0c4ccdd491921502\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1eba0c4ccdd491921502/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1eba0c4ccdd491921502?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4802a641708179ad15f8\n",
+      "View: https://api.biosimulations.org/runs/66bb4802a641708179ad15f8\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4802a641708179ad15f8/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4802a641708179ad15f8?includeOutput=true\n"
      ]
     },
     {
@@ -164,7 +164,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=fe00670b96934c8c8194595a424f7329\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=29e999bc0cb84fd0ac823cc1638f9c3a\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -172,10 +172,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ebcf29e09b32cb6f52c\n",
-      "View: https://api.biosimulations.org/runs/66bb1ebcf29e09b32cb6f52c\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ebcf29e09b32cb6f52c/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ebcf29e09b32cb6f52c?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4804f29e09b32cb6fce9\n",
+      "View: https://api.biosimulations.org/runs/66bb4804f29e09b32cb6fce9\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4804f29e09b32cb6fce9/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4804f29e09b32cb6fce9?includeOutput=true\n"
      ]
     },
     {
@@ -187,7 +187,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=970ebf139ad34bb99d29a34cecf95601\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4acbdcfb5103452fa97c71bb81e13df6\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -195,10 +195,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ebea641708179ad0e9e\n",
-      "View: https://api.biosimulations.org/runs/66bb1ebea641708179ad0e9e\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ebea641708179ad0e9e/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ebea641708179ad0e9e?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4806f29e09b32cb6fcfa\n",
+      "View: https://api.biosimulations.org/runs/66bb4806f29e09b32cb6fcfa\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4806f29e09b32cb6fcfa/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4806f29e09b32cb6fcfa?includeOutput=true\n"
      ]
     },
     {
@@ -210,7 +210,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5ce0e4f76267429299ec6ae1716c6c8c\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a45e33c2762f4b93a708044c7147c2dc\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -218,10 +218,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec0a641708179ad0ea3\n",
-      "View: https://api.biosimulations.org/runs/66bb1ec0a641708179ad0ea3\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ec0a641708179ad0ea3/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ec0a641708179ad0ea3?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb48080c4ccdd491921cd8\n",
+      "View: https://api.biosimulations.org/runs/66bb48080c4ccdd491921cd8\n",
+      "Downloads: https://api.biosimulations.org/results/66bb48080c4ccdd491921cd8/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb48080c4ccdd491921cd8?includeOutput=true\n"
      ]
     },
     {
@@ -233,7 +233,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=8b90c1b4b7b1499a8dae09a03adf23c7\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4b6d898aab684ebab25f52e18880f4ba\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -241,10 +241,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec20c4ccdd491921506\n",
-      "View: https://api.biosimulations.org/runs/66bb1ec20c4ccdd491921506\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ec20c4ccdd491921506/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ec20c4ccdd491921506?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb480bf29e09b32cb6fd01\n",
+      "View: https://api.biosimulations.org/runs/66bb480bf29e09b32cb6fd01\n",
+      "Downloads: https://api.biosimulations.org/results/66bb480bf29e09b32cb6fd01/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb480bf29e09b32cb6fd01?includeOutput=true\n"
      ]
     },
     {
@@ -256,7 +256,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=774ff499104a46bd9870b755062b136a\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a2561cb8036a466eafed80d23548601a\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -264,10 +264,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec4f29e09b32cb6f536\n",
-      "View: https://api.biosimulations.org/runs/66bb1ec4f29e09b32cb6f536\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ec4f29e09b32cb6f536/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ec4f29e09b32cb6f536?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb480c0c4ccdd491921cdc\n",
+      "View: https://api.biosimulations.org/runs/66bb480c0c4ccdd491921cdc\n",
+      "Downloads: https://api.biosimulations.org/results/66bb480c0c4ccdd491921cdc/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb480c0c4ccdd491921cdc?includeOutput=true\n"
      ]
     },
     {
@@ -279,7 +279,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=ec0e7ae509274148adf3c88bd16b6e38\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=afdba8fa9da7404f8e18ac291644f0a5\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -287,10 +287,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec6a641708179ad0eaa\n",
-      "View: https://api.biosimulations.org/runs/66bb1ec6a641708179ad0eaa\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ec6a641708179ad0eaa/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ec6a641708179ad0eaa?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb480ef29e09b32cb6fd06\n",
+      "View: https://api.biosimulations.org/runs/66bb480ef29e09b32cb6fd06\n",
+      "Downloads: https://api.biosimulations.org/results/66bb480ef29e09b32cb6fd06/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb480ef29e09b32cb6fd06?includeOutput=true\n"
      ]
     },
     {
@@ -302,7 +302,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=2a7a32dd648f410ca5774405d10d7029\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=e64064a51bd84f84b584449891ce0400\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -310,10 +310,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ec80c4ccdd491921511\n",
-      "View: https://api.biosimulations.org/runs/66bb1ec80c4ccdd491921511\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ec80c4ccdd491921511/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ec80c4ccdd491921511?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4810f29e09b32cb6fd1d\n",
+      "View: https://api.biosimulations.org/runs/66bb4810f29e09b32cb6fd1d\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4810f29e09b32cb6fd1d/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4810f29e09b32cb6fd1d?includeOutput=true\n"
      ]
     },
     {
@@ -325,7 +325,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=8e2c7805085f4d25b40f0a7d4206a530\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=3fa4b04644054a55bfd03f2dee99479b\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -333,10 +333,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eca0c4ccdd491921514\n",
-      "View: https://api.biosimulations.org/runs/66bb1eca0c4ccdd491921514\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1eca0c4ccdd491921514/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1eca0c4ccdd491921514?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb48120c4ccdd491921d0b\n",
+      "View: https://api.biosimulations.org/runs/66bb48120c4ccdd491921d0b\n",
+      "Downloads: https://api.biosimulations.org/results/66bb48120c4ccdd491921d0b/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb48120c4ccdd491921d0b?includeOutput=true\n"
      ]
     },
     {
@@ -348,7 +348,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=1cf8970faf3643ea8d17adc021047a43\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c9c96acc9e3748c4bc25d31c10c21344\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -356,10 +356,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ecba641708179ad0eba\n",
-      "View: https://api.biosimulations.org/runs/66bb1ecba641708179ad0eba\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ecba641708179ad0eba/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ecba641708179ad0eba?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4814f29e09b32cb6fd2b\n",
+      "View: https://api.biosimulations.org/runs/66bb4814f29e09b32cb6fd2b\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4814f29e09b32cb6fd2b/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4814f29e09b32cb6fd2b?includeOutput=true\n"
      ]
     },
     {
@@ -371,7 +371,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=63f9f78ddeae4a02b00b525a31eeafd7\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7c952d2e73094a259c624bfca1a26013\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -379,10 +379,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ecd0c4ccdd49192153c\n",
-      "View: https://api.biosimulations.org/runs/66bb1ecd0c4ccdd49192153c\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ecd0c4ccdd49192153c/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ecd0c4ccdd49192153c?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4815f29e09b32cb6fd42\n",
+      "View: https://api.biosimulations.org/runs/66bb4815f29e09b32cb6fd42\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4815f29e09b32cb6fd42/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4815f29e09b32cb6fd42?includeOutput=true\n"
      ]
     },
     {
@@ -394,7 +394,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=999bbaa17e9a4781acc6deb3ac4f0fe8\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a49ca6f742234dfeaf523a88f36532c9\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -402,10 +402,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ecea641708179ad0ec4\n",
-      "View: https://api.biosimulations.org/runs/66bb1ecea641708179ad0ec4\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ecea641708179ad0ec4/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ecea641708179ad0ec4?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb48170c4ccdd491921d27\n",
+      "View: https://api.biosimulations.org/runs/66bb48170c4ccdd491921d27\n",
+      "Downloads: https://api.biosimulations.org/results/66bb48170c4ccdd491921d27/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb48170c4ccdd491921d27?includeOutput=true\n"
      ]
     },
     {
@@ -417,7 +417,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=bedad17524724f85b49fd5d7507208ab\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f0852adb02794e10a5db9a003051157d\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -425,10 +425,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ed0f29e09b32cb6f55f\n",
-      "View: https://api.biosimulations.org/runs/66bb1ed0f29e09b32cb6f55f\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ed0f29e09b32cb6f55f/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ed0f29e09b32cb6f55f?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4819f29e09b32cb6fd65\n",
+      "View: https://api.biosimulations.org/runs/66bb4819f29e09b32cb6fd65\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4819f29e09b32cb6fd65/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4819f29e09b32cb6fd65?includeOutput=true\n"
      ]
     },
     {
@@ -440,7 +440,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=07eacaf016564cd991943f763e90ff30\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5baaa90850ee4d62ac95e31838da4244\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -448,10 +448,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ed2f29e09b32cb6f569\n",
-      "View: https://api.biosimulations.org/runs/66bb1ed2f29e09b32cb6f569\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ed2f29e09b32cb6f569/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ed2f29e09b32cb6f569?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb481bf29e09b32cb6fd77\n",
+      "View: https://api.biosimulations.org/runs/66bb481bf29e09b32cb6fd77\n",
+      "Downloads: https://api.biosimulations.org/results/66bb481bf29e09b32cb6fd77/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb481bf29e09b32cb6fd77?includeOutput=true\n"
      ]
     },
     {
@@ -463,7 +463,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=28a10abf17534f26bf5e0e92a677bd49\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4510539d7b534c45874c59acfbdcdf5d\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -471,10 +471,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ed4f29e09b32cb6f585\n",
-      "View: https://api.biosimulations.org/runs/66bb1ed4f29e09b32cb6f585\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ed4f29e09b32cb6f585/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ed4f29e09b32cb6f585?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb481ea641708179ad1671\n",
+      "View: https://api.biosimulations.org/runs/66bb481ea641708179ad1671\n",
+      "Downloads: https://api.biosimulations.org/results/66bb481ea641708179ad1671/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb481ea641708179ad1671?includeOutput=true\n"
      ]
     },
     {
@@ -486,7 +486,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=555fe9cb8c14494ba1a20573b70f8866\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7d34e66703f4436b992d01ae6f9caac4\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -494,10 +494,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1ed6a641708179ad0ee9\n",
-      "View: https://api.biosimulations.org/runs/66bb1ed6a641708179ad0ee9\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1ed6a641708179ad0ee9/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1ed6a641708179ad0ee9?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4820a641708179ad1674\n",
+      "View: https://api.biosimulations.org/runs/66bb4820a641708179ad1674\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4820a641708179ad1674/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4820a641708179ad1674?includeOutput=true\n"
      ]
     },
     {
@@ -509,7 +509,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f58ee5d4ad6a441a9c8a6bf68eb55b70\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4eb251ba57e3405ebf954a697127d423\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -517,10 +517,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1eda0c4ccdd491921592\n",
-      "View: https://api.biosimulations.org/runs/66bb1eda0c4ccdd491921592\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1eda0c4ccdd491921592/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1eda0c4ccdd491921592?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb48240c4ccdd491921d5e\n",
+      "View: https://api.biosimulations.org/runs/66bb48240c4ccdd491921d5e\n",
+      "Downloads: https://api.biosimulations.org/results/66bb48240c4ccdd491921d5e/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb48240c4ccdd491921d5e?includeOutput=true\n"
      ]
     },
     {
@@ -532,7 +532,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=aeeb96cd32ae426fa80173e3317ffc45\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=73f4e7a2900f4bb38c20e8761f1b1a79\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -540,10 +540,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb1edca641708179ad0f0d\n",
-      "View: https://api.biosimulations.org/runs/66bb1edca641708179ad0f0d\n",
-      "Downloads: https://api.biosimulations.org/results/66bb1edca641708179ad0f0d/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb1edca641708179ad0f0d?includeOutput=true\n",
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4826f29e09b32cb6fdab\n",
+      "View: https://api.biosimulations.org/runs/66bb4826f29e09b32cb6fdab\n",
+      "Downloads: https://api.biosimulations.org/results/66bb4826f29e09b32cb6fdab/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bb4826f29e09b32cb6fdab?includeOutput=true\n",
       "Downloading amici results...\n",
       "Downloading brian2 results...\n",
       "Downloading bionetgen results...\n",
@@ -565,19 +565,19 @@
       "Downloading tellurium results...\n",
       "Downloading vcell results...\n",
       "Downloading xpp results...\n",
-      "Moving remote_results\\amici\\outputs\\tmp262364\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
-      "Moving remote_results\\bionetgen\\outputs\\tmp98719\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
-      "Moving remote_results\\boolnet\\outputs\\tmp813849\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
-      "Moving remote_results\\cbmpy\\outputs\\tmp979743\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
-      "Moving remote_results\\cobrapy\\outputs\\tmp981863\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
-      "Moving remote_results\\copasi\\outputs\\tmp423266\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
-      "Moving remote_results\\gillespy2\\outputs\\tmp146730\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
-      "Moving remote_results\\ginsim\\outputs\\tmp968356\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
-      "Moving remote_results\\libsbmlsim\\outputs\\tmp247930\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
-      "Moving remote_results\\masspy\\outputs\\tmp905203\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
-      "Moving remote_results\\pysces\\outputs\\tmp260212\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
-      "Moving remote_results\\rbapy\\outputs\\tmp516019\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
-      "Moving remote_results\\tellurium\\outputs\\tmp540535\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
+      "Moving remote_results\\amici\\outputs\\tmp904901\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
+      "Moving remote_results\\bionetgen\\outputs\\tmp896149\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
+      "Moving remote_results\\boolnet\\outputs\\tmp638536\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
+      "Moving remote_results\\cbmpy\\outputs\\tmp231472\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
+      "Moving remote_results\\cobrapy\\outputs\\tmp607739\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
+      "Moving remote_results\\copasi\\outputs\\tmp661623\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
+      "Moving remote_results\\gillespy2\\outputs\\tmp345818\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
+      "Moving remote_results\\ginsim\\outputs\\tmp721937\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
+      "Moving remote_results\\libsbmlsim\\outputs\\tmp543113\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
+      "Moving remote_results\\masspy\\outputs\\tmp783032\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
+      "Moving remote_results\\pysces\\outputs\\tmp449843\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
+      "Moving remote_results\\rbapy\\outputs\\tmp868501\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
+      "Moving remote_results\\tellurium\\outputs\\tmp613094\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
       "Removed remote_results folder\n",
       "Running amici\n",
       "Running brian2\n",
@@ -682,33 +682,158 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "engines = {\n",
+    "    'amici': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_AMICI/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'brian2': {\n",
+    "        'formats': [('nml', 'sedml'), ('lems', 'sedml'), ('sbml', 'sedml')],\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'bionetgen': {\n",
+    "        'formats': ('bngl', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_BioNetGen/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'boolnet': {\n",
+    "        'formats': ('sbmlqual', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_BoolNet/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'cbmpy': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_CBMPy/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'cobrapy': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_COBRApy/',\n",
+    "        'status': \"Only allows steady state simulations\"\n",
+    "    },\n",
+    "    'copasi': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_COPASI/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'gillespy2': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_GillesPy2/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'ginsim': {\n",
+    "        'formats': ('sbmlqual', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_GINsim/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'libsbmlsim': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_LibSBMLSim/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'masspy': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_MASSpy/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'netpyne': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'neuron': {\n",
+    "        'formats': [('nml', 'sedml'), ('lems', 'sedml')],\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'opencor': {\n",
+    "        'formats': ('cellml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_OpenCOR/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'pyneuroml': {\n",
+    "        'formats': [('nml', 'sedml'), ('lems', 'sedml')],\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'pysces': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_PySCeS/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'rbapy': {\n",
+    "        'formats': ('rbapy', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_RBApy/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'smoldyn': {\n",
+    "        'formats': None,\n",
+    "        'url': 'https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'tellurium': {\n",
+    "        'formats': ('sbml', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_tellurium/',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'vcell': {\n",
+    "        'formats': [('sbml', 'sedml'),('bngl', 'sedml')],\n",
+    "        'url': 'https://github.com/virtualcell/vcell',\n",
+    "        'status': \"\"\n",
+    "    },\n",
+    "    'xpp': {\n",
+    "        'formats': ('xpp', 'sedml'),\n",
+    "        'url': 'https://docs.biosimulators.org/Biosimulators_XPP/',\n",
+    "        'status': \"\"\n",
+    "    }\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
    "outputs": [
     {
      "data": {
       "text/markdown": [
-       "|    | Engine                                                                                                          | pass / FAIL (remote)                                                                                                                                                       | pass / FAIL (local)                                                                                                                                                        | Compat (remote)                                                                                                                                                                                                                                                                                                                        | Compat (local)                                                                                                                                                                                                                                                                                                                         | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |\n",
-       "|---:|:----------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|\n",
-       "|  0 | <a href=\"https://docs.biosimulators.org/Biosimulators_AMICI/\">amici</a>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
-       "|  1 | <a href=\"https://docs.biosimulators.org/Biosimulators_BioNetGen/\">bionetgen</a>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
-       "|  2 | <a href=\"https://docs.biosimulators.org/Biosimulators_BoolNet/\">boolnet</a>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
-       "|  3 | <a href=\"https://docs.biosimulators.org/Biosimulators_CBMPy/\">cbmpy</a>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
-       "|  4 | <a href=\"https://docs.biosimulators.org/Biosimulators_COBRApy/\">cobrapy</a>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
-       "|  5 | <a href=\"https://docs.biosimulators.org/Biosimulators_COPASI/\">copasi</a>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
-       "|  6 | <a href=\"https://docs.biosimulators.org/Biosimulators_GINsim/\">ginsim</a>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
-       "|  7 | <a href=\"https://docs.biosimulators.org/Biosimulators_GillesPy2/\">gillespy2</a>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
-       "|  8 | <a href=\"https://docs.biosimulators.org/Biosimulators_LibSBMLSim/\">libsbmlsim</a>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
-       "|  9 | <a href=\"https://docs.biosimulators.org/Biosimulators_MASSpy/\">masspy</a>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
-       "| 10 | <a href=\"https://docs.biosimulators.org/Biosimulators_OpenCOR/\">opencor</a>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 11 | <a href=\"https://docs.biosimulators.org/Biosimulators_PySCeS/\">pysces</a>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpi0f2z0io/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpi0f2z0io/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
-       "| 12 | <a href=\"https://docs.biosimulators.org/Biosimulators_RBApy/\">rbapy</a>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
-       "| 13 | <a href=\"https://docs.biosimulators.org/Biosimulators_XPP/\">xpp</a>                                             | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 14 | <a href=\"https://docs.biosimulators.org/Biosimulators_pyNeuroML/\">brian2</a>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 15 | <a href=\"https://docs.biosimulators.org/Biosimulators_pyNeuroML/\">netpyne</a>                                   | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 16 | <a href=\"https://docs.biosimulators.org/Biosimulators_pyNeuroML/\">neuron</a>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 17 | <a href=\"https://docs.biosimulators.org/Biosimulators_pyNeuroML/\">pyneuroml</a>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'SED-ML', 'NeuroML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 18 | <a href=\"https://docs.biosimulators.org/Biosimulators_tellurium/\">tellurium</a>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
-       "| 19 | <a href=\"https://github.com/virtualcell/vcell\">vcell</a>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 20 | <a href=\"https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api\">smoldyn</a> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
+       "## Compatibility Biosimulator engines (L = local, R = remote)"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/markdown": [
+       "|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                             | Compat (L)                                                                                                                                                                                                                                                                                                                             | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                   | d1 (R)                                               | d1 (L)                                              |\n",
+       "|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|\n",
+       "|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
+       "|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
+       "|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
+       "|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
+       "|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
+       "|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
+       "|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
+       "|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
+       "|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
+       "| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
+       "| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpr_05sxok/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpr_05sxok/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
+       "| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
+       "| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
+       "| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
       ]
      },
      "metadata": {},
@@ -716,29 +841,88 @@
     }
    ],
    "source": [
+    "import re\n",
+    "\n",
+    "def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, output_dir):\n",
+    "    \"\"\"\n",
+    "    Create a markdown table of the results.\n",
+    "    \n",
+    "    Input: results, types_dict, sbml_filepath, sedml_filepath, engines, output_dir\n",
+    "    Output: results_md_table\n",
+    "\n",
+    "    \"\"\"\n",
+    "    \n",
+    "    link_green_square = \"https://via.placeholder.com/15/00dd00/00dd00.png\"\n",
+    "    link_orange_square = \"https://via.placeholder.com/15/ec9706/ec9706.png\"\n",
+    "    link_red_square = \"https://via.placeholder.com/15/dd0000/dd0000.png\"\n",
+    "\n",
+    "    # Create a table of the results\n",
+    "    results_table = pd.DataFrame.from_dict(results).T\n",
+    "    # if list is three elements \n",
+    "    if results_table.shape[1] == 3:\n",
+    "        results_table.columns = ['pass / FAIL', 'Error', 'Type']\n",
+    "    elif results_table.shape[1] == 2:\n",
+    "        results_table.columns = ['pass / FAIL', 'Error']\n",
+    "   \n",
+    "    results_table.index.name = 'Engine'\n",
+    "    results_table.reset_index(inplace=True)\n",
+    "    \n",
+    "    # Error\n",
+    "    results_table['Error'] = results_table.apply(lambda x: None if x['pass / FAIL'] == x['Error'] else x['Error'], axis=1)\n",
+    "    results_table['pass / FAIL'] = results_table['pass / FAIL'].replace('other', 'FAIL')\n",
+    "\n",
+    "    results_table['Error'] = results_table['Error'].apply(lambda x:  utils.ansi_to_html(x))\n",
+    "    results_table['Error'] = results_table['Error'].apply(lambda x:  utils.collapsible_content(x))\n",
+    "\n",
+    "    # compatibility_message\n",
+    "    results_table['Compat'] = results_table['Engine'].apply(lambda x:  utils.check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))\n",
+    "    results_table['Compat'] = results_table['Compat'].apply(lambda x:  utils.collapsible_content(x[1], title=x[0]))\n",
+    "    results_table['Compat'] = results_table['Compat'].apply(lambda x: f'<span style=\"color:darkred;\"><img src={link_red_square}/> {x}</span>'\\\n",
+    "                                                             if 'FAIL' in x else f'<img src={link_green_square}/>{x}')\n",
+    "\n",
+    "    # pass / FAIL\n",
+    "    results_table['pass / FAIL'] = results_table['pass / FAIL'].apply(lambda x: f'<span style=\"color:darkred;\">\\\n",
+    "                                                                      <img src={link_red_square}/> {x}</span>' if x == 'FAIL' \\\n",
+    "                                                                        else f'<img src={link_green_square}/> {x}')\n",
+    "\n",
+    "    # d1 plot clickable link\n",
+    "    results_table['d1'] = results_table['Engine'].apply(lambda x:  utils.d1_plots_dict(engines, output_dir).get(x, None))\n",
+    "    results_table['d1'] = results_table['d1'].apply(lambda x: utils.create_hyperlink(x,title='plot'))\n",
+    "    \n",
+    "    # if Type is in the table add message with collapsible content\n",
+    "    if 'Type' in results_table.columns:\n",
+    "        results_table['Type'] = results_table['Type'].apply(lambda x:  utils.collapsible_content(x,\"\".join(re.findall(r'[A-Z]', x))))\n",
+    "\n",
+    "    results_table['Engine'] = results_table['Engine'].apply(lambda x:  utils.collapsible_content(f'{engines[x][\"url\"]}<br>{engines[x][\"status\"]}', x))\n",
+    "\n",
+    "    return results_table\n",
+    "\n",
+    "\n",
     "#########################################################################################\n",
     "# process results and save markdown table\n",
     "#########################################################################################\n",
     "\n",
-    "results_table = utils.create_results_table(results_remote, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)\n",
-    "results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)\n",
+    "results_table = create_results_table(results_remote, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)\n",
+    "results_table_local = create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)\n",
     "\n",
     "# rename cols to distinguish between local and remote results except for Engine column\n",
-    "results_table.columns = [str(col) + ' (remote)' if col != 'Engine' else str(col) for col in results_table.columns]\n",
-    "results_table_local.columns = [str(col) + ' (local)' if col != 'Engine' else str(col) for col in results_table_local.columns]\n",
+    "results_table.columns = [str(col) + ' (R)' if col != 'Engine' else str(col) for col in results_table.columns]\n",
+    "results_table_local.columns = [str(col) + ' (L)' if col != 'Engine' else str(col) for col in results_table_local.columns]\n",
     "\n",
     "# combine remote and local results\n",
     "combined_results = pd.merge(results_table, results_table_local, on='Engine', how='outer')\n",
-    "combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))\n",
+    "# combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))\n",
     "\n",
-    "cols_order = ['Engine', 'pass / FAIL (remote)', 'pass / FAIL (local)',\\\n",
-    "               'Compat (remote)', 'Compat (local)', \\\n",
-    "               'Type (remote)', \\\n",
-    "               'Error (remote)', 'Error (local)', \\\n",
-    "               'd1 (remote)', 'd1 (local)']\n",
+    "cols_order = ['Engine', 'pass / FAIL (R)', 'pass / FAIL (L)',\\\n",
+    "               'Compat (R)', 'Compat (L)', \\\n",
+    "               'Type (R)', \\\n",
+    "               'Error (R)', 'Error (L)', \\\n",
+    "               'd1 (R)', 'd1 (L)']\n",
     "\n",
     "combined_results = combined_results[cols_order]\n",
-    "display_markdown(combined_results.to_markdown(), raw=True)"
+    "# add a table title\n",
+    "display_markdown('## Compatibility Biosimulator engines (L = local, R = remote)', raw=True)\n",
+    "display_markdown(combined_results.to_markdown(), raw=True)\n"
    ]
   }
  ],
diff --git a/utils/__init__.py b/utils/__init__.py
index 69ad87f..535ba3a 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -21,141 +21,115 @@
 from pyneuroml import biosimulations
 import pandas as pd
 
-# 
-engines = {
-                        'amici': ('sbml', 'sedml'),\
-                        'brian2': [('nml', 'sedml'),('lems', 'sedml'),('sbml', 'sedml')],\
-                        'bionetgen': ('bngl', 'sedml'),\
-                        'boolnet': ('sbmlqual', 'sedml'),\
-                        'cbmpy': ('sbml', 'sedml'),\
-                        'cobrapy': ('sbml', 'sedml'),\
-                        'copasi': ('sbml', 'sedml'),\
-                        'gillespy2': ('sbml', 'sedml'),\
-                        'ginsim': ('sbmlqual', 'sedml'),\
-                        'libsbmlsim': ('sbml', 'sedml'),\
-                        'masspy': ('sbml', 'sedml'),\
-                        'netpyne': ('sbml', 'sedml'),\
-                        'neuron': [('nml', 'sedml'),('lems', 'sedml')],\
-                        'opencor': ('cellml', 'sedml'),\
-                        'pyneuroml': [('nml', 'sedml'),('lems', 'sedml')],\
-                        'pysces': ('sbml', 'sedml'),\
-                        'rbapy': ('rbapy', 'sedml'),\
-                        'smoldyn':None ,\
-                        'tellurium': ('sbml', 'sedml'),\
-                        'vcell': None,\
-                        'xpp': ('xpp', 'sedml')               
-            }
-
 engines = {
     'amici': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_AMICI/',
-        'status': ''
+        'status': ""
     },
     'brian2': {
         'formats': [('nml', 'sedml'), ('lems', 'sedml'), ('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
-        'status': ''
+        'status': ""
     },
     'bionetgen': {
         'formats': ('bngl', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_BioNetGen/',
-        'status': ''
+        'status': ""
     },
     'boolnet': {
         'formats': ('sbmlqual', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_BoolNet/',
-        'status': ''
+        'status': ""
     },
     'cbmpy': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_CBMPy/',
-        'status': ''
+        'status': ""
     },
     'cobrapy': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_COBRApy/',
-        'status': 'Only allows steady state simulations'
+        'status': "Only allows steady state simulations"
     },
     'copasi': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_COPASI/',
-        'status': ''
+        'status': ""
     },
     'gillespy2': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_GillesPy2/',
-        'status': ''
+        'status': ""
     },
     'ginsim': {
         'formats': ('sbmlqual', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_GINsim/',
-        'status': ''
+        'status': ""
     },
     'libsbmlsim': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_LibSBMLSim/',
-        'status': ''
+        'status': ""
     },
     'masspy': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_MASSpy/',
-        'status': ''
+        'status': ""
     },
     'netpyne': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
-        'status': ''
+        'status': ""
     },
     'neuron': {
         'formats': [('nml', 'sedml'), ('lems', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
-        'status': ''
+        'status': ""
     },
     'opencor': {
         'formats': ('cellml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_OpenCOR/',
-        'status': ''
+        'status': ""
     },
     'pyneuroml': {
         'formats': [('nml', 'sedml'), ('lems', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
-        'status': ''
+        'status': ""
     },
     'pysces': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_PySCeS/',
-        'status': ''
+        'status': ""
     },
     'rbapy': {
         'formats': ('rbapy', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_RBApy/',
-        'status': ''
+        'status': ""
     },
     'smoldyn': {
         'formats': None,
         'url': 'https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api',
-        'status': 'inactive'
+        'status': ""
     },
     'tellurium': {
         'formats': ('sbml', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_tellurium/',
-        'status': ''
+        'status': ""
     },
     'vcell': {
         'formats': [('sbml', 'sedml'),('bngl', 'sedml')],
         'url': 'https://github.com/virtualcell/vcell',
-        'status': ''
+        'status': ""
     },
     'xpp': {
         'formats': ('xpp', 'sedml'),
         'url': 'https://docs.biosimulators.org/Biosimulators_XPP/',
-        'status': ''
+        'status': ""
     }
 }
 
 
-
 types_dict = {
                 'sbml':'SBML',\
                 'sedml':'SED-ML',\
@@ -170,8 +144,6 @@
              }
 
 
-
-
 #define error categories for detailed error counting per engine
 # (currently only tellurium)
 # key is the tag/category used to report the category, value is a regex matching the error message
@@ -1139,7 +1111,7 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng
     if 'Type' in results_table.columns:
         results_table['Type'] = results_table['Type'].apply(lambda x: collapsible_content(x,"".join(re.findall(r'[A-Z]', x))))
 
-    # Engine add hyperlink
-    results_table['Engine'] = results_table['Engine'].apply(lambda x: create_hyperlink(engines[x]['url'], title=x))
+
+    results_table['Engine'] = results_table['Engine'].apply(lambda x:  collapsible_content(f'{engines[x]["url"]}<br>{engines[x]["status"]}', x))
 
     return results_table

From facc3959b9c551939f7caaeb1ce17d2d7720b887 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Tue, 13 Aug 2024 14:43:52 +0100
Subject: [PATCH 26/71] Regenerated files

---
 .gitignore                        | 2 ++
 LEMS/BIOMD0000000127_url_LEMS.xml | 8 ++++----
 LEMS/BIOMD0000000184_LEMS.xml     | 6 +++---
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/.gitignore b/.gitignore
index af268f9..e837a44 100644
--- a/.gitignore
+++ b/.gitignore
@@ -43,3 +43,5 @@ arm64
 __pycache__
 venv
 /SBML/.DS_Store
+/SBML/LEMS_NML2_Ex9_FN_missing_xmlns.omex
+/SBML/output
diff --git a/LEMS/BIOMD0000000127_url_LEMS.xml b/LEMS/BIOMD0000000127_url_LEMS.xml
index 33b4a1c..d3f6263 100644
--- a/LEMS/BIOMD0000000127_url_LEMS.xml
+++ b/LEMS/BIOMD0000000127_url_LEMS.xml
@@ -1,9 +1,9 @@
 <Lems>
 <!--
     This LEMS file has been generated by org.neuroml.importer.sbml.SBMLImporter (see https://github.com/NeuroML/org.neuroml.import)
-         org.neuroml.import  v1.10.0
-         org.neuroml.model   v1.10.0
-         jLEMS               v0.11.0
+         org.neuroml.import  v1.10.1
+         org.neuroml.model   v1.10.1
+         jLEMS               v0.11.1
 -->
 
     <Dimension name="time" m="0" l="0" t="1" i="0" k="0" n="0" j="0"/>
@@ -197,7 +197,7 @@
             <TimeDerivative variable="i" value="tscale * 0"/>
             <TimeDerivative variable="v" value="tscale * ((((((0.04 * (v ^ 2.0)) + (5.0 * v)) + 140.0) - U) + i))"/>
             <TimeDerivative variable="U" value="tscale * ((a * ((b * v) - U)))"/>
-            <TimeDerivative variable="time" value="1"/>
+            <TimeDerivative variable="time" value="tscale* 1"/>
             <OnStart>
                 <StateAssignment variable="i" value="0.0"/>
                 <StateAssignment variable="v" value="-70.0"/>
diff --git a/LEMS/BIOMD0000000184_LEMS.xml b/LEMS/BIOMD0000000184_LEMS.xml
index 8c1713c..7e3e374 100644
--- a/LEMS/BIOMD0000000184_LEMS.xml
+++ b/LEMS/BIOMD0000000184_LEMS.xml
@@ -1,9 +1,9 @@
 <Lems>
 <!--
     This LEMS file has been generated by org.neuroml.importer.sbml.SBMLImporter (see https://github.com/NeuroML/org.neuroml.import)
-         org.neuroml.import  v1.10.0
-         org.neuroml.model   v1.10.0
-         jLEMS               v0.11.0
+         org.neuroml.import  v1.10.1
+         org.neuroml.model   v1.10.1
+         jLEMS               v0.11.1
 -->
 
     <Dimension name="time" m="0" l="0" t="1" i="0" k="0" n="0" j="0"/>

From 036cf12cbe8ea45c3fb9c1fed0a5db156fe899b8 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 14 Aug 2024 08:58:30 +0100
Subject: [PATCH 27/71] Update table column names for remote and local results
 (R, L) in py script

---
 SBML/test_compatibility_biosimulators.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/test_compatibility_biosimulators.py
index 3d41b52..000d316 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/test_compatibility_biosimulators.py
@@ -107,18 +107,18 @@
 results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)
 
 # rename cols to distinguish between local and remote results except for Engine column
-results_table.columns = [str(col) + ' (remote)' if col != 'Engine' else str(col) for col in results_table.columns]
-results_table_local.columns = [str(col) + ' (local)' if col != 'Engine' else str(col) for col in results_table_local.columns]
+results_table.columns = [str(col) + ' (R)' if col != 'Engine' else str(col) for col in results_table.columns]
+results_table_local.columns = [str(col) + ' (L)' if col != 'Engine' else str(col) for col in results_table_local.columns]
 
 # combine remote and local results
 combined_results = pd.merge(results_table, results_table_local, on='Engine', how='outer')
 combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))
 
-cols_order = ['Engine', 'pass / FAIL (remote)', 'pass / FAIL (local)',\
-               'Compat (remote)', 'Compat (local)', \
-               'Type (remote)', \
-               'Error (remote)', 'Error (local)', \
-               'd1 (remote)', 'd1 (local)']
+cols_order = ['Engine', 'pass / FAIL (R)', 'pass / FAIL (L)',\
+               'Compat (R)', 'Compat (L)', \
+               'Type (R)', \
+               'Error (R)', 'Error (L)', \
+               'd1 (R)', 'd1 (L)']
 
 combined_results = combined_results[cols_order]
 

From daee6ad77556ff0f7ba9646597ffcc7fc258e568 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 14 Aug 2024 09:03:50 +0100
Subject: [PATCH 28/71] tidy up jpynb script for trouble shooting

---
 SBML/test_compatibility_biosimulators.ipynb | 452 ++++++--------------
 1 file changed, 140 insertions(+), 312 deletions(-)

diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/test_compatibility_biosimulators.ipynb
index f0abcdd..42a78fd 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/test_compatibility_biosimulators.ipynb
@@ -72,7 +72,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=98aa4f1cb44c4f11a059359d7d9be91a\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4f4d0d71858746cab44391b232bfdeb1\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -80,10 +80,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb47fcf29e09b32cb6fcdb\n",
-      "View: https://api.biosimulations.org/runs/66bb47fcf29e09b32cb6fcdb\n",
-      "Downloads: https://api.biosimulations.org/results/66bb47fcf29e09b32cb6fcdb/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb47fcf29e09b32cb6fcdb?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc643ea641708179ad2dd7\n",
+      "View: https://api.biosimulations.org/runs/66bc643ea641708179ad2dd7\n",
+      "Downloads: https://api.biosimulations.org/results/66bc643ea641708179ad2dd7/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc643ea641708179ad2dd7?includeOutput=true\n"
      ]
     },
     {
@@ -95,7 +95,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=8ac4ce046ceb4ce99c059ecefd0159ed\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=bf3a11a48a234cdd98c4513e86e75a69\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -103,10 +103,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb47fea641708179ad15f5\n",
-      "View: https://api.biosimulations.org/runs/66bb47fea641708179ad15f5\n",
-      "Downloads: https://api.biosimulations.org/results/66bb47fea641708179ad15f5/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb47fea641708179ad15f5?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6440a641708179ad2e01\n",
+      "View: https://api.biosimulations.org/runs/66bc6440a641708179ad2e01\n",
+      "Downloads: https://api.biosimulations.org/results/66bc6440a641708179ad2e01/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc6440a641708179ad2e01?includeOutput=true\n"
      ]
     },
     {
@@ -118,7 +118,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c730000074a24c25a7cd35d979b1f0df\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7351ffe3fce7434581ec6a356aff7a36\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -126,10 +126,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4800f29e09b32cb6fce2\n",
-      "View: https://api.biosimulations.org/runs/66bb4800f29e09b32cb6fce2\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4800f29e09b32cb6fce2/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4800f29e09b32cb6fce2?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64420c4ccdd491923499\n",
+      "View: https://api.biosimulations.org/runs/66bc64420c4ccdd491923499\n",
+      "Downloads: https://api.biosimulations.org/results/66bc64420c4ccdd491923499/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc64420c4ccdd491923499?includeOutput=true\n"
      ]
     },
     {
@@ -141,7 +141,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5e83dbb3cee2421ea87a09d4a5ee6160\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b4c82db1ce4f411c97a8d62e880b5765\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -149,10 +149,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4802a641708179ad15f8\n",
-      "View: https://api.biosimulations.org/runs/66bb4802a641708179ad15f8\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4802a641708179ad15f8/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4802a641708179ad15f8?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6445f29e09b32cb71538\n",
+      "View: https://api.biosimulations.org/runs/66bc6445f29e09b32cb71538\n",
+      "Downloads: https://api.biosimulations.org/results/66bc6445f29e09b32cb71538/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc6445f29e09b32cb71538?includeOutput=true\n"
      ]
     },
     {
@@ -164,7 +164,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=29e999bc0cb84fd0ac823cc1638f9c3a\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b1f3fedd0d7e450c8d6a22225609703b\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -172,10 +172,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4804f29e09b32cb6fce9\n",
-      "View: https://api.biosimulations.org/runs/66bb4804f29e09b32cb6fce9\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4804f29e09b32cb6fce9/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4804f29e09b32cb6fce9?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6448f29e09b32cb7156f\n",
+      "View: https://api.biosimulations.org/runs/66bc6448f29e09b32cb7156f\n",
+      "Downloads: https://api.biosimulations.org/results/66bc6448f29e09b32cb7156f/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc6448f29e09b32cb7156f?includeOutput=true\n"
      ]
     },
     {
@@ -187,7 +187,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4acbdcfb5103452fa97c71bb81e13df6\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f75f20204474457a841b39b84cf86b7c\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -195,10 +195,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4806f29e09b32cb6fcfa\n",
-      "View: https://api.biosimulations.org/runs/66bb4806f29e09b32cb6fcfa\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4806f29e09b32cb6fcfa/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4806f29e09b32cb6fcfa?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc644aa641708179ad2e93\n",
+      "View: https://api.biosimulations.org/runs/66bc644aa641708179ad2e93\n",
+      "Downloads: https://api.biosimulations.org/results/66bc644aa641708179ad2e93/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc644aa641708179ad2e93?includeOutput=true\n"
      ]
     },
     {
@@ -210,7 +210,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a45e33c2762f4b93a708044c7147c2dc\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7f46f52689e940499d58544bc679cbf4\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -218,10 +218,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb48080c4ccdd491921cd8\n",
-      "View: https://api.biosimulations.org/runs/66bb48080c4ccdd491921cd8\n",
-      "Downloads: https://api.biosimulations.org/results/66bb48080c4ccdd491921cd8/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb48080c4ccdd491921cd8?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc644c0c4ccdd49192354c\n",
+      "View: https://api.biosimulations.org/runs/66bc644c0c4ccdd49192354c\n",
+      "Downloads: https://api.biosimulations.org/results/66bc644c0c4ccdd49192354c/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc644c0c4ccdd49192354c?includeOutput=true\n"
      ]
     },
     {
@@ -233,7 +233,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4b6d898aab684ebab25f52e18880f4ba\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a95da07b0eed4b0c81b8efea3865cdd2\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -241,10 +241,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb480bf29e09b32cb6fd01\n",
-      "View: https://api.biosimulations.org/runs/66bb480bf29e09b32cb6fd01\n",
-      "Downloads: https://api.biosimulations.org/results/66bb480bf29e09b32cb6fd01/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb480bf29e09b32cb6fd01?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc644ef29e09b32cb715ff\n",
+      "View: https://api.biosimulations.org/runs/66bc644ef29e09b32cb715ff\n",
+      "Downloads: https://api.biosimulations.org/results/66bc644ef29e09b32cb715ff/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc644ef29e09b32cb715ff?includeOutput=true\n"
      ]
     },
     {
@@ -256,7 +256,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a2561cb8036a466eafed80d23548601a\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f196d9eb63c44771b057607e142425ef\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -264,10 +264,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb480c0c4ccdd491921cdc\n",
-      "View: https://api.biosimulations.org/runs/66bb480c0c4ccdd491921cdc\n",
-      "Downloads: https://api.biosimulations.org/results/66bb480c0c4ccdd491921cdc/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb480c0c4ccdd491921cdc?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64510c4ccdd4919235ce\n",
+      "View: https://api.biosimulations.org/runs/66bc64510c4ccdd4919235ce\n",
+      "Downloads: https://api.biosimulations.org/results/66bc64510c4ccdd4919235ce/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc64510c4ccdd4919235ce?includeOutput=true\n"
      ]
     },
     {
@@ -279,7 +279,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=afdba8fa9da7404f8e18ac291644f0a5\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=9abf44470197427eb5d0e537386631a4\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -287,10 +287,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb480ef29e09b32cb6fd06\n",
-      "View: https://api.biosimulations.org/runs/66bb480ef29e09b32cb6fd06\n",
-      "Downloads: https://api.biosimulations.org/results/66bb480ef29e09b32cb6fd06/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb480ef29e09b32cb6fd06?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64530c4ccdd491923630\n",
+      "View: https://api.biosimulations.org/runs/66bc64530c4ccdd491923630\n",
+      "Downloads: https://api.biosimulations.org/results/66bc64530c4ccdd491923630/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc64530c4ccdd491923630?includeOutput=true\n"
      ]
     },
     {
@@ -302,7 +302,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=e64064a51bd84f84b584449891ce0400\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=0555dafc508d434d99eb0deac879dc66\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -310,10 +310,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4810f29e09b32cb6fd1d\n",
-      "View: https://api.biosimulations.org/runs/66bb4810f29e09b32cb6fd1d\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4810f29e09b32cb6fd1d/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4810f29e09b32cb6fd1d?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6456a641708179ad2fdf\n",
+      "View: https://api.biosimulations.org/runs/66bc6456a641708179ad2fdf\n",
+      "Downloads: https://api.biosimulations.org/results/66bc6456a641708179ad2fdf/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc6456a641708179ad2fdf?includeOutput=true\n"
      ]
     },
     {
@@ -325,7 +325,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=3fa4b04644054a55bfd03f2dee99479b\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7c5d87f9e90b4084ab78d7f2395e0047\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -333,10 +333,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb48120c4ccdd491921d0b\n",
-      "View: https://api.biosimulations.org/runs/66bb48120c4ccdd491921d0b\n",
-      "Downloads: https://api.biosimulations.org/results/66bb48120c4ccdd491921d0b/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb48120c4ccdd491921d0b?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6458a641708179ad304e\n",
+      "View: https://api.biosimulations.org/runs/66bc6458a641708179ad304e\n",
+      "Downloads: https://api.biosimulations.org/results/66bc6458a641708179ad304e/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc6458a641708179ad304e?includeOutput=true\n"
      ]
     },
     {
@@ -348,7 +348,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c9c96acc9e3748c4bc25d31c10c21344\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=0b9c70f0c9c7462cb1be21f774e1615e\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -356,10 +356,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4814f29e09b32cb6fd2b\n",
-      "View: https://api.biosimulations.org/runs/66bb4814f29e09b32cb6fd2b\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4814f29e09b32cb6fd2b/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4814f29e09b32cb6fd2b?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc645af29e09b32cb717bf\n",
+      "View: https://api.biosimulations.org/runs/66bc645af29e09b32cb717bf\n",
+      "Downloads: https://api.biosimulations.org/results/66bc645af29e09b32cb717bf/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc645af29e09b32cb717bf?includeOutput=true\n"
      ]
     },
     {
@@ -371,7 +371,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7c952d2e73094a259c624bfca1a26013\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c3b9c2080d334b74a6f468d540e2bf32\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -379,10 +379,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4815f29e09b32cb6fd42\n",
-      "View: https://api.biosimulations.org/runs/66bb4815f29e09b32cb6fd42\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4815f29e09b32cb6fd42/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4815f29e09b32cb6fd42?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc645cf29e09b32cb71813\n",
+      "View: https://api.biosimulations.org/runs/66bc645cf29e09b32cb71813\n",
+      "Downloads: https://api.biosimulations.org/results/66bc645cf29e09b32cb71813/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc645cf29e09b32cb71813?includeOutput=true\n"
      ]
     },
     {
@@ -394,7 +394,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a49ca6f742234dfeaf523a88f36532c9\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=3eb15093c60140898d6bfe71685568fc\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -402,10 +402,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb48170c4ccdd491921d27\n",
-      "View: https://api.biosimulations.org/runs/66bb48170c4ccdd491921d27\n",
-      "Downloads: https://api.biosimulations.org/results/66bb48170c4ccdd491921d27/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb48170c4ccdd491921d27?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc645fa641708179ad3112\n",
+      "View: https://api.biosimulations.org/runs/66bc645fa641708179ad3112\n",
+      "Downloads: https://api.biosimulations.org/results/66bc645fa641708179ad3112/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc645fa641708179ad3112?includeOutput=true\n"
      ]
     },
     {
@@ -417,7 +417,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f0852adb02794e10a5db9a003051157d\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c7ed6cc225864a2fb918db765ec00557\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -425,10 +425,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4819f29e09b32cb6fd65\n",
-      "View: https://api.biosimulations.org/runs/66bb4819f29e09b32cb6fd65\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4819f29e09b32cb6fd65/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4819f29e09b32cb6fd65?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64630c4ccdd491923827\n",
+      "View: https://api.biosimulations.org/runs/66bc64630c4ccdd491923827\n",
+      "Downloads: https://api.biosimulations.org/results/66bc64630c4ccdd491923827/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc64630c4ccdd491923827?includeOutput=true\n"
      ]
     },
     {
@@ -440,7 +440,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5baaa90850ee4d62ac95e31838da4244\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=762c8555ab614c258f06df395558c712\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -448,10 +448,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb481bf29e09b32cb6fd77\n",
-      "View: https://api.biosimulations.org/runs/66bb481bf29e09b32cb6fd77\n",
-      "Downloads: https://api.biosimulations.org/results/66bb481bf29e09b32cb6fd77/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb481bf29e09b32cb6fd77?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64660c4ccdd49192382a\n",
+      "View: https://api.biosimulations.org/runs/66bc64660c4ccdd49192382a\n",
+      "Downloads: https://api.biosimulations.org/results/66bc64660c4ccdd49192382a/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc64660c4ccdd49192382a?includeOutput=true\n"
      ]
     },
     {
@@ -463,7 +463,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4510539d7b534c45874c59acfbdcdf5d\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=53c6f673860c44bdb476c8afa656ccdd\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -471,10 +471,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb481ea641708179ad1671\n",
-      "View: https://api.biosimulations.org/runs/66bb481ea641708179ad1671\n",
-      "Downloads: https://api.biosimulations.org/results/66bb481ea641708179ad1671/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb481ea641708179ad1671?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64680c4ccdd491923847\n",
+      "View: https://api.biosimulations.org/runs/66bc64680c4ccdd491923847\n",
+      "Downloads: https://api.biosimulations.org/results/66bc64680c4ccdd491923847/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc64680c4ccdd491923847?includeOutput=true\n"
      ]
     },
     {
@@ -486,7 +486,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7d34e66703f4436b992d01ae6f9caac4\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5ea5711967054c93a35895fab7fc782c\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -494,10 +494,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4820a641708179ad1674\n",
-      "View: https://api.biosimulations.org/runs/66bb4820a641708179ad1674\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4820a641708179ad1674/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4820a641708179ad1674?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc646aa641708179ad31a4\n",
+      "View: https://api.biosimulations.org/runs/66bc646aa641708179ad31a4\n",
+      "Downloads: https://api.biosimulations.org/results/66bc646aa641708179ad31a4/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc646aa641708179ad31a4?includeOutput=true\n"
      ]
     },
     {
@@ -509,7 +509,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4eb251ba57e3405ebf954a697127d423\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f97f781db1ec4812b2769295024b8c7c\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -517,10 +517,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb48240c4ccdd491921d5e\n",
-      "View: https://api.biosimulations.org/runs/66bb48240c4ccdd491921d5e\n",
-      "Downloads: https://api.biosimulations.org/results/66bb48240c4ccdd491921d5e/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb48240c4ccdd491921d5e?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc646e0c4ccdd491923866\n",
+      "View: https://api.biosimulations.org/runs/66bc646e0c4ccdd491923866\n",
+      "Downloads: https://api.biosimulations.org/results/66bc646e0c4ccdd491923866/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc646e0c4ccdd491923866?includeOutput=true\n"
      ]
     },
     {
@@ -532,7 +532,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=73f4e7a2900f4bb38c20e8761f1b1a79\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b0571c54189246b5acfbdc36c592583f\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -540,10 +540,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bb4826f29e09b32cb6fdab\n",
-      "View: https://api.biosimulations.org/runs/66bb4826f29e09b32cb6fdab\n",
-      "Downloads: https://api.biosimulations.org/results/66bb4826f29e09b32cb6fdab/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bb4826f29e09b32cb6fdab?includeOutput=true\n",
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6470f29e09b32cb71907\n",
+      "View: https://api.biosimulations.org/runs/66bc6470f29e09b32cb71907\n",
+      "Downloads: https://api.biosimulations.org/results/66bc6470f29e09b32cb71907/download\n",
+      "Logs: https://api.biosimulations.org/logs/66bc6470f29e09b32cb71907?includeOutput=true\n",
       "Downloading amici results...\n",
       "Downloading brian2 results...\n",
       "Downloading bionetgen results...\n",
@@ -565,19 +565,19 @@
       "Downloading tellurium results...\n",
       "Downloading vcell results...\n",
       "Downloading xpp results...\n",
-      "Moving remote_results\\amici\\outputs\\tmp904901\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
-      "Moving remote_results\\bionetgen\\outputs\\tmp896149\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
-      "Moving remote_results\\boolnet\\outputs\\tmp638536\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
-      "Moving remote_results\\cbmpy\\outputs\\tmp231472\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
-      "Moving remote_results\\cobrapy\\outputs\\tmp607739\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
-      "Moving remote_results\\copasi\\outputs\\tmp661623\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
-      "Moving remote_results\\gillespy2\\outputs\\tmp345818\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
-      "Moving remote_results\\ginsim\\outputs\\tmp721937\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
-      "Moving remote_results\\libsbmlsim\\outputs\\tmp543113\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
-      "Moving remote_results\\masspy\\outputs\\tmp783032\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
-      "Moving remote_results\\pysces\\outputs\\tmp449843\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
-      "Moving remote_results\\rbapy\\outputs\\tmp868501\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
-      "Moving remote_results\\tellurium\\outputs\\tmp613094\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
+      "Moving remote_results\\amici\\outputs\\tmp472787\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
+      "Moving remote_results\\bionetgen\\outputs\\tmp345301\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
+      "Moving remote_results\\boolnet\\outputs\\tmp110064\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
+      "Moving remote_results\\cbmpy\\outputs\\tmp806249\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
+      "Moving remote_results\\cobrapy\\outputs\\tmp591048\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
+      "Moving remote_results\\copasi\\outputs\\tmp631588\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
+      "Moving remote_results\\gillespy2\\outputs\\tmp681509\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
+      "Moving remote_results\\ginsim\\outputs\\tmp705876\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
+      "Moving remote_results\\libsbmlsim\\outputs\\tmp986325\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
+      "Moving remote_results\\masspy\\outputs\\tmp374428\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
+      "Moving remote_results\\pysces\\outputs\\tmp757204\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
+      "Moving remote_results\\rbapy\\outputs\\tmp601277\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
+      "Moving remote_results\\tellurium\\outputs\\tmp774548\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
       "Removed remote_results folder\n",
       "Running amici\n",
       "Running brian2\n",
@@ -678,122 +678,6 @@
     "    print('Removed ' + output_folder + ' folder')"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "engines = {\n",
-    "    'amici': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_AMICI/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'brian2': {\n",
-    "        'formats': [('nml', 'sedml'), ('lems', 'sedml'), ('sbml', 'sedml')],\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'bionetgen': {\n",
-    "        'formats': ('bngl', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_BioNetGen/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'boolnet': {\n",
-    "        'formats': ('sbmlqual', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_BoolNet/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'cbmpy': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_CBMPy/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'cobrapy': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_COBRApy/',\n",
-    "        'status': \"Only allows steady state simulations\"\n",
-    "    },\n",
-    "    'copasi': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_COPASI/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'gillespy2': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_GillesPy2/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'ginsim': {\n",
-    "        'formats': ('sbmlqual', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_GINsim/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'libsbmlsim': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_LibSBMLSim/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'masspy': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_MASSpy/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'netpyne': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'neuron': {\n",
-    "        'formats': [('nml', 'sedml'), ('lems', 'sedml')],\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'opencor': {\n",
-    "        'formats': ('cellml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_OpenCOR/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'pyneuroml': {\n",
-    "        'formats': [('nml', 'sedml'), ('lems', 'sedml')],\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'pysces': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_PySCeS/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'rbapy': {\n",
-    "        'formats': ('rbapy', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_RBApy/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'smoldyn': {\n",
-    "        'formats': None,\n",
-    "        'url': 'https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'tellurium': {\n",
-    "        'formats': ('sbml', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_tellurium/',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'vcell': {\n",
-    "        'formats': [('sbml', 'sedml'),('bngl', 'sedml')],\n",
-    "        'url': 'https://github.com/virtualcell/vcell',\n",
-    "        'status': \"\"\n",
-    "    },\n",
-    "    'xpp': {\n",
-    "        'formats': ('xpp', 'sedml'),\n",
-    "        'url': 'https://docs.biosimulators.org/Biosimulators_XPP/',\n",
-    "        'status': \"\"\n",
-    "    }\n",
-    "}"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 4,
@@ -813,27 +697,27 @@
       "text/markdown": [
        "|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                             | Compat (L)                                                                                                                                                                                                                                                                                                                             | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                   | d1 (R)                                               | d1 (L)                                              |\n",
        "|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|\n",
-       "|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
-       "|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
-       "|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
-       "|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
-       "|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
-       "|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
-       "|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
-       "|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
-       "|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
-       "| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
-       "| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpr_05sxok/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpr_05sxok/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
-       "| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
+       "|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
+       "|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
+       "|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
+       "|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
+       "|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
+       "|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
+       "|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
+       "|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
+       "|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
+       "| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
+       "| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span>    | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmprlw_6w38/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmprlw_6w38/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
+       "| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
        "| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
-       "| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
+       "| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
+       "| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
+       "| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
       ]
      },
      "metadata": {},
@@ -841,69 +725,13 @@
     }
    ],
    "source": [
-    "import re\n",
-    "\n",
-    "def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, output_dir):\n",
-    "    \"\"\"\n",
-    "    Create a markdown table of the results.\n",
-    "    \n",
-    "    Input: results, types_dict, sbml_filepath, sedml_filepath, engines, output_dir\n",
-    "    Output: results_md_table\n",
-    "\n",
-    "    \"\"\"\n",
-    "    \n",
-    "    link_green_square = \"https://via.placeholder.com/15/00dd00/00dd00.png\"\n",
-    "    link_orange_square = \"https://via.placeholder.com/15/ec9706/ec9706.png\"\n",
-    "    link_red_square = \"https://via.placeholder.com/15/dd0000/dd0000.png\"\n",
-    "\n",
-    "    # Create a table of the results\n",
-    "    results_table = pd.DataFrame.from_dict(results).T\n",
-    "    # if list is three elements \n",
-    "    if results_table.shape[1] == 3:\n",
-    "        results_table.columns = ['pass / FAIL', 'Error', 'Type']\n",
-    "    elif results_table.shape[1] == 2:\n",
-    "        results_table.columns = ['pass / FAIL', 'Error']\n",
-    "   \n",
-    "    results_table.index.name = 'Engine'\n",
-    "    results_table.reset_index(inplace=True)\n",
-    "    \n",
-    "    # Error\n",
-    "    results_table['Error'] = results_table.apply(lambda x: None if x['pass / FAIL'] == x['Error'] else x['Error'], axis=1)\n",
-    "    results_table['pass / FAIL'] = results_table['pass / FAIL'].replace('other', 'FAIL')\n",
-    "\n",
-    "    results_table['Error'] = results_table['Error'].apply(lambda x:  utils.ansi_to_html(x))\n",
-    "    results_table['Error'] = results_table['Error'].apply(lambda x:  utils.collapsible_content(x))\n",
-    "\n",
-    "    # compatibility_message\n",
-    "    results_table['Compat'] = results_table['Engine'].apply(lambda x:  utils.check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))\n",
-    "    results_table['Compat'] = results_table['Compat'].apply(lambda x:  utils.collapsible_content(x[1], title=x[0]))\n",
-    "    results_table['Compat'] = results_table['Compat'].apply(lambda x: f'<span style=\"color:darkred;\"><img src={link_red_square}/> {x}</span>'\\\n",
-    "                                                             if 'FAIL' in x else f'<img src={link_green_square}/>{x}')\n",
-    "\n",
-    "    # pass / FAIL\n",
-    "    results_table['pass / FAIL'] = results_table['pass / FAIL'].apply(lambda x: f'<span style=\"color:darkred;\">\\\n",
-    "                                                                      <img src={link_red_square}/> {x}</span>' if x == 'FAIL' \\\n",
-    "                                                                        else f'<img src={link_green_square}/> {x}')\n",
-    "\n",
-    "    # d1 plot clickable link\n",
-    "    results_table['d1'] = results_table['Engine'].apply(lambda x:  utils.d1_plots_dict(engines, output_dir).get(x, None))\n",
-    "    results_table['d1'] = results_table['d1'].apply(lambda x: utils.create_hyperlink(x,title='plot'))\n",
-    "    \n",
-    "    # if Type is in the table add message with collapsible content\n",
-    "    if 'Type' in results_table.columns:\n",
-    "        results_table['Type'] = results_table['Type'].apply(lambda x:  utils.collapsible_content(x,\"\".join(re.findall(r'[A-Z]', x))))\n",
-    "\n",
-    "    results_table['Engine'] = results_table['Engine'].apply(lambda x:  utils.collapsible_content(f'{engines[x][\"url\"]}<br>{engines[x][\"status\"]}', x))\n",
-    "\n",
-    "    return results_table\n",
-    "\n",
     "\n",
     "#########################################################################################\n",
     "# process results and save markdown table\n",
     "#########################################################################################\n",
     "\n",
-    "results_table = create_results_table(results_remote, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)\n",
-    "results_table_local = create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)\n",
+    "results_table = utils.create_results_table(results_remote, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)\n",
+    "results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)\n",
     "\n",
     "# rename cols to distinguish between local and remote results except for Engine column\n",
     "results_table.columns = [str(col) + ' (R)' if col != 'Engine' else str(col) for col in results_table.columns]\n",

From b1e509ef7e926acd657619f6ce5dbbafcef8a3e1 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 14 Aug 2024 09:06:24 +0100
Subject: [PATCH 29/71] Update results table

---
 SBML/results_compatibility_biosimulators.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/SBML/results_compatibility_biosimulators.md b/SBML/results_compatibility_biosimulators.md
index 019e5c9..4eb2820 100644
--- a/SBML/results_compatibility_biosimulators.md
+++ b/SBML/results_compatibility_biosimulators.md
@@ -1,4 +1,4 @@
-|    | Engine                                                                                                                                     | pass / FAIL (remote)                                                                                                                                                       | pass / FAIL (local)                                                                                                                                                        | Compat (remote)                                                                                                                                                                                                                                                                                                                        | Compat (local)                                                                                                                                                                                                                                                                                                                         | Type (remote)                                                          | Error (remote)                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Error (local)                                                                                                                                               | d1 (remote)                                          | d1 (local)                                          |
+|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                             | Compat (L)                                                                                                                                                                                                                                                                                                                             | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                   | d1 (R)                                               | d1 (L)                                              |
 |---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
 |  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="d1_plots_local\amici_d1.pdf">plot</a>      |
 |  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="d1_plots_local\bionetgen_d1.pdf">plot</a>  |
@@ -12,10 +12,10 @@
 |  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
 | 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="d1_plots_local\masspy_d1.pdf">plot</a>     |
 | 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
 | 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp0ouw2n9o/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp0ouw2n9o/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmph2fvlpzq/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmph2fvlpzq/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
 | 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_d1.pdf">plot</a>      |
 | 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
 | 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_d1.pdf">plot</a>  |

From cf33fc671d29e6ee2e308ee12fa3d0de7dfa7fdf Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 14 Aug 2024 09:31:06 +0100
Subject: [PATCH 30/71] fix typo Tese --> These

---
 utils/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/utils/__init__.py b/utils/__init__.py
index 535ba3a..0161227 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -445,7 +445,7 @@ def check_file_compatibility_test(engine, types_dict, model_filepath, experiment
         if input_filetypes.issubset(engine_filetypes):
             return 'pass', (f"The file extensions suggest the input file types are '{input_file_types_text}'. These are compatible with {engine}")
         else:
-            return 'FAIL', (f"The file extensions suggest the input file types are '{input_file_types_text}'. Tese are not compatible with {engine}. The following file types will be compatible {engine_file_types_text}")
+            return 'FAIL', (f"The file extensions suggest the input file types are '{input_file_types_text}'. These are not compatible with {engine}. The following file types will be compatible {engine_file_types_text}")
     else:
         return 'FAIL', (f"{engine} compatible file types unknown.")
 

From 505a3fdb74d04c78d861b7476308460fc80a3983 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 14 Aug 2024 09:40:26 +0100
Subject: [PATCH 31/71] ammend results table (local run failed in last table)

---
 SBML/results_compatibility_biosimulators.md | 46 ++++++++++-----------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/SBML/results_compatibility_biosimulators.md b/SBML/results_compatibility_biosimulators.md
index 4eb2820..4044be1 100644
--- a/SBML/results_compatibility_biosimulators.md
+++ b/SBML/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                             | Compat (L)                                                                                                                                                                                                                                                                                                                             | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                   | d1 (R)                                               | d1 (L)                                              |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="d1_plots_local\amici_d1.pdf">plot</a>      |
-|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="d1_plots_local\bionetgen_d1.pdf">plot</a>  |
-|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="d1_plots_local\boolnet_d1.pdf">plot</a>    |
-|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="d1_plots_local\cbmpy_d1.pdf">plot</a>      |
-|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="d1_plots_local\cobrapy_d1.pdf">plot</a>    |
-|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="d1_plots_local\copasi_d1.pdf">plot</a>     |
-|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="d1_plots_local\gillespy2_d1.pdf">plot</a>  |
-|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="d1_plots_local\ginsim_d1.pdf">plot</a>     |
-|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
-| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="d1_plots_local\masspy_d1.pdf">plot</a>     |
-| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmph2fvlpzq/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmph2fvlpzq/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
-| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_d1.pdf">plot</a>      |
-| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href="d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_d1.pdf">plot</a>  |
-| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
-| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |
\ No newline at end of file
+|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                              | Compat (L)                                                                                                                                                                                                                                                                                                                              | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                                                            | d1 (R)                                               | d1 (L)                                              |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
+|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="d1_plots_local\amici_d1.pdf">plot</a>      |
+|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="d1_plots_local\bionetgen_d1.pdf">plot</a>  |
+|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="d1_plots_local\boolnet_d1.pdf">plot</a>    |
+|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                      |                                                     |
+|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="d1_plots_local\cbmpy_d1.pdf">plot</a>      |
+|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="d1_plots_local\cobrapy_d1.pdf">plot</a>    |
+|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="d1_plots_local\copasi_d1.pdf">plot</a>     |
+|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="d1_plots_local\gillespy2_d1.pdf">plot</a>  |
+|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="d1_plots_local\ginsim_d1.pdf">plot</a>     |
+|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
+| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="d1_plots_local\masspy_d1.pdf">plot</a>     |
+| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                      |                                                     |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                      |                                                     |
+| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                      |                                                     |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                      |                                                     |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp4u2w7p7f/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp4u2w7p7f/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
+| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_d1.pdf">plot</a>      |
+| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                      |                                                     |
+| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_d1.pdf">plot</a>  |
+| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>No such container: e94149ab5804bb6b56c44a27b83c2d3030c2764438cdeed95d90285f837aee7f</details>                                                                     |                                                      |                                                     |
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                      |                                                     |
\ No newline at end of file

From d33c661eb60887abc3566569611df717e25367d4 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Tue, 20 Aug 2024 13:56:24 +0100
Subject: [PATCH 32/71] Minor tweak to validate test script

---
 SBML/.test.validate.sbml.omt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SBML/.test.validate.sbml.omt b/SBML/.test.validate.sbml.omt
index eb508a1..6925fc6 100644
--- a/SBML/.test.validate.sbml.omt
+++ b/SBML/.test.validate.sbml.omt
@@ -1,5 +1,5 @@
 # Script for running automated tests on OSB using github actions, see https://github.com/OpenSourceBrain/osb-model-validation 
 
-# This test will validate the SBML files in the current directory using: pyneuroml -validate-sbml *.xml *.sbml
+# This test will validate the SBML files in the current directory using: pynml -validate-sbml *.xml *.sbml
 target: "*.xml *.sbml"
 engine: pyNeuroML_validate_sbml
\ No newline at end of file

From c0c95daac023af8d7edeb763dd3800778574d79f Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 20 Aug 2024 17:47:01 +0100
Subject: [PATCH 33/71] Restructure SBML directory structure

- Move SBML tests to a separate "tests" folder.
- Update the file paths in the test scripts to reflect the new directory structure.
- Update filepaths in github actions
---
 .github/workflows/non-omv.yml                 |    6 +-
 SBML/Copasi184.cps                            | 1587 -----------------
 SBML/test_biosimulators_docker.py             |   19 -
 SBML/{ => tests}/d1_plots_local/amici_d1.pdf  |  Bin 13644 -> 13644 bytes
 .../d1_plots_local/bionetgen_d1.pdf           |  Bin 5948 -> 5948 bytes
 .../{ => tests}/d1_plots_local/boolnet_d1.pdf |  Bin 5948 -> 5948 bytes
 SBML/{ => tests}/d1_plots_local/cbmpy_d1.pdf  |  Bin 5948 -> 5948 bytes
 .../{ => tests}/d1_plots_local/cobrapy_d1.pdf |  Bin 5948 -> 5948 bytes
 SBML/{ => tests}/d1_plots_local/copasi_d1.pdf |  Bin 5948 -> 5948 bytes
 .../d1_plots_local/gillespy2_d1.pdf           |  Bin 8877 -> 8877 bytes
 SBML/{ => tests}/d1_plots_local/ginsim_d1.pdf |  Bin 5948 -> 5948 bytes
 .../d1_plots_local/libsbmlsim_d1.pdf          |  Bin 14643 -> 14643 bytes
 SBML/{ => tests}/d1_plots_local/masspy_d1.pdf |  Bin 5948 -> 5948 bytes
 SBML/{ => tests}/d1_plots_local/pysces_d1.pdf |  Bin 5948 -> 5948 bytes
 SBML/{ => tests}/d1_plots_local/rbapy_d1.pdf  |  Bin 5948 -> 5948 bytes
 .../d1_plots_local/tellurium_d1.pdf           |  Bin 14664 -> 14664 bytes
 SBML/{ => tests}/d1_plots_remote/amici_d1.pdf |  Bin 13650 -> 13650 bytes
 .../d1_plots_remote/bionetgen_d1.pdf          |  Bin 5954 -> 5954 bytes
 .../d1_plots_remote/boolnet_d1.pdf            |  Bin 5954 -> 5954 bytes
 SBML/{ => tests}/d1_plots_remote/cbmpy_d1.pdf |  Bin 5954 -> 5954 bytes
 .../d1_plots_remote/cobrapy_d1.pdf            |  Bin 5954 -> 5954 bytes
 .../{ => tests}/d1_plots_remote/copasi_d1.pdf |  Bin 5954 -> 5954 bytes
 .../d1_plots_remote/gillespy2_d1.pdf          |  Bin 8883 -> 8883 bytes
 .../{ => tests}/d1_plots_remote/ginsim_d1.pdf |  Bin 5954 -> 5954 bytes
 .../d1_plots_remote/libsbmlsim_d1.pdf         |  Bin 14649 -> 14649 bytes
 .../{ => tests}/d1_plots_remote/masspy_d1.pdf |  Bin 5954 -> 5954 bytes
 .../{ => tests}/d1_plots_remote/pysces_d1.pdf |  Bin 5954 -> 5954 bytes
 SBML/{ => tests}/d1_plots_remote/rbapy_d1.pdf |  Bin 5954 -> 5954 bytes
 .../d1_plots_remote/tellurium_d1.pdf          |  Bin 14670 -> 14670 bytes
 .../results_compatibility_biosimulators.md    |   46 +-
 SBML/tests/test_biosimulators_docker.py       |   29 +
 .../test_compatibility_biosimulators.ipynb    |  443 ++---
 .../test_compatibility_biosimulators.py       |   70 +-
 SBML/{ => tests}/test_tellurium.py            |    8 +-
 SBML/{ => tests}/validateAll.sh               |    3 +
 35 files changed, 358 insertions(+), 1853 deletions(-)
 delete mode 100755 SBML/Copasi184.cps
 delete mode 100755 SBML/test_biosimulators_docker.py
 rename SBML/{ => tests}/d1_plots_local/amici_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/bionetgen_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/boolnet_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/cbmpy_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/cobrapy_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/copasi_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/gillespy2_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/ginsim_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/libsbmlsim_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/masspy_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/pysces_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/rbapy_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_local/tellurium_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/amici_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/bionetgen_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/boolnet_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/cbmpy_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/cobrapy_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/copasi_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/gillespy2_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/ginsim_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/libsbmlsim_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/masspy_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/pysces_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/rbapy_d1.pdf (99%)
 rename SBML/{ => tests}/d1_plots_remote/tellurium_d1.pdf (99%)
 rename SBML/{ => tests}/results_compatibility_biosimulators.md (87%)
 create mode 100644 SBML/tests/test_biosimulators_docker.py
 rename SBML/{ => tests}/test_compatibility_biosimulators.ipynb (61%)
 rename SBML/{ => tests}/test_compatibility_biosimulators.py (65%)
 rename SBML/{ => tests}/test_tellurium.py (80%)
 rename SBML/{ => tests}/validateAll.sh (86%)
 mode change 100755 => 100644

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index b06792c..985664c 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -47,19 +47,19 @@ jobs:
       run: |
         pip install pyNeuroML pyNeuroML[annotations]
         cd SBML
-        ./validateAll.sh
+        ./tests/alidateAll.sh
 
     - name: test omex file creation
       run: |
         pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
         cd SBML        
-        ./test_biosimulators_docker.py
+        ./tests/test_biosimulators_docker.py
 
     - name: test biosimulators compatibility table creation
       run: |
         cd SBML
         sudo rm -rf output
-        python ./test_compatibility_biosimulators.py --output-dir=tmp_plots
+        python ./tests/test_compatibility_biosimulators.py --output-dir=tmp_plots
 
 
     - name: Test test_suite output regeneration
diff --git a/SBML/Copasi184.cps b/SBML/Copasi184.cps
deleted file mode 100755
index 51bd328..0000000
--- a/SBML/Copasi184.cps
+++ /dev/null
@@ -1,1587 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- generated with COPASI 4.27 (Build 217) (http://www.copasi.org) at 2020-01-21T10:07:36Z -->
-<?oxygen RNGSchema="http://www.copasi.org/static/schema/CopasiML.rng" type="xml"?>
-<COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="27" versionDevel="217" copasiSourcesModified="0">
-  <ListOfFunctions>
-    <Function key="Function_6" name="Constant flux (irreversible)" type="PreDefined" reversible="false">
-      <MiriamAnnotation>
-<rdf:RDF
-xmlns:dcterms="http://purl.org/dc/terms/"
-xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
-<rdf:Description rdf:about="#Function_6">
-<dcterms:created>
-<rdf:Description>
-<dcterms:W3CDTF>2020-01-21T10:03:15Z</dcterms:W3CDTF>
-</rdf:Description>
-</dcterms:created>
-</rdf:Description>
-</rdf:RDF>
-      </MiriamAnnotation>
-      <Expression>
-        v
-      </Expression>
-      <ListOfParameterDescriptions>
-        <ParameterDescription key="FunctionParameter_49" name="v" order="0" role="constant"/>
-      </ListOfParameterDescriptions>
-    </Function>
-    <Function key="Function_13" name="Mass action (irreversible)" type="MassAction" reversible="false">
-      <MiriamAnnotation>
-<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
-   <rdf:Description rdf:about="#Function_13">
-   <CopasiMT:is rdf:resource="urn:miriam:obo.sbo:SBO:0000163" />
-   </rdf:Description>
-   </rdf:RDF>
-      </MiriamAnnotation>
-      <Comment>
-        <body xmlns="http://www.w3.org/1999/xhtml">
-<b>Mass action rate law for irreversible reactions</b>
-<p>
-Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant.
-</p>
-</body>
-      </Comment>
-      <Expression>
-        k1*PRODUCT&lt;substrate_i>
-      </Expression>
-      <ListOfParameterDescriptions>
-        <ParameterDescription key="FunctionParameter_80" name="k1" order="0" role="constant"/>
-        <ParameterDescription key="FunctionParameter_81" name="substrate" order="1" role="substrate"/>
-      </ListOfParameterDescriptions>
-    </Function>
-    <Function key="Function_40" name="Function for CICR" type="UserDefined" reversible="false">
-      <MiriamAnnotation>
-<rdf:RDF
-xmlns:dcterms="http://purl.org/dc/terms/"
-xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
-<rdf:Description rdf:about="#Function_40">
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-      <StateTemplateVariable objectReference="Metabolite_1"/>
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-      <StateTemplateVariable objectReference="ModelValue_0"/>
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-      <StateTemplateVariable objectReference="ModelValue_2"/>
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-      <StateTemplateVariable objectReference="ModelValue_4"/>
-      <StateTemplateVariable objectReference="ModelValue_5"/>
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-      <StateTemplateVariable objectReference="ModelValue_7"/>
-      <StateTemplateVariable objectReference="ModelValue_8"/>
-      <StateTemplateVariable objectReference="ModelValue_9"/>
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-      <StateTemplateVariable objectReference="ModelValue_11"/>
-      <StateTemplateVariable objectReference="ModelValue_12"/>
-      <StateTemplateVariable objectReference="ModelValue_13"/>
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-      0 60221408570000000 60221408570000000 9.0332112855e+17 1 1 0.050000000000000003 0.5 40 0.14999999999999999 2.02 0.14999999999999999 2.2000000000000002 0.10000000000000001 15 0.10000000000000001 0.5 0.050000000000000003 0.29999999999999999 0.080000000000000002 
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-        <Parameter name="Values" type="string" value=""/>
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-</rdf:Description>
-</rdf:RDF>
-      </MiriamAnnotation>
-      <Expression>
-        1
-      </Expression>
-    </UnitDefinition>
-    <UnitDefinition key="Unit_17" name="item" symbol="#">
-      <MiriamAnnotation>
-<rdf:RDF
-xmlns:dcterms="http://purl.org/dc/terms/"
-xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
-<rdf:Description rdf:about="#Unit_16">
-<dcterms:created>
-<rdf:Description>
-<dcterms:W3CDTF>2020-01-21T10:03:15Z</dcterms:W3CDTF>
-</rdf:Description>
-</dcterms:created>
-</rdf:Description>
-</rdf:RDF>
-      </MiriamAnnotation>
-      <Expression>
-        #
-      </Expression>
-    </UnitDefinition>
-    <UnitDefinition key="Unit_35" name="liter" symbol="l">
-      <MiriamAnnotation>
-<rdf:RDF
-xmlns:dcterms="http://purl.org/dc/terms/"
-xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
-<rdf:Description rdf:about="#Unit_34">
-<dcterms:created>
-<rdf:Description>
-<dcterms:W3CDTF>2020-01-21T10:03:15Z</dcterms:W3CDTF>
-</rdf:Description>
-</dcterms:created>
-</rdf:Description>
-</rdf:RDF>
-      </MiriamAnnotation>
-      <Expression>
-        0.001*m^3
-      </Expression>
-    </UnitDefinition>
-    <UnitDefinition key="Unit_41" name="mole" symbol="mol">
-      <MiriamAnnotation>
-<rdf:RDF
-xmlns:dcterms="http://purl.org/dc/terms/"
-xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
-<rdf:Description rdf:about="#Unit_40">
-<dcterms:created>
-<rdf:Description>
-<dcterms:W3CDTF>2020-01-21T10:03:15Z</dcterms:W3CDTF>
-</rdf:Description>
-</dcterms:created>
-</rdf:Description>
-</rdf:RDF>
-      </MiriamAnnotation>
-      <Expression>
-        Avogadro*#
-      </Expression>
-    </UnitDefinition>
-  </ListOfUnitDefinitions>
-</COPASI>
diff --git a/SBML/test_biosimulators_docker.py b/SBML/test_biosimulators_docker.py
deleted file mode 100755
index 473a607..0000000
--- a/SBML/test_biosimulators_docker.py
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env python
-
-'''
-use pymetadata module to create a minimal valid combine archive
-using LEMS_NML2_Ex9_FN.sbml and LEMS_NML2_Ex9_FN.sedml
-'''
-
-import sys
-sys.path.append("..")
-import utils
-
-sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml'
-#sedml_filepath = 'LEMS_NML2_Ex9_FN.sedml' #xmlns:sbml added manually
-sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
-omex_filepath = utils.create_omex(sedml_filepath,sbml_filepath)
-
-utils.biosimulators_core('tellurium',omex_filepath)
-
-print('Finished')
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diff --git a/SBML/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
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+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                              | Compat (L)                                                                                                                                                                                                                                                                                                                              | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                                                            | d1 (R)                                               | d1 (L)                                              |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="d1_plots_local\amici_d1.pdf">plot</a>      |
-|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="d1_plots_local\bionetgen_d1.pdf">plot</a>  |
-|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="d1_plots_local\boolnet_d1.pdf">plot</a>    |
-|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                      |                                                     |
-|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="d1_plots_local\cbmpy_d1.pdf">plot</a>      |
-|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="d1_plots_local\cobrapy_d1.pdf">plot</a>    |
-|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="d1_plots_local\copasi_d1.pdf">plot</a>     |
-|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="d1_plots_local\gillespy2_d1.pdf">plot</a>  |
-|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="d1_plots_local\ginsim_d1.pdf">plot</a>     |
-|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
-| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="d1_plots_local\masspy_d1.pdf">plot</a>     |
-| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                      |                                                     |
-| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with neuron. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                      |                                                     |
-| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                      |                                                     |
-| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with pyneuroml. The following file types will be compatible ['LEMS', 'NeuroML', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                      |                                                     |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp4u2w7p7f/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp4u2w7p7f/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
-| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_d1.pdf">plot</a>      |
-| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                      |                                                     |
-| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_d1.pdf">plot</a>  |
-| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>No such container: e94149ab5804bb6b56c44a27b83c2d3030c2764438cdeed95d90285f837aee7f</details>                                                                     |                                                      |                                                     |
-| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                      |                                                     |
\ No newline at end of file
+|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                              | Compat (L)                                                                                                                                                                                                                                                                                                                              | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                                                            | d1 (R)                                                     | d1 (L)                                                    |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|:----------------------------------------------------------|
+|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_d1.pdf">plot</a>      |
+|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_d1.pdf">plot</a>  |
+|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_d1.pdf">plot</a>    |
+|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                            |                                                           |
+|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_d1.pdf">plot</a>      |
+|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_d1.pdf">plot</a>    |
+|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_d1.pdf">plot</a>     |
+|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_d1.pdf">plot</a>  |
+|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_d1.pdf">plot</a>     |
+|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
+| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_d1.pdf">plot</a>     |
+| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                            |                                                           |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                            |                                                           |
+| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                            |                                                           |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                            |                                                           |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp091bjymu/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp091bjymu/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_d1.pdf">plot</a>     |
+| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_d1.pdf">plot</a>      |
+| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                            |                                                           |
+| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_d1.pdf">plot</a>  |
+| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                            |                                                           |
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                            |                                                           |
\ No newline at end of file
diff --git a/SBML/tests/test_biosimulators_docker.py b/SBML/tests/test_biosimulators_docker.py
new file mode 100644
index 0000000..d0b4a40
--- /dev/null
+++ b/SBML/tests/test_biosimulators_docker.py
@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+
+'''
+use pymetadata module to create a minimal valid combine archive
+using LEMS_NML2_Ex9_FN.sbml and LEMS_NML2_Ex9_FN.sedml
+'''
+import os
+import sys
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
+import utils
+
+
+cwd = os.getcwd()
+print("Current working directory:", cwd)
+path_to_sbml_folder = os.path.abspath(os.path.join(cwd, os.pardir))
+print("Path to SBML folder:", path_to_sbml_folder)
+os.chdir(path_to_sbml_folder)
+print("Changed working directory to:", os.getcwd())
+
+sbml_file_name = 'LEMS_NML2_Ex9_FN.sbml'
+#sedml_filepath = 'LEMS_NML2_Ex9_FN.sedml' #xmlns:sbml added manually
+sedml_file_name = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
+
+omex_filepath = utils.create_omex(sedml_file_name,sbml_file_name)
+
+print('Testing biosimulators-core (tellurium)')
+message = utils.biosimulators_core('tellurium',omex_filepath)
+print('..................')
+print('Finished')
diff --git a/SBML/test_compatibility_biosimulators.ipynb b/SBML/tests/test_compatibility_biosimulators.ipynb
similarity index 61%
rename from SBML/test_compatibility_biosimulators.ipynb
rename to SBML/tests/test_compatibility_biosimulators.ipynb
index 42a78fd..3649820 100644
--- a/SBML/test_compatibility_biosimulators.ipynb
+++ b/SBML/tests/test_compatibility_biosimulators.ipynb
@@ -23,39 +23,52 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\n"
+      "Path to SED-ML file: c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\LEMS_NML2_Ex9_FN_missing_xmlns.sedml\n",
+      "Path to SBML file: c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\LEMS_NML2_Ex9_FN.sbml\n",
+      "d1 plots will be saved in: tests\\d1_plots_remote and tests\\d1_plots_local\n"
      ]
     }
    ],
    "source": [
-    "#!/usr/bin/env python\n",
-    "\n",
-    "'''\n",
-    "use pymetadata module to create a minimal valid combine archive\n",
-    "using LEMS_NML2_Ex9_FN.sbml and LEMS_NML2_Ex9_FN.sedml\n",
-    "'''\n",
-    "\n",
-    "import sys\n",
-    "sys.path.append(\"..\")\n",
-    "import utils\n",
     "import os\n",
     "import pandas as pd\n",
     "from IPython.display import display_markdown\n",
     "import shutil\n",
     "import yaml\n",
     "\n",
-    "\n",
+    "# Save the current working directory\n",
     "cwd = os.getcwd()\n",
-    "print(cwd)\n",
+    "\n",
+    "# Change directory to the import utils \n",
+    "os.chdir('../../')\n",
+    "import utils\n",
+    "path_to_sbml_folder = os.path.join(os.getcwd(), 'SBML')\n",
+    "\n",
+    "# Change back to the original working directory\n",
+    "os.chdir(path_to_sbml_folder)\n",
     "\n",
     "d1_plots_remote_dir = 'd1_plots'+ '_remote'\n",
     "d1_plots_local_dir = 'd1_plots' + '_local'\n",
     "\n",
-    "sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml'\n",
-    "sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing\n",
+    "sbml_file_name = 'LEMS_NML2_Ex9_FN.sbml'\n",
+    "sedml_file_name = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing\n",
+    "\n",
+    "sbml_file_path = os.path.join(path_to_sbml_folder, sbml_file_name)\n",
+    "sedml_file_path = os.path.join(path_to_sbml_folder, sedml_file_name)\n",
+    "\n",
+    "print('Path to SED-ML file:', sedml_file_path)\n",
+    "print('Path to SBML file:', sbml_file_path)\n",
     "\n",
     "engines = utils.engines\n",
-    "types_dict = utils.types_dict\n"
+    "types_dict = utils.types_dict\n",
+    "\n",
+    "test_folder = 'tests'\n",
+    "output_dir = 'd1_plots'\n",
+    "\n",
+    "d1_plots_remote_dir = os.path.join(test_folder, output_dir + '_remote')\n",
+    "d1_plots_local_dir = os.path.join(test_folder, output_dir + '_local')\n",
+    "\n",
+    "print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir)"
    ]
   },
   {
@@ -72,7 +85,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"amici\",\"simulatorVersion\":\"0.18.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=4f4d0d71858746cab44391b232bfdeb1\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=afb2be9d281b4e768e7619adea6bea08\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -80,10 +93,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc643ea641708179ad2dd7\n",
-      "View: https://api.biosimulations.org/runs/66bc643ea641708179ad2dd7\n",
-      "Downloads: https://api.biosimulations.org/results/66bc643ea641708179ad2dd7/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc643ea641708179ad2dd7?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c7029f535bb92ffefba7\n",
+      "View: https://api.biosimulations.org/runs/66c4c7029f535bb92ffefba7\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c7029f535bb92ffefba7/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c7029f535bb92ffefba7?includeOutput=true\n"
      ]
     },
     {
@@ -95,7 +108,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"brian2\",\"simulatorVersion\":\"2.5.0.3\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=bf3a11a48a234cdd98c4513e86e75a69\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=854eedd4a17243468f540f3b47ff70d8\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -103,10 +116,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6440a641708179ad2e01\n",
-      "View: https://api.biosimulations.org/runs/66bc6440a641708179ad2e01\n",
-      "Downloads: https://api.biosimulations.org/results/66bc6440a641708179ad2e01/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc6440a641708179ad2e01?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c70493c284abde6a09a2\n",
+      "View: https://api.biosimulations.org/runs/66c4c70493c284abde6a09a2\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c70493c284abde6a09a2/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c70493c284abde6a09a2?includeOutput=true\n"
      ]
     },
     {
@@ -118,7 +131,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"bionetgen\",\"simulatorVersion\":\"2.8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7351ffe3fce7434581ec6a356aff7a36\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=e7f22dd135a346fea09e9b899522afbe\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -126,10 +139,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64420c4ccdd491923499\n",
-      "View: https://api.biosimulations.org/runs/66bc64420c4ccdd491923499\n",
-      "Downloads: https://api.biosimulations.org/results/66bc64420c4ccdd491923499/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc64420c4ccdd491923499?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c7059f535bb92ffefbab\n",
+      "View: https://api.biosimulations.org/runs/66c4c7059f535bb92ffefbab\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c7059f535bb92ffefbab/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c7059f535bb92ffefbab?includeOutput=true\n"
      ]
     },
     {
@@ -141,7 +154,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"boolnet\",\"simulatorVersion\":\"2.1.5\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b4c82db1ce4f411c97a8d62e880b5765\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c1c0dbb21ff1468e8a3de3da7e4ee989\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -149,10 +162,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6445f29e09b32cb71538\n",
-      "View: https://api.biosimulations.org/runs/66bc6445f29e09b32cb71538\n",
-      "Downloads: https://api.biosimulations.org/results/66bc6445f29e09b32cb71538/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc6445f29e09b32cb71538?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c70793c284abde6a09a6\n",
+      "View: https://api.biosimulations.org/runs/66c4c70793c284abde6a09a6\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c70793c284abde6a09a6/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c70793c284abde6a09a6?includeOutput=true\n"
      ]
     },
     {
@@ -164,7 +177,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cbmpy\",\"simulatorVersion\":\"0.7.25\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b1f3fedd0d7e450c8d6a22225609703b\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f94d1a5421e74764a8d3bca1668b24ea\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -172,10 +185,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6448f29e09b32cb7156f\n",
-      "View: https://api.biosimulations.org/runs/66bc6448f29e09b32cb7156f\n",
-      "Downloads: https://api.biosimulations.org/results/66bc6448f29e09b32cb7156f/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc6448f29e09b32cb7156f?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c7099f535bb92ffefbae\n",
+      "View: https://api.biosimulations.org/runs/66c4c7099f535bb92ffefbae\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c7099f535bb92ffefbae/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c7099f535bb92ffefbae?includeOutput=true\n"
      ]
     },
     {
@@ -187,7 +200,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"cobrapy\",\"simulatorVersion\":\"0.24.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f75f20204474457a841b39b84cf86b7c\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=bb90b9b79e2a432e99cc9bae089a01cf\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -195,10 +208,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc644aa641708179ad2e93\n",
-      "View: https://api.biosimulations.org/runs/66bc644aa641708179ad2e93\n",
-      "Downloads: https://api.biosimulations.org/results/66bc644aa641708179ad2e93/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc644aa641708179ad2e93?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c70b93c284abde6a09a9\n",
+      "View: https://api.biosimulations.org/runs/66c4c70b93c284abde6a09a9\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c70b93c284abde6a09a9/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c70b93c284abde6a09a9?includeOutput=true\n"
      ]
     },
     {
@@ -210,7 +223,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"copasi\",\"simulatorVersion\":\"4.42.284\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7f46f52689e940499d58544bc679cbf4\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=1f2116f724624a68a372cebc158125d5\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -218,10 +231,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc644c0c4ccdd49192354c\n",
-      "View: https://api.biosimulations.org/runs/66bc644c0c4ccdd49192354c\n",
-      "Downloads: https://api.biosimulations.org/results/66bc644c0c4ccdd49192354c/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc644c0c4ccdd49192354c?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c70d93c284abde6a09ad\n",
+      "View: https://api.biosimulations.org/runs/66c4c70d93c284abde6a09ad\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c70d93c284abde6a09ad/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c70d93c284abde6a09ad?includeOutput=true\n"
      ]
     },
     {
@@ -233,7 +246,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"gillespy2\",\"simulatorVersion\":\"1.6.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=a95da07b0eed4b0c81b8efea3865cdd2\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=25ad040d50cd4f3b98daf0a9314681af\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -241,10 +254,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc644ef29e09b32cb715ff\n",
-      "View: https://api.biosimulations.org/runs/66bc644ef29e09b32cb715ff\n",
-      "Downloads: https://api.biosimulations.org/results/66bc644ef29e09b32cb715ff/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc644ef29e09b32cb715ff?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c71093c284abde6a09b2\n",
+      "View: https://api.biosimulations.org/runs/66c4c71093c284abde6a09b2\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c71093c284abde6a09b2/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c71093c284abde6a09b2?includeOutput=true\n"
      ]
     },
     {
@@ -256,7 +269,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"ginsim\",\"simulatorVersion\":\"3.0.0b\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f196d9eb63c44771b057607e142425ef\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=bb903e82d8204c029e36bd6f8cc024d9\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -264,10 +277,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64510c4ccdd4919235ce\n",
-      "View: https://api.biosimulations.org/runs/66bc64510c4ccdd4919235ce\n",
-      "Downloads: https://api.biosimulations.org/results/66bc64510c4ccdd4919235ce/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc64510c4ccdd4919235ce?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c71293c284abde6a09b7\n",
+      "View: https://api.biosimulations.org/runs/66c4c71293c284abde6a09b7\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c71293c284abde6a09b7/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c71293c284abde6a09b7?includeOutput=true\n"
      ]
     },
     {
@@ -279,7 +292,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"libsbmlsim\",\"simulatorVersion\":\"1.4.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=9abf44470197427eb5d0e537386631a4\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f0117d681cea479496e06434fb72cbd2\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -287,10 +300,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64530c4ccdd491923630\n",
-      "View: https://api.biosimulations.org/runs/66bc64530c4ccdd491923630\n",
-      "Downloads: https://api.biosimulations.org/results/66bc64530c4ccdd491923630/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc64530c4ccdd491923630?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c7139f535bb92ffefbbc\n",
+      "View: https://api.biosimulations.org/runs/66c4c7139f535bb92ffefbbc\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c7139f535bb92ffefbbc/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c7139f535bb92ffefbbc?includeOutput=true\n"
      ]
     },
     {
@@ -302,7 +315,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"masspy\",\"simulatorVersion\":\"0.1.6\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=0555dafc508d434d99eb0deac879dc66\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=d9188e27cf524560ace345df3a95b794\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -310,10 +323,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6456a641708179ad2fdf\n",
-      "View: https://api.biosimulations.org/runs/66bc6456a641708179ad2fdf\n",
-      "Downloads: https://api.biosimulations.org/results/66bc6456a641708179ad2fdf/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc6456a641708179ad2fdf?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c7159f535bb92ffefbc5\n",
+      "View: https://api.biosimulations.org/runs/66c4c7159f535bb92ffefbc5\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c7159f535bb92ffefbc5/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c7159f535bb92ffefbc5?includeOutput=true\n"
      ]
     },
     {
@@ -325,7 +338,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"netpyne\",\"simulatorVersion\":\"1.0.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=7c5d87f9e90b4084ab78d7f2395e0047\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=2082f0d4ead94d5c8dd22184f83ee888\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -333,10 +346,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6458a641708179ad304e\n",
-      "View: https://api.biosimulations.org/runs/66bc6458a641708179ad304e\n",
-      "Downloads: https://api.biosimulations.org/results/66bc6458a641708179ad304e/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc6458a641708179ad304e?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c71793c284abde6a09c2\n",
+      "View: https://api.biosimulations.org/runs/66c4c71793c284abde6a09c2\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c71793c284abde6a09c2/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c71793c284abde6a09c2?includeOutput=true\n"
      ]
     },
     {
@@ -348,7 +361,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"neuron\",\"simulatorVersion\":\"8.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=0b9c70f0c9c7462cb1be21f774e1615e\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=fe7bb5b685074bedbab22e697a258d00\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -356,10 +369,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc645af29e09b32cb717bf\n",
-      "View: https://api.biosimulations.org/runs/66bc645af29e09b32cb717bf\n",
-      "Downloads: https://api.biosimulations.org/results/66bc645af29e09b32cb717bf/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc645af29e09b32cb717bf?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c71993c284abde6a09d1\n",
+      "View: https://api.biosimulations.org/runs/66c4c71993c284abde6a09d1\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c71993c284abde6a09d1/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c71993c284abde6a09d1?includeOutput=true\n"
      ]
     },
     {
@@ -371,7 +384,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"opencor\",\"simulatorVersion\":\"2021-10-05\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c3b9c2080d334b74a6f468d540e2bf32\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=3b76339f0c9e4d609d648c8e18a53ae5\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -379,10 +392,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc645cf29e09b32cb71813\n",
-      "View: https://api.biosimulations.org/runs/66bc645cf29e09b32cb71813\n",
-      "Downloads: https://api.biosimulations.org/results/66bc645cf29e09b32cb71813/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc645cf29e09b32cb71813?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c71b4da143765fa7870d\n",
+      "View: https://api.biosimulations.org/runs/66c4c71b4da143765fa7870d\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c71b4da143765fa7870d/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c71b4da143765fa7870d?includeOutput=true\n"
      ]
     },
     {
@@ -394,7 +407,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pyneuroml\",\"simulatorVersion\":\"0.5.20\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=3eb15093c60140898d6bfe71685568fc\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=0c4a0cb42fcd4afd8499f37eed6e4725\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -402,10 +415,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc645fa641708179ad3112\n",
-      "View: https://api.biosimulations.org/runs/66bc645fa641708179ad3112\n",
-      "Downloads: https://api.biosimulations.org/results/66bc645fa641708179ad3112/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc645fa641708179ad3112?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c71d93c284abde6a09e2\n",
+      "View: https://api.biosimulations.org/runs/66c4c71d93c284abde6a09e2\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c71d93c284abde6a09e2/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c71d93c284abde6a09e2?includeOutput=true\n"
      ]
     },
     {
@@ -417,7 +430,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"pysces\",\"simulatorVersion\":\"1.2.1\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=c7ed6cc225864a2fb918db765ec00557\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=828e5d99b16545c6bd12470db30f9923\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -425,10 +438,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64630c4ccdd491923827\n",
-      "View: https://api.biosimulations.org/runs/66bc64630c4ccdd491923827\n",
-      "Downloads: https://api.biosimulations.org/results/66bc64630c4ccdd491923827/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc64630c4ccdd491923827?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c71e9f535bb92ffefbeb\n",
+      "View: https://api.biosimulations.org/runs/66c4c71e9f535bb92ffefbeb\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c71e9f535bb92ffefbeb/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c71e9f535bb92ffefbeb?includeOutput=true\n"
      ]
     },
     {
@@ -440,7 +453,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"rbapy\",\"simulatorVersion\":\"1.0.2\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=762c8555ab614c258f06df395558c712\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=1fb55551f1564f45b85cc3e62576dc6e\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -448,10 +461,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64660c4ccdd49192382a\n",
-      "View: https://api.biosimulations.org/runs/66bc64660c4ccdd49192382a\n",
-      "Downloads: https://api.biosimulations.org/results/66bc64660c4ccdd49192382a/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc64660c4ccdd49192382a?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c7204da143765fa78738\n",
+      "View: https://api.biosimulations.org/runs/66c4c7204da143765fa78738\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c7204da143765fa78738/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c7204da143765fa78738?includeOutput=true\n"
      ]
     },
     {
@@ -463,7 +476,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"smoldyn\",\"simulatorVersion\":\"2.72\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=53c6f673860c44bdb476c8afa656ccdd\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f0044384e7b041f5a9ec67dcd10183fa\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -471,10 +484,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc64680c4ccdd491923847\n",
-      "View: https://api.biosimulations.org/runs/66bc64680c4ccdd491923847\n",
-      "Downloads: https://api.biosimulations.org/results/66bc64680c4ccdd491923847/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc64680c4ccdd491923847?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c7224da143765fa7873d\n",
+      "View: https://api.biosimulations.org/runs/66c4c7224da143765fa7873d\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c7224da143765fa7873d/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c7224da143765fa7873d?includeOutput=true\n"
      ]
     },
     {
@@ -486,7 +499,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"tellurium\",\"simulatorVersion\":\"2.2.8\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=5ea5711967054c93a35895fab7fc782c\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=873875592d194849b7cdf3f69eb53e67\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -494,10 +507,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc646aa641708179ad31a4\n",
-      "View: https://api.biosimulations.org/runs/66bc646aa641708179ad31a4\n",
-      "Downloads: https://api.biosimulations.org/results/66bc646aa641708179ad31a4/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc646aa641708179ad31a4?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c7249f535bb92ffefc19\n",
+      "View: https://api.biosimulations.org/runs/66c4c7249f535bb92ffefc19\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c7249f535bb92ffefc19/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c7249f535bb92ffefc19?includeOutput=true\n"
      ]
     },
     {
@@ -509,7 +522,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"vcell\",\"simulatorVersion\":\"7.5.0.99\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=f97f781db1ec4812b2769295024b8c7c\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=327013065b91432ea3e5b3addb6a0427\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -517,10 +530,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc646e0c4ccdd491923866\n",
-      "View: https://api.biosimulations.org/runs/66bc646e0c4ccdd491923866\n",
-      "Downloads: https://api.biosimulations.org/results/66bc646e0c4ccdd491923866/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc646e0c4ccdd491923866?includeOutput=true\n"
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c72893c284abde6a0a1a\n",
+      "View: https://api.biosimulations.org/runs/66c4c72893c284abde6a0a1a\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c72893c284abde6a0a1a/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c72893c284abde6a0a1a?includeOutput=true\n"
      ]
     },
     {
@@ -532,7 +545,7 @@
       "pyNeuroML >>> DEBUG - data is:\n",
       "{'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}\n",
       "pyNeuroML >>> INFO - multipart encoded data is <MultipartEncoder: {'file': ('LEMS_NML2_Ex9_FN_missing_xmlns.omex', <_io.BufferedReader name='LEMS_NML2_Ex9_FN_missing_xmlns.omex'>), 'simulationRun': (None, '{\"name\":\"test\",\"simulator\":\"xpp\",\"simulatorVersion\":\"8.0\",\"maxTime\":20,\"cpus\":1,\"memory\":8,\"purpose\":\"academic\",\"email\":\"\",\"envVars\":[]}')}>\n",
-      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=b0571c54189246b5acfbdc36c592583f\n",
+      "pyNeuroML >>> INFO - with content type: multipart/form-data; boundary=cbb375f0b6794f548c8b243a48ed9eb9\n",
       "pyNeuroML >>> INFO - Submitting archive to biosimulations\n"
      ]
     },
@@ -540,10 +553,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66bc6470f29e09b32cb71907\n",
-      "View: https://api.biosimulations.org/runs/66bc6470f29e09b32cb71907\n",
-      "Downloads: https://api.biosimulations.org/results/66bc6470f29e09b32cb71907/download\n",
-      "Logs: https://api.biosimulations.org/logs/66bc6470f29e09b32cb71907?includeOutput=true\n",
+      "Submitted LEMS_NML2_Ex9_FN_missing_xmlns.omex successfully with id: 66c4c72a9f535bb92ffefc37\n",
+      "View: https://api.biosimulations.org/runs/66c4c72a9f535bb92ffefc37\n",
+      "Downloads: https://api.biosimulations.org/results/66c4c72a9f535bb92ffefc37/download\n",
+      "Logs: https://api.biosimulations.org/logs/66c4c72a9f535bb92ffefc37?includeOutput=true\n",
       "Downloading amici results...\n",
       "Downloading brian2 results...\n",
       "Downloading bionetgen results...\n",
@@ -565,57 +578,132 @@
       "Downloading tellurium results...\n",
       "Downloading vcell results...\n",
       "Downloading xpp results...\n",
-      "Moving remote_results\\amici\\outputs\\tmp472787\\d1.pdf to d1_plots_remote\\amici_d1.pdf\n",
-      "Moving remote_results\\bionetgen\\outputs\\tmp345301\\d1.pdf to d1_plots_remote\\bionetgen_d1.pdf\n",
-      "Moving remote_results\\boolnet\\outputs\\tmp110064\\d1.pdf to d1_plots_remote\\boolnet_d1.pdf\n",
-      "Moving remote_results\\cbmpy\\outputs\\tmp806249\\d1.pdf to d1_plots_remote\\cbmpy_d1.pdf\n",
-      "Moving remote_results\\cobrapy\\outputs\\tmp591048\\d1.pdf to d1_plots_remote\\cobrapy_d1.pdf\n",
-      "Moving remote_results\\copasi\\outputs\\tmp631588\\d1.pdf to d1_plots_remote\\copasi_d1.pdf\n",
-      "Moving remote_results\\gillespy2\\outputs\\tmp681509\\d1.pdf to d1_plots_remote\\gillespy2_d1.pdf\n",
-      "Moving remote_results\\ginsim\\outputs\\tmp705876\\d1.pdf to d1_plots_remote\\ginsim_d1.pdf\n",
-      "Moving remote_results\\libsbmlsim\\outputs\\tmp986325\\d1.pdf to d1_plots_remote\\libsbmlsim_d1.pdf\n",
-      "Moving remote_results\\masspy\\outputs\\tmp374428\\d1.pdf to d1_plots_remote\\masspy_d1.pdf\n",
-      "Moving remote_results\\pysces\\outputs\\tmp757204\\d1.pdf to d1_plots_remote\\pysces_d1.pdf\n",
-      "Moving remote_results\\rbapy\\outputs\\tmp601277\\d1.pdf to d1_plots_remote\\rbapy_d1.pdf\n",
-      "Moving remote_results\\tellurium\\outputs\\tmp774548\\d1.pdf to d1_plots_remote\\tellurium_d1.pdf\n",
-      "Removed remote_results folder\n",
+      "Moving tests\\remote_results\\amici\\outputs\\tmp445545\\d1.pdf to tests\\d1_plots_remote\\amici_d1.pdf\n",
+      "Moving tests\\remote_results\\bionetgen\\outputs\\tmp713444\\d1.pdf to tests\\d1_plots_remote\\bionetgen_d1.pdf\n",
+      "Moving tests\\remote_results\\boolnet\\outputs\\tmp993713\\d1.pdf to tests\\d1_plots_remote\\boolnet_d1.pdf\n",
+      "Moving tests\\remote_results\\cbmpy\\outputs\\tmp924986\\d1.pdf to tests\\d1_plots_remote\\cbmpy_d1.pdf\n",
+      "Moving tests\\remote_results\\cobrapy\\outputs\\tmp796378\\d1.pdf to tests\\d1_plots_remote\\cobrapy_d1.pdf\n",
+      "Moving tests\\remote_results\\copasi\\outputs\\tmp39638\\d1.pdf to tests\\d1_plots_remote\\copasi_d1.pdf\n",
+      "Moving tests\\remote_results\\gillespy2\\outputs\\tmp785210\\d1.pdf to tests\\d1_plots_remote\\gillespy2_d1.pdf\n",
+      "Moving tests\\remote_results\\ginsim\\outputs\\tmp311223\\d1.pdf to tests\\d1_plots_remote\\ginsim_d1.pdf\n",
+      "Moving tests\\remote_results\\libsbmlsim\\outputs\\tmp733415\\d1.pdf to tests\\d1_plots_remote\\libsbmlsim_d1.pdf\n",
+      "Moving tests\\remote_results\\masspy\\outputs\\tmp970012\\d1.pdf to tests\\d1_plots_remote\\masspy_d1.pdf\n",
+      "Moving tests\\remote_results\\pysces\\outputs\\tmp729410\\d1.pdf to tests\\d1_plots_remote\\pysces_d1.pdf\n",
+      "Moving tests\\remote_results\\rbapy\\outputs\\tmp656630\\d1.pdf to tests\\d1_plots_remote\\rbapy_d1.pdf\n",
+      "Moving tests\\remote_results\\tellurium\\outputs\\tmp33488\\d1.pdf to tests\\d1_plots_remote\\tellurium_d1.pdf\n",
+      "Removed tests\\remote_results folder\n",
       "Running amici\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\amici\n",
       "Running brian2\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\brian2\n",
       "Running bionetgen\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\bionetgen\n",
       "Running boolnet\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\boolnet\n",
       "Running cbmpy\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\cbmpy\n",
       "Running cobrapy\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\cobrapy\n",
       "Running copasi\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\copasi\n",
       "Running gillespy2\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\gillespy2\n",
       "Running ginsim\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\ginsim\n",
       "Running libsbmlsim\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\libsbmlsim\n",
       "Running masspy\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\masspy\n",
       "Running netpyne\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\netpyne\n",
       "Running neuron\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\neuron\n",
       "Running opencor\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\opencor\n",
       "Running pyneuroml\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\pyneuroml\n",
       "Running pysces\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\pysces\n",
       "Running rbapy\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\rbapy\n",
       "Running smoldyn\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\smoldyn\n",
       "Running tellurium\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\tellurium\n",
       "Running vcell\n",
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\vcell\n",
       "Running xpp\n",
-      "Removed output folder\n"
+      "c:\\Users\\prins\\GitHub\\SBMLShowcase\\SBML\\tests\\local_results\\xpp\n",
+      "file paths: ['tests\\\\local_results\\\\amici\\\\tmp570097\\\\d1.pdf', 'tests\\\\local_results\\\\bionetgen\\\\tmp137382\\\\d1.pdf', 'tests\\\\local_results\\\\boolnet\\\\tmp324009\\\\d1.pdf', 'tests\\\\local_results\\\\cbmpy\\\\tmp359591\\\\d1.pdf', 'tests\\\\local_results\\\\cobrapy\\\\tmp259926\\\\d1.pdf', 'tests\\\\local_results\\\\copasi\\\\tmp179627\\\\d1.pdf', 'tests\\\\local_results\\\\gillespy2\\\\tmp466262\\\\d1.pdf', 'tests\\\\local_results\\\\ginsim\\\\tmp931151\\\\d1.pdf', 'tests\\\\local_results\\\\libsbmlsim\\\\tmp489428\\\\d1.pdf', 'tests\\\\local_results\\\\masspy\\\\tmp159869\\\\d1.pdf', 'tests\\\\local_results\\\\pysces\\\\tmp959556\\\\d1.pdf', 'tests\\\\local_results\\\\rbapy\\\\tmp804849\\\\d1.pdf', 'tests\\\\local_results\\\\tellurium\\\\tmp614468\\\\d1.pdf']\n",
+      "Moving tests\\local_results\\amici\\tmp570097\\d1.pdf to tests\\d1_plots_local\\amici_d1.pdf\n",
+      "Moving tests\\local_results\\bionetgen\\tmp137382\\d1.pdf to tests\\d1_plots_local\\bionetgen_d1.pdf\n",
+      "Moving tests\\local_results\\boolnet\\tmp324009\\d1.pdf to tests\\d1_plots_local\\boolnet_d1.pdf\n",
+      "Moving tests\\local_results\\cbmpy\\tmp359591\\d1.pdf to tests\\d1_plots_local\\cbmpy_d1.pdf\n",
+      "Moving tests\\local_results\\cobrapy\\tmp259926\\d1.pdf to tests\\d1_plots_local\\cobrapy_d1.pdf\n",
+      "Moving tests\\local_results\\copasi\\tmp179627\\d1.pdf to tests\\d1_plots_local\\copasi_d1.pdf\n",
+      "Moving tests\\local_results\\gillespy2\\tmp466262\\d1.pdf to tests\\d1_plots_local\\gillespy2_d1.pdf\n",
+      "Moving tests\\local_results\\ginsim\\tmp931151\\d1.pdf to tests\\d1_plots_local\\ginsim_d1.pdf\n",
+      "Moving tests\\local_results\\libsbmlsim\\tmp489428\\d1.pdf to tests\\d1_plots_local\\libsbmlsim_d1.pdf\n",
+      "Moving tests\\local_results\\masspy\\tmp159869\\d1.pdf to tests\\d1_plots_local\\masspy_d1.pdf\n",
+      "Moving tests\\local_results\\pysces\\tmp959556\\d1.pdf to tests\\d1_plots_local\\pysces_d1.pdf\n",
+      "Moving tests\\local_results\\rbapy\\tmp804849\\d1.pdf to tests\\d1_plots_local\\rbapy_d1.pdf\n",
+      "Moving tests\\local_results\\tellurium\\tmp614468\\d1.pdf to tests\\d1_plots_local\\tellurium_d1.pdf\n",
+      "Removed tests\\local_results folder\n"
      ]
+    },
+    {
+     "data": {
+      "text/markdown": [
+       "## Compatibility Biosimulator engines (L = local, R = remote)"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/markdown": [
+       "|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                              | Compat (L)                                                                                                                                                                                                                                                                                                                              | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                                                            | d1 (R)                                                     | d1 (L)                                                    |\n",
+       "|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|:----------------------------------------------------------|\n",
+       "|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with amici</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href=\"tests\\d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"tests\\d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
+       "|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href=\"tests\\d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"tests\\d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
+       "|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href=\"tests\\d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"tests\\d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
+       "|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with brian2</details>                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                            |                                                           |\n",
+       "|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cbmpy</details>                                                                                                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href=\"tests\\d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"tests\\d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
+       "|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with cobrapy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href=\"tests\\d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"tests\\d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
+       "|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with copasi</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href=\"tests\\d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"tests\\d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
+       "|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with gillespy2</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href=\"tests\\d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"tests\\d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
+       "|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href=\"tests\\d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"tests\\d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
+       "|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with libsbmlsim</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href=\"tests\\d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"tests\\d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
+       "| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with masspy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href=\"tests\\d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"tests\\d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
+       "| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with netpyne</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                            |                                                           |\n",
+       "| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                            |                                                           |\n",
+       "| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                            |                                                           |\n",
+       "| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                            |                                                           |\n",
+       "| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with pysces</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpr1stywf8/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpr1stywf8/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href=\"tests\\d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"tests\\d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
+       "| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href=\"tests\\d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"tests\\d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
+       "| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                            |                                                           |\n",
+       "| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with tellurium</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href=\"tests\\d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"tests\\d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
+       "| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are compatible with vcell</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                            |                                                           |\n",
+       "| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SBML', 'SED-ML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                            |                                                           |"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
     }
    ],
    "source": [
-    "\n",
     "\n",
     "#########################################################################################\n",
     "# Run remotely\n",
     "#########################################################################################\n",
     "\n",
     "remote_output_dir = 'remote_results'\n",
+    "remote_output_dir = os.path.join(test_folder, remote_output_dir)\n",
     "\n",
     "download_links_dict = dict()\n",
     "for e in engines.keys():\n",
-    "    download_link = utils.run_biosimulators_remote(e, sedml_filepath, sbml_filepath)\n",
+    "    download_link = utils.run_biosimulators_remote(e, sedml_file_name, sbml_file_name)\n",
     "    download_links_dict[e] = download_link\n",
     "\n",
     "extract_dir_dict = dict()\n",
@@ -623,7 +711,7 @@
     "    extract_dir = utils.get_remote_results(e, link, remote_output_dir)\n",
     "    extract_dir_dict[e] = extract_dir\n",
     "\n",
-    "results_remote = dict()\n",
+    "results = dict()\n",
     "for e, extract_dir in extract_dir_dict.items():\n",
     "    status = \"\"\n",
     "    error_message = \"\"\n",
@@ -645,7 +733,7 @@
     "            exception_type = exception['type'] \n",
     "        else:\n",
     "            status = None\n",
-    "        results_remote[e] = [status, error_message, exception_type] \n",
+    "        results[e] = [status, error_message, exception_type] \n",
     "\n",
     "file_paths = utils.find_files(remote_output_dir, '.pdf')\n",
     "utils.move_d1_files(file_paths, d1_plots_remote_dir)\n",
@@ -661,77 +749,31 @@
     "\n",
     "results_local = {}\n",
     "\n",
-    "output_folder = 'output'\n",
+    "output_folder = 'local_results'\n",
+    "local_output_dir = os.path.join(test_folder, output_folder)\n",
     "\n",
     "for e in engines.keys():\n",
     "    print('Running ' + e)\n",
-    "    output_dir = os.path.abspath(os.path.join(output_folder, e))\n",
-    "    record = utils.run_biosimulators_docker(e, sedml_filepath, sbml_filepath, output_dir=output_dir)\n",
+    "    local_output_dir_e = os.path.abspath(os.path.join(local_output_dir, e))\n",
+    "    print(local_output_dir_e)\n",
+    "    record = utils.run_biosimulators_docker(e, sedml_file_name, sbml_file_name, output_dir=local_output_dir_e)\n",
     "    results_local[e] = record\n",
     "\n",
-    "file_paths = utils.find_files(output_folder, '.pdf')\n",
+    "file_paths = utils.find_files(local_output_dir, '.pdf')\n",
+    "print('file paths:', file_paths)\n",
     "utils.move_d1_files(file_paths, d1_plots_local_dir)\n",
     "\n",
     "# if it exists remove the output folder\n",
-    "if os.path.exists(output_folder):\n",
-    "    shutil.rmtree(output_folder)\n",
-    "    print('Removed ' + output_folder + ' folder')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/markdown": [
-       "## Compatibility Biosimulator engines (L = local, R = remote)"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/markdown": [
-       "|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                             | Compat (L)                                                                                                                                                                                                                                                                                                                             | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                   | d1 (R)                                               | d1 (L)                                              |\n",
-       "|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|\n",
-       "|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\amici_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\amici_d1.pdf\">plot</a>      |\n",
-       "|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\bionetgen_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\bionetgen_d1.pdf\">plot</a>  |\n",
-       "|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\boolnet_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\boolnet_d1.pdf\">plot</a>    |\n",
-       "|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cbmpy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\cbmpy_d1.pdf\">plot</a>      |\n",
-       "|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\cobrapy_d1.pdf\">plot</a>    | <a href=\"d1_plots_local\\cobrapy_d1.pdf\">plot</a>    |\n",
-       "|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\copasi_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\copasi_d1.pdf\">plot</a>     |\n",
-       "|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\gillespy2_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\gillespy2_d1.pdf\">plot</a>  |\n",
-       "|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\ginsim_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\ginsim_d1.pdf\">plot</a>     |\n",
-       "|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                   |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\libsbmlsim_d1.pdf\">plot</a> | <a href=\"d1_plots_local\\libsbmlsim_d1.pdf\">plot</a> |\n",
-       "| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    \t`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\masspy_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\masspy_d1.pdf\">plot</a>     |\n",
-       "| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span>    | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with neuron. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with pyneuroml. The following file types will be compatible ['SED-ML', 'LEMS', 'NeuroML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmprlw_6w38/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmprlw_6w38/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\pysces_d1.pdf\">plot</a>     | <a href=\"d1_plots_local\\pysces_d1.pdf\">plot</a>     |\n",
-       "| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style=\"color:red;\">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\rbapy_d1.pdf\">plot</a>      | <a href=\"d1_plots_local\\rbapy_d1.pdf\">plot</a>      |\n",
-       "| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> | <a href=\"d1_plots_remote\\tellurium_d1.pdf\">plot</a>  | <a href=\"d1_plots_local\\tellurium_d1.pdf\">plot</a>  |\n",
-       "| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |\n",
-       "| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style=\"color:darkred;\"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. Tese are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```</details> |                                                      |                                                     |"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
+    "if os.path.exists(local_output_dir):\n",
+    "    shutil.rmtree(local_output_dir)\n",
+    "    print('Removed ' + local_output_dir + ' folder')\n",
     "\n",
     "#########################################################################################\n",
     "# process results and save markdown table\n",
     "#########################################################################################\n",
     "\n",
-    "results_table = utils.create_results_table(results_remote, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)\n",
-    "results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)\n",
+    "results_table = utils.create_results_table(results, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_remote_dir)\n",
+    "results_table_local = utils.create_results_table(results_local, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_local_dir)\n",
     "\n",
     "# rename cols to distinguish between local and remote results except for Engine column\n",
     "results_table.columns = [str(col) + ' (R)' if col != 'Engine' else str(col) for col in results_table.columns]\n",
@@ -739,7 +781,7 @@
     "\n",
     "# combine remote and local results\n",
     "combined_results = pd.merge(results_table, results_table_local, on='Engine', how='outer')\n",
-    "# combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))\n",
+    "combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))\n",
     "\n",
     "cols_order = ['Engine', 'pass / FAIL (R)', 'pass / FAIL (L)',\\\n",
     "               'Compat (R)', 'Compat (L)', \\\n",
@@ -748,9 +790,10 @@
     "               'd1 (R)', 'd1 (L)']\n",
     "\n",
     "combined_results = combined_results[cols_order]\n",
+    "\n",
     "# add a table title\n",
     "display_markdown('## Compatibility Biosimulator engines (L = local, R = remote)', raw=True)\n",
-    "display_markdown(combined_results.to_markdown(), raw=True)\n"
+    "display_markdown(combined_results.to_markdown(), raw=True)"
    ]
   }
  ],
diff --git a/SBML/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py
similarity index 65%
rename from SBML/test_compatibility_biosimulators.py
rename to SBML/tests/test_compatibility_biosimulators.py
index 000d316..6c50b1b 100644
--- a/SBML/test_compatibility_biosimulators.py
+++ b/SBML/tests/test_compatibility_biosimulators.py
@@ -7,7 +7,11 @@
 '''
 
 import sys
-sys.path.append("..")
+import os
+
+# Add the parent directory to the Python path
+parent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
 import utils
 import os
 import pandas as pd
@@ -15,29 +19,51 @@
 import yaml
 import argparse
 
-parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines')
-parser.add_argument('--output-dir',action='store',default='d1_plots',help='prefix of the output directory where the d1 plots will be saved')
-args = parser.parse_args()
+# Save the current working directory
+cwd = os.getcwd()
+print('Current working directory:', cwd)
+
+# SBML folder is one folder up relative to cwd
+path_to_sbml_folder = os.path.abspath(os.path.join(cwd, os.pardir))
+print('Path to SBML folder:', path_to_sbml_folder)
+
+# change the working directory to the SBML folder
+os.chdir(path_to_sbml_folder)
+print('Changed working directory to:', os.getcwd())
 
-d1_plots_remote_dir = args.output_dir + '_remote'
-d1_plots_local_dir = args.output_dir + '_local'
+sbml_file_name = 'LEMS_NML2_Ex9_FN.sbml'
+sedml_file_name = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
 
-sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml'
-sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
+sbml_file_path = os.path.join(path_to_sbml_folder, sbml_file_name)
+sedml_file_path = os.path.join(path_to_sbml_folder, sedml_file_name)
 
 engines = utils.engines
 types_dict = utils.types_dict
 
+print('Path to SED-ML file:', sedml_file_path)
+print('Path to SBML file:', sbml_file_path)
+
+parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines')
+parser.add_argument('--output-dir',action='store',default='d1_plots',help='prefix of the output directory where the d1 plots will be saved')
+args = parser.parse_args()
+
+test_folder = 'tests'
+
+d1_plots_remote_dir = os.path.join(test_folder, args.output_dir + '_remote')
+d1_plots_local_dir = os.path.join(test_folder, args.output_dir + '_local')
+
+print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir)
 
 #########################################################################################
 # Run remotely
 #########################################################################################
 
 remote_output_dir = 'remote_results'
+remote_output_dir = os.path.join(test_folder, remote_output_dir)
 
 download_links_dict = dict()
 for e in engines.keys():
-    download_link = utils.run_biosimulators_remote(e, sedml_filepath, sbml_filepath)
+    download_link = utils.run_biosimulators_remote(e, sedml_file_name, sbml_file_name)
     download_links_dict[e] = download_link
 
 extract_dir_dict = dict()
@@ -83,28 +109,31 @@
 
 results_local = {}
 
-output_folder = 'output'
+output_folder = 'local_results'
+local_output_dir = os.path.join(test_folder, output_folder)
 
 for e in engines.keys():
     print('Running ' + e)
-    output_dir = os.path.abspath(os.path.join(output_folder, e))
-    record = utils.run_biosimulators_docker(e, sedml_filepath, sbml_filepath, output_dir=output_dir)
+    local_output_dir_e = os.path.abspath(os.path.join(local_output_dir, e))
+    print(local_output_dir_e)
+    record = utils.run_biosimulators_docker(e, sedml_file_name, sbml_file_name, output_dir=local_output_dir_e)
     results_local[e] = record
 
-file_paths = utils.find_files(output_folder, '.pdf')
+file_paths = utils.find_files(local_output_dir, '.pdf')
+print('file paths:', file_paths)
 utils.move_d1_files(file_paths, d1_plots_local_dir)
 
 # if it exists remove the output folder
-if os.path.exists(output_folder):
-    shutil.rmtree(output_folder)
-    print('Removed ' + output_folder + ' folder')
+if os.path.exists(local_output_dir):
+    shutil.rmtree(local_output_dir)
+    print('Removed ' + local_output_dir + ' folder')
 
 #########################################################################################
 # process results and save markdown table
 #########################################################################################
 
-results_table = utils.create_results_table(results, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_remote_dir)
-results_table_local = utils.create_results_table(results_local, types_dict, sbml_filepath, sedml_filepath, engines, d1_plots_local_dir)
+results_table = utils.create_results_table(results, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_remote_dir)
+results_table_local = utils.create_results_table(results_local, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_local_dir)
 
 # rename cols to distinguish between local and remote results except for Engine column
 results_table.columns = [str(col) + ' (R)' if col != 'Engine' else str(col) for col in results_table.columns]
@@ -122,6 +151,7 @@
 
 combined_results = combined_results[cols_order]
 
-# save the results to a markdown file
-with open('results_compatibility_biosimulators.md', 'w') as f:
+path_to_results = os.path.join(test_folder, 'results_compatibility_biosimulators.md')
+print('Saving results to:', path_to_results)
+with open(path_to_results, 'w') as f:
     f.write(combined_results.to_markdown())
diff --git a/SBML/test_tellurium.py b/SBML/tests/test_tellurium.py
similarity index 80%
rename from SBML/test_tellurium.py
rename to SBML/tests/test_tellurium.py
index 362bf02..8f2e101 100644
--- a/SBML/test_tellurium.py
+++ b/SBML/tests/test_tellurium.py
@@ -1,9 +1,15 @@
 
 import tellurium as te
 te.setDefaultPlottingEngine('matplotlib')
-
+import os
 import sys
 
+path_to_sbml_folder = os.path.abspath(os.path.join(os.getcwd(), os.pardir))
+
+# change the working directory to the SBML folder
+os.chdir(path_to_sbml_folder)
+print('Changed working directory to:', os.getcwd())
+
 sedml_file='LEMS_NML2_Ex9_FN.sedml'
 if len(sys.argv)>1:
     sedml_file=sys.argv[1]
diff --git a/SBML/validateAll.sh b/SBML/tests/validateAll.sh
old mode 100755
new mode 100644
similarity index 86%
rename from SBML/validateAll.sh
rename to SBML/tests/validateAll.sh
index 12ad860..f54b99a
--- a/SBML/validateAll.sh
+++ b/SBML/tests/validateAll.sh
@@ -3,6 +3,9 @@ set -ex
 
 ### A script to validate SBML & SED-ML files using pyNeuroML
 
+# change directory to one folder up
+cd ..
+
 pynml -validate-sbml *.sbml
 
 echo "All SBML files valid"

From 5cc1317d6a074da79210c61e7489636d60efda50 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 21 Aug 2024 08:29:10 +0100
Subject: [PATCH 34/71] Fix typo in validateAll.sh script

---
 .github/workflows/non-omv.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index 985664c..bb422a6 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -47,7 +47,7 @@ jobs:
       run: |
         pip install pyNeuroML pyNeuroML[annotations]
         cd SBML
-        ./tests/alidateAll.sh
+        ./tests/validateAll.sh
 
     - name: test omex file creation
       run: |

From 8e0182c947e5ab6047da2906408cc7b1afce00f1 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 21 Aug 2024 10:02:17 +0100
Subject: [PATCH 35/71] refactor test_compatability_biosimulators

---
 .../results_compatibility_biosimulators.md    |   6 +-
 .../tests/test_compatibility_biosimulators.py |   4 +-
 utils/__init__.py                             | 149 ++++++++++++++++++
 3 files changed, 154 insertions(+), 5 deletions(-)

diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index 7a25681..995762c 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -12,10 +12,10 @@
 |  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
 | 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_d1.pdf">plot</a>     |
 | 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                            |                                                           |
-| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                            |                                                           |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                            |                                                           |
 | 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                            |                                                           |
-| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'LEMS', 'SED-ML']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                            |                                                           |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp091bjymu/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp091bjymu/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_d1.pdf">plot</a>     |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                            |                                                           |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp36492nwm/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp36492nwm/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_d1.pdf">plot</a>     |
 | 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_d1.pdf">plot</a>      |
 | 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                            |                                                           |
 | 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_d1.pdf">plot</a>  |
diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py
index 6c50b1b..b2c1d24 100644
--- a/SBML/tests/test_compatibility_biosimulators.py
+++ b/SBML/tests/test_compatibility_biosimulators.py
@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 
-'''
+"""
 This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file.
 It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation.
 The results are then displayed in a table and saved to a markdown file.
-'''
+"""
 
 import sys
 import os
diff --git a/utils/__init__.py b/utils/__init__.py
index 0161227..b617427 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -1115,3 +1115,152 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng
     results_table['Engine'] = results_table['Engine'].apply(lambda x:  collapsible_content(f'{engines[x]["url"]}<br>{engines[x]["status"]}', x))
 
     return results_table
+
+
+
+def run_biosimulators_remotely(sedml_file_name, 
+                               sbml_file_name, 
+                               d1_plots_remote_dir, 
+                               engines=engines, 
+                               test_folder='tests'):
+    
+    """ run with directory pointing towards the location of the sedml and sbml files"""
+    
+    remote_output_dir = 'remote_results'
+    remote_output_dir = os.path.join(test_folder, remote_output_dir)
+
+    download_links_dict = dict()
+    for e in engines.keys():
+        download_link = run_biosimulators_remote(e, sedml_file_name, sbml_file_name)
+        download_links_dict[e] = download_link
+
+    extract_dir_dict = dict()
+    for e, link in download_links_dict.items():
+        extract_dir = get_remote_results(e, link, remote_output_dir)
+        extract_dir_dict[e] = extract_dir
+
+    results_remote = dict()
+    for e, extract_dir in extract_dir_dict.items():
+        status = ""
+        error_message = ""
+        exception_type = ""
+
+        log_yml_path = find_file_in_dir('log.yml', extract_dir)[0]
+        if not log_yml_path:
+            status = None
+            error_message = 'log.yml not found'
+            continue
+        with open(log_yml_path) as f:
+            log_yml_dict = yaml.safe_load(f)
+            if log_yml_dict['status'] == 'SUCCEEDED':
+                status = 'pass'
+            elif log_yml_dict['status'] == 'FAILED':
+                status = 'FAIL'
+                exception = log_yml_dict['exception']
+                error_message = exception['message']
+                exception_type = exception['type'] 
+            else:
+                status = None
+            results_remote[e] = [status, error_message, exception_type] 
+
+    file_paths = find_files(remote_output_dir, '.pdf')
+    move_d1_files(file_paths, d1_plots_remote_dir)
+
+    # remove the remote results directory
+    if os.path.exists(remote_output_dir):
+        shutil.rmtree(remote_output_dir)
+        print('Removed ' + remote_output_dir + ' folder')
+
+    return results_remote
+
+def run_biosimulators_locally(sedml_file_name, 
+                              sbml_file_name, 
+                              d1_plots_local_dir, 
+                              engines=engines, 
+                              test_folder='tests'):
+    results_local = {}
+
+    output_folder = 'local_results'
+    local_output_dir = os.path.join(test_folder, output_folder)
+
+    for e in engines.keys():
+        print('Running ' + e)
+        local_output_dir_e = os.path.abspath(os.path.join(local_output_dir, e))
+        print(local_output_dir_e)
+        record = run_biosimulators_docker(e, sedml_file_name, sbml_file_name, output_dir=local_output_dir_e)
+        results_local[e] = record
+
+    file_paths = find_files(local_output_dir, '.pdf')
+    print('file paths:', file_paths)
+    move_d1_files(file_paths, d1_plots_local_dir)
+
+    # if it exists remove the output folder
+    if os.path.exists(local_output_dir):
+        shutil.rmtree(local_output_dir)
+        print('Removed ' + local_output_dir + ' folder')
+
+    return results_local
+
+
+def create_combined_results_table(results_remote, 
+                                  results_local, 
+                                  sedml_file_name, 
+                                  sbml_file_name, 
+                                  d1_plots_local_dir, 
+                                  d1_plots_remote_dir,
+                                  engines=engines, 
+                                  test_folder='tests'):
+    
+    results_table_remote = create_results_table(results_remote, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_remote_dir)
+    results_table_local = create_results_table(results_local, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_local_dir)
+
+    # rename cols to distinguish between local and remote results except for Engine column
+    results_table_remote.columns = [str(col) + ' (R)' if col != 'Engine' else str(col) for col in results_table_remote.columns]
+    results_table_local.columns = [str(col) + ' (L)' if col != 'Engine' else str(col) for col in results_table_local.columns]
+
+    # combine remote and local results
+    combined_results = pd.merge(results_table_remote, results_table_local, on='Engine', how='outer')
+    combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))
+
+    cols_order = ['Engine', 'pass / FAIL (R)', 'pass / FAIL (L)',\
+                'Compat (R)', 'Compat (L)', \
+                'Type (R)', \
+                'Error (R)', 'Error (L)', \
+                'd1 (R)', 'd1 (L)']
+
+    combined_results = combined_results[cols_order]
+
+    path_to_results = os.path.join(test_folder, 'results_compatibility_biosimulators.md')
+    print('Saving results to:', path_to_results)
+    with open(path_to_results, 'w') as f:
+        f.write(combined_results.to_markdown())
+
+    return combined_results
+
+
+def run_biosimulators_remotely_and_locally(sedml_file_name, 
+                                 sbml_file_name,
+                                 d1_plots_remote_dir, 
+                                 d1_plots_local_dir,
+                                 engines=engines, test_folder='tests'):
+    
+    results_remote = run_biosimulators_remotely(sedml_file_name=sedml_file_name, 
+                                    sbml_file_name=sbml_file_name,
+                                    d1_plots_remote_dir=d1_plots_remote_dir, 
+                                    engines=engines, test_folder=test_folder)
+    
+    results_local = run_biosimulators_locally(sedml_file_name=sedml_file_name, 
+                                    sbml_file_name=sbml_file_name,
+                                    d1_plots_local_dir=d1_plots_local_dir, 
+                                    engines=engines, test_folder=test_folder)
+
+    results_table = create_combined_results_table(results_remote, 
+                                    results_local, 
+                                    sedml_file_name=sedml_file_name, 
+                                    sbml_file_name=sbml_file_name,
+                                    d1_plots_local_dir=d1_plots_local_dir,
+                                    d1_plots_remote_dir=d1_plots_remote_dir, 
+                                    engines=engines, 
+                                    test_folder=test_folder)
+    
+    return results_table
\ No newline at end of file

From 9239b3af732e039d23f437cd165d7422a497ebd5 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 21 Aug 2024 10:08:30 +0100
Subject: [PATCH 36/71] update test_tellurium.py path for github actions

---
 .github/workflows/non-omv.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index bb422a6..1f59741 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -41,7 +41,7 @@ jobs:
 
         cd ../SBML
         pip install python-libsedml
-        python test_tellurium.py 
+        python ./tests/test_tellurium.py 
 
     - name: Test validity of files
       run: |

From e840822d5f8c60037df4cac9aff8f96f98941d40 Mon Sep 17 00:00:00 2001
From: Robert Vickerstaff <r.vickerstaff@ucl.ac.uk>
Date: Wed, 21 Aug 2024 09:25:25 +0000
Subject: [PATCH 37/71] set execute permission for test script

---
 SBML/tests/validateAll.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 SBML/tests/validateAll.sh

diff --git a/SBML/tests/validateAll.sh b/SBML/tests/validateAll.sh
old mode 100644
new mode 100755

From 13547f6790c7765859f222558685c10e87e52a4a Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 21 Aug 2024 10:46:58 +0100
Subject: [PATCH 38/71] change path for running Test validity of files in
 github actions

---
 .github/workflows/non-omv.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index 1f59741..6428d52 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -46,7 +46,7 @@ jobs:
     - name: Test validity of files
       run: |
         pip install pyNeuroML pyNeuroML[annotations]
-        cd SBML
+        cd SBML/tests
         ./tests/validateAll.sh
 
     - name: test omex file creation

From 8d72303073f6672f5e595c63b265ac73997faf5c Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 21 Aug 2024 10:49:14 +0100
Subject: [PATCH 39/71] Adjust file path for running file validity tests in
 GitHub Actions

---
 .github/workflows/non-omv.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index 6428d52..82b76a4 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -47,7 +47,7 @@ jobs:
       run: |
         pip install pyNeuroML pyNeuroML[annotations]
         cd SBML/tests
-        ./tests/validateAll.sh
+        ./validateAll.sh
 
     - name: test omex file creation
       run: |

From 818fde163853200d1c5877ede52c7a9e2e7e5c63 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 21 Aug 2024 10:57:08 +0100
Subject: [PATCH 40/71] Switch to using the 'python script_name.py' form for
 test omex file creation

---
 .github/workflows/non-omv.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index 82b76a4..26a228b 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -53,7 +53,7 @@ jobs:
       run: |
         pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
         cd SBML        
-        ./tests/test_biosimulators_docker.py
+        python ./tests/test_biosimulators_docker.py
 
     - name: test biosimulators compatibility table creation
       run: |

From 74c64eeb020f756292243d83b683845fff74a08b Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 21 Aug 2024 11:00:16 +0100
Subject: [PATCH 41/71] Change test omex file creation path in GitHub Actions
 workflow

---
 .github/workflows/non-omv.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index 26a228b..e952b9b 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -52,8 +52,8 @@ jobs:
     - name: test omex file creation
       run: |
         pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
-        cd SBML        
-        python ./tests/test_biosimulators_docker.py
+        cd SBML/tests    
+        python ./test_biosimulators_docker.py
 
     - name: test biosimulators compatibility table creation
       run: |

From 798dd104f94f5a8778e1d743fbee8cb3058e1ccb Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 21 Aug 2024 11:04:29 +0100
Subject: [PATCH 42/71] Adjust file path for running
 test_compatibility_biosimulators.py in GitHub Actions workflow

---
 .github/workflows/non-omv.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index e952b9b..3cf4579 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -57,9 +57,9 @@ jobs:
 
     - name: test biosimulators compatibility table creation
       run: |
-        cd SBML
+        cd SBML/tests
         sudo rm -rf output
-        python ./tests/test_compatibility_biosimulators.py --output-dir=tmp_plots
+        python ./test_compatibility_biosimulators.py --output-dir=tmp_plots
 
 
     - name: Test test_suite output regeneration

From 8f7157d42b5bfce2b10c137a823111a89cde15e7 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 22 Aug 2024 09:41:11 +0100
Subject: [PATCH 43/71] Adjust test tellurium file paths for running tests in
 GitHub Actions workflow and print out the number of columns and rows, and
 first rows of test_compatibility_biosimulators results table for double check
 in GitHub actions

---
 .github/workflows/non-omv.yml                  | 4 ++--
 SBML/tests/test_compatibility_biosimulators.py | 4 ++++
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index 3cf4579..08d4fd1 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -39,9 +39,9 @@ jobs:
         cd tellurium
         python simple.py -nogui
 
-        cd ../SBML
+        cd ../SBML/tests
         pip install python-libsedml
-        python ./tests/test_tellurium.py 
+        python ./test_tellurium.py 
 
     - name: Test validity of files
       run: |
diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py
index b2c1d24..07f37ba 100644
--- a/SBML/tests/test_compatibility_biosimulators.py
+++ b/SBML/tests/test_compatibility_biosimulators.py
@@ -155,3 +155,7 @@
 print('Saving results to:', path_to_results)
 with open(path_to_results, 'w') as f:
     f.write(combined_results.to_markdown())
+
+print('Number of columns in md table:', len(combined_results.columns))
+print('Number of rows in md table:', len(combined_results))
+print(combined_results.head())

From 45313ff9ea5a2142cf31f96b349b548afb2819ce Mon Sep 17 00:00:00 2001
From: Stella Prins <s.prins@ucl.ac.uk>
Date: Thu, 22 Aug 2024 15:04:59 +0100
Subject: [PATCH 44/71] Adjust github actions names so that they all start with
 capital letter

---
 .github/workflows/non-omv.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index 08d4fd1..de3a9b4 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -49,13 +49,13 @@ jobs:
         cd SBML/tests
         ./validateAll.sh
 
-    - name: test omex file creation
+    - name: Test omex file creation
       run: |
         pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
         cd SBML/tests    
         python ./test_biosimulators_docker.py
 
-    - name: test biosimulators compatibility table creation
+    - name: Test biosimulators compatibility table creation
       run: |
         cd SBML/tests
         sudo rm -rf output

From a426c21219cc9f8930ef5bc60139e0fcd003f6cc Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 27 Aug 2024 09:51:13 +0100
Subject: [PATCH 45/71] Refactor test_compatibility_biosimulators.py to use a
 unified function for running biosimulators remotely and locally

---
 .../tests/test_compatibility_biosimulators.py | 110 +-----------------
 1 file changed, 5 insertions(+), 105 deletions(-)

diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py
index 07f37ba..5616050 100644
--- a/SBML/tests/test_compatibility_biosimulators.py
+++ b/SBML/tests/test_compatibility_biosimulators.py
@@ -54,108 +54,8 @@
 
 print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir)
 
-#########################################################################################
-# Run remotely
-#########################################################################################
-
-remote_output_dir = 'remote_results'
-remote_output_dir = os.path.join(test_folder, remote_output_dir)
-
-download_links_dict = dict()
-for e in engines.keys():
-    download_link = utils.run_biosimulators_remote(e, sedml_file_name, sbml_file_name)
-    download_links_dict[e] = download_link
-
-extract_dir_dict = dict()
-for e, link in download_links_dict.items():
-    extract_dir = utils.get_remote_results(e, link, remote_output_dir)
-    extract_dir_dict[e] = extract_dir
-
-results = dict()
-for e, extract_dir in extract_dir_dict.items():
-    status = ""
-    error_message = ""
-    exception_type = ""
-
-    log_yml_path = utils.find_file_in_dir('log.yml', extract_dir)[0]
-    if not log_yml_path:
-        status = None
-        error_message = 'log.yml not found'
-        continue
-    with open(log_yml_path) as f:
-        log_yml_dict = yaml.safe_load(f)
-        if log_yml_dict['status'] == 'SUCCEEDED':
-            status = 'pass'
-        elif log_yml_dict['status'] == 'FAILED':
-            status = 'FAIL'
-            exception = log_yml_dict['exception']
-            error_message = exception['message']
-            exception_type = exception['type'] 
-        else:
-            status = None
-        results[e] = [status, error_message, exception_type] 
-
-file_paths = utils.find_files(remote_output_dir, '.pdf')
-utils.move_d1_files(file_paths, d1_plots_remote_dir)
-
-# remove the remote results directory
-if os.path.exists(remote_output_dir):
-    shutil.rmtree(remote_output_dir)
-    print('Removed ' + remote_output_dir + ' folder')
-
-#########################################################################################
-# Run locally
-#########################################################################################
-
-results_local = {}
-
-output_folder = 'local_results'
-local_output_dir = os.path.join(test_folder, output_folder)
-
-for e in engines.keys():
-    print('Running ' + e)
-    local_output_dir_e = os.path.abspath(os.path.join(local_output_dir, e))
-    print(local_output_dir_e)
-    record = utils.run_biosimulators_docker(e, sedml_file_name, sbml_file_name, output_dir=local_output_dir_e)
-    results_local[e] = record
-
-file_paths = utils.find_files(local_output_dir, '.pdf')
-print('file paths:', file_paths)
-utils.move_d1_files(file_paths, d1_plots_local_dir)
-
-# if it exists remove the output folder
-if os.path.exists(local_output_dir):
-    shutil.rmtree(local_output_dir)
-    print('Removed ' + local_output_dir + ' folder')
-
-#########################################################################################
-# process results and save markdown table
-#########################################################################################
-
-results_table = utils.create_results_table(results, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_remote_dir)
-results_table_local = utils.create_results_table(results_local, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_local_dir)
-
-# rename cols to distinguish between local and remote results except for Engine column
-results_table.columns = [str(col) + ' (R)' if col != 'Engine' else str(col) for col in results_table.columns]
-results_table_local.columns = [str(col) + ' (L)' if col != 'Engine' else str(col) for col in results_table_local.columns]
-
-# combine remote and local results
-combined_results = pd.merge(results_table, results_table_local, on='Engine', how='outer')
-combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))
-
-cols_order = ['Engine', 'pass / FAIL (R)', 'pass / FAIL (L)',\
-               'Compat (R)', 'Compat (L)', \
-               'Type (R)', \
-               'Error (R)', 'Error (L)', \
-               'd1 (R)', 'd1 (L)']
-
-combined_results = combined_results[cols_order]
-
-path_to_results = os.path.join(test_folder, 'results_compatibility_biosimulators.md')
-print('Saving results to:', path_to_results)
-with open(path_to_results, 'w') as f:
-    f.write(combined_results.to_markdown())
-
-print('Number of columns in md table:', len(combined_results.columns))
-print('Number of rows in md table:', len(combined_results))
-print(combined_results.head())
+utils.run_biosimulators_remotely_and_locally(sedml_file_name, 
+                                 sbml_file_name,
+                                 d1_plots_remote_dir, 
+                                 d1_plots_local_dir,
+                                 engines=engines, test_folder='tests')
\ No newline at end of file

From 613d8e80d40931b641b9404e99882d86d27352cf Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 27 Aug 2024 09:52:13 +0100
Subject: [PATCH 46/71] Refactor  utils create_combined_results_table function
 to print table information

---
 utils/__init__.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/utils/__init__.py b/utils/__init__.py
index b617427..af152b1 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -1235,6 +1235,10 @@ def create_combined_results_table(results_remote,
     with open(path_to_results, 'w') as f:
         f.write(combined_results.to_markdown())
 
+    print('Number of columns in md table:', len(combined_results.columns))
+    print('Number of rows in md table:', len(combined_results))
+    print(combined_results.head())    
+
     return combined_results
 
 

From 7637a9cfadbfad04a49496063f3d449ab7675dcd Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 27 Aug 2024 10:02:00 +0100
Subject: [PATCH 47/71] Remove unnecessary imports and lines from
 test_compatibility_biosimulators.py

---
 SBML/tests/test_compatibility_biosimulators.py | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py
index 5616050..f6c7af4 100644
--- a/SBML/tests/test_compatibility_biosimulators.py
+++ b/SBML/tests/test_compatibility_biosimulators.py
@@ -8,15 +8,8 @@
 
 import sys
 import os
-
-# Add the parent directory to the Python path
-parent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
-sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils
 import utils
-import os
-import pandas as pd
-import shutil
-import yaml
 import argparse
 
 # Save the current working directory

From 9884ddc239aeb46366fb0f90443a1982b509b987 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 27 Aug 2024 10:14:09 +0100
Subject: [PATCH 48/71] Remove redundent lines from
 test_compatibility_biosimulators.py and add a little more documentation

---
 SBML/tests/test_compatibility_biosimulators.py | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py
index f6c7af4..c801471 100644
--- a/SBML/tests/test_compatibility_biosimulators.py
+++ b/SBML/tests/test_compatibility_biosimulators.py
@@ -12,6 +12,9 @@
 import utils
 import argparse
 
+engines = utils.engines
+types_dict = utils.types_dict
+
 # Save the current working directory
 cwd = os.getcwd()
 print('Current working directory:', cwd)
@@ -20,22 +23,14 @@
 path_to_sbml_folder = os.path.abspath(os.path.join(cwd, os.pardir))
 print('Path to SBML folder:', path_to_sbml_folder)
 
-# change the working directory to the SBML folder
+# change the working directory to the SBML folder (because here the SBML and SED-ML files are located)
 os.chdir(path_to_sbml_folder)
 print('Changed working directory to:', os.getcwd())
 
 sbml_file_name = 'LEMS_NML2_Ex9_FN.sbml'
 sedml_file_name = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
 
-sbml_file_path = os.path.join(path_to_sbml_folder, sbml_file_name)
-sedml_file_path = os.path.join(path_to_sbml_folder, sedml_file_name)
-
-engines = utils.engines
-types_dict = utils.types_dict
-
-print('Path to SED-ML file:', sedml_file_path)
-print('Path to SBML file:', sbml_file_path)
-
+# output_dir is set to 'd1_plots' by default but can be changed using the --output-dir argument (required to deal with GitHub Actions permission issues)
 parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines')
 parser.add_argument('--output-dir',action='store',default='d1_plots',help='prefix of the output directory where the d1 plots will be saved')
 args = parser.parse_args()

From ab94d5f502e918bfad0e502ad22220e53ce47c60 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 27 Aug 2024 11:04:40 +0100
Subject: [PATCH 49/71] update README to use sbml-level_version instead of
 suite-glob in process_test_suite.py

---
 test_suite/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite/README.md b/test_suite/README.md
index 6f5d9e7..e4ae43d 100644
--- a/test_suite/README.md
+++ b/test_suite/README.md
@@ -35,7 +35,7 @@ pip install docker
 Navigate to the directory containing the `process_test_suite.py` script and execute it, specifying the path to the extracted test files. For example if the extraction folder is  `C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic` and the `process_test_suite.py` script is in the current directory.
 
 ```
- python process_test_suite.py --suite-path C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic  --suite-glob '*/*-sbml-l3v2.xml' --output-file ./results_test.md --limit 5       
+ python process_test_suite.py --suite-path C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic  --sbml-level_version 'l3v2' --output-file ./results_test.md --limit 5       
 ```
 
 ## Command Line Options

From fac0715591687c6edfa482ccdb44b71f33b4045e Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:08:16 +0100
Subject: [PATCH 50/71] Adjust README to use sbml-level_version instead of
 suite-glob and allow level_version to be set to 'highest' or to a specific
 level

---
 test_suite/README.md             | 10 +++++-----
 test_suite/process_test_suite.py | 26 +++++++++++++-------------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/test_suite/README.md b/test_suite/README.md
index e4ae43d..2c26a5e 100644
--- a/test_suite/README.md
+++ b/test_suite/README.md
@@ -35,7 +35,7 @@ pip install docker
 Navigate to the directory containing the `process_test_suite.py` script and execute it, specifying the path to the extracted test files. For example if the extraction folder is  `C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic` and the `process_test_suite.py` script is in the current directory.
 
 ```
- python process_test_suite.py --suite-path C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic  --sbml-level_version 'l3v2' --output-file ./results_test.md --limit 5       
+ python process_test_suite.py --suite-path C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic  --sbml-level_version 'sbml-l3v2' --output-file ./results_test.md --limit 5       
 ```
 
 ## Command Line Options
@@ -52,10 +52,10 @@ The `process_test_suite.py` script provides various command-line options to cust
   **Usage:** `--suite-path <path>`  
   **Default:** `.` (current directory)
 
-- `--suite-glob`  
-  **Description:** Shell-style glob pattern to match SBML files within the specified suite path.  
-  **Usage:** `--suite-glob <pattern>`  
-  **Default:** `000*/*-sbml-l3v2.xml`
+- `--sbml-level_version'
+  **Description:** String that specifies level and version of files to select for processing (e.g. 'l3v2')
+  **Usage:** `--sbml-level_version <string>`  
+  **Default:** `highest`
 
 - `--suite-url-base`  
   **Description:** Base URL for the online test case files to include as links in the results. Set to an empty string to disable links.  
diff --git a/test_suite/process_test_suite.py b/test_suite/process_test_suite.py
index 73d8b83..1a2862c 100755
--- a/test_suite/process_test_suite.py
+++ b/test_suite/process_test_suite.py
@@ -57,8 +57,8 @@ def parse_arguments():
         "--sbml-level_version",
         action="store",
         type=str,
-        default="sbml-l3v2",
-        help="SBML level and version to test, default is 'sbml-l3v2'",
+        default="highest",
+        help="SBML level and version to test (e.g. 'l3v2'), default is '' which will try to find the highest level and version in the folder",
     )
 
     parser.add_argument(
@@ -119,21 +119,21 @@ def process_cases(args):
     subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit]    
     
     for subfolder in subfolders:
-        # find relevant files in the subfolder
-        sbml_file_name = f"*-{args.sbml_level_version}.xml"
-        sedml_file_name = f"*-{args.sbml_level_version}-sedml.xml"
-        sbml_file_path = glob.glob(os.path.join(subfolder, sbml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sbml_file_name))) > 0 else []
-        sedml_file_path = glob.glob(os.path.join(subfolder, sedml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sedml_file_name))) > 0 else []
-
-        # if no files found with the specified sbml_level_version, try to find any sbml or sedml files
-        if sbml_file_path == [] or sedml_file_path == []:
-            print(f"Folder {subfolder} has no {args.sbml_level_version} SBML or SED-ML files")
+        # if sbml_level_version is empty string (default), find the highest level and version in the folder
+        if args.sbml_level_version == "highest":
             sedml_file_paths = glob.glob(os.path.join(subfolder, "*-sbml-*sedml.xml"))
             # get last entry in list of sedml_file_paths (because it has the highest level and version number considering the alphabetical order and naming convention)
             sedml_file_path = sedml_file_paths[-1] if sedml_file_paths != [] else []
             sbml_file_path = sedml_file_path.replace("-sedml.xml",".xml") if sedml_file_path != [] else []
-            if sbml_file_path == [] or sedml_file_path == []:
-                print(f"Folder {subfolder} has no SBML or SED-ML files")
+        else:
+            # find relevant files in the subfolder
+            sbml_file_name = f"*-sbml-{args.sbml_level_version}.xml"
+            sedml_file_name = f"*-sbml-{args.sbml_level_version}-sedml.xml"
+            sbml_file_path = glob.glob(os.path.join(subfolder, sbml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sbml_file_name))) > 0 else []
+            sedml_file_path = glob.glob(os.path.join(subfolder, sedml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sedml_file_name))) > 0 else []
+        
+        if sbml_file_path == [] or sedml_file_path == []:
+                print(f"Folder {subfolder} has no SBML or SED-ML files {args.sbml_level_version}")
                 continue
         print(f"Processing {sbml_file_path} and {sedml_file_path}")
         

From a0b7cff5368f621991d344c9091df149a6f4f292 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 28 Aug 2024 08:46:39 +0100
Subject: [PATCH 51/71] Create test_compatibility_biosimulators results table
 for first three examples in SBML test suite. Change
 check_file_compatibility_test and dependencies so that it deals with .xml
 extensions as well.

---
 .../results_compatibility_biosimulators.md    |  46 +++---
 .../test_00001/00001-sbml-l3v2-sedml.omex     | Bin 0 -> 1989 bytes
 .../test_00001/00001-sbml-l3v2-sedml.xml      |  66 ++++++++
 test_suite/test_00001/00001-sbml-l3v2.xml     |  52 +++++++
 .../tests/d1_plots_local/amici_plot_1.pdf     | Bin 0 -> 9578 bytes
 .../tests/d1_plots_local/bionetgen_plot_1.pdf | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/boolnet_plot_1.pdf   | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/cbmpy_plot_1.pdf     | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/cobrapy_plot_1.pdf   | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/copasi_plot_1.pdf    | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/gillespy2_plot_1.pdf | Bin 0 -> 9592 bytes
 .../tests/d1_plots_local/ginsim_plot_1.pdf    | Bin 0 -> 5948 bytes
 .../d1_plots_local/libsbmlsim_plot_1.pdf      | Bin 0 -> 9597 bytes
 .../tests/d1_plots_local/masspy_plot_1.pdf    | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/pysces_plot_1.pdf    | Bin 0 -> 9590 bytes
 .../tests/d1_plots_local/rbapy_plot_1.pdf     | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/tellurium_plot_1.pdf | Bin 0 -> 9580 bytes
 .../tests/d1_plots_remote/amici_plot_1.pdf    | Bin 0 -> 9584 bytes
 .../d1_plots_remote/bionetgen_plot_1.pdf      | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/boolnet_plot_1.pdf  | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/cbmpy_plot_1.pdf    | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/cobrapy_plot_1.pdf  | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/copasi_plot_1.pdf   | Bin 0 -> 5954 bytes
 .../d1_plots_remote/gillespy2_plot_1.pdf      | Bin 0 -> 9598 bytes
 .../tests/d1_plots_remote/ginsim_plot_1.pdf   | Bin 0 -> 5954 bytes
 .../d1_plots_remote/libsbmlsim_plot_1.pdf     | Bin 0 -> 9603 bytes
 .../tests/d1_plots_remote/masspy_plot_1.pdf   | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/pysces_plot_1.pdf   | Bin 0 -> 9596 bytes
 .../tests/d1_plots_remote/rbapy_plot_1.pdf    | Bin 0 -> 5954 bytes
 .../d1_plots_remote/tellurium_plot_1.pdf      | Bin 0 -> 9586 bytes
 .../results_compatibility_biosimulators.md    |  23 +++
 .../test_00002/00002-sbml-l3v2-sedml.omex     | Bin 0 -> 2029 bytes
 .../test_00002/00002-sbml-l3v2-sedml.xml      |  66 ++++++++
 test_suite/test_00002/00002-sbml-l3v2.xml     |  71 +++++++++
 .../tests/d1_plots_local/amici_plot_1.pdf     | Bin 0 -> 9601 bytes
 .../tests/d1_plots_local/bionetgen_plot_1.pdf | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/boolnet_plot_1.pdf   | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/cbmpy_plot_1.pdf     | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/cobrapy_plot_1.pdf   | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/copasi_plot_1.pdf    | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/gillespy2_plot_1.pdf | Bin 0 -> 9585 bytes
 .../tests/d1_plots_local/ginsim_plot_1.pdf    | Bin 0 -> 5948 bytes
 .../d1_plots_local/libsbmlsim_plot_1.pdf      | Bin 0 -> 9591 bytes
 .../tests/d1_plots_local/masspy_plot_1.pdf    | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/pysces_plot_1.pdf    | Bin 0 -> 9587 bytes
 .../tests/d1_plots_local/rbapy_plot_1.pdf     | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/tellurium_plot_1.pdf | Bin 0 -> 9589 bytes
 .../tests/d1_plots_remote/amici_plot_1.pdf    | Bin 0 -> 9607 bytes
 .../d1_plots_remote/bionetgen_plot_1.pdf      | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/boolnet_plot_1.pdf  | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/cbmpy_plot_1.pdf    | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/cobrapy_plot_1.pdf  | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/copasi_plot_1.pdf   | Bin 0 -> 5954 bytes
 .../d1_plots_remote/gillespy2_plot_1.pdf      | Bin 0 -> 9591 bytes
 .../tests/d1_plots_remote/ginsim_plot_1.pdf   | Bin 0 -> 5954 bytes
 .../d1_plots_remote/libsbmlsim_plot_1.pdf     | Bin 0 -> 9597 bytes
 .../tests/d1_plots_remote/masspy_plot_1.pdf   | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/pysces_plot_1.pdf   | Bin 0 -> 9593 bytes
 .../tests/d1_plots_remote/rbapy_plot_1.pdf    | Bin 0 -> 5954 bytes
 .../d1_plots_remote/tellurium_plot_1.pdf      | Bin 0 -> 9595 bytes
 .../results_compatibility_biosimulators.md    |  23 +++
 .../test_00003/00003-sbml-l3v2-sedml.omex     | Bin 0 -> 1993 bytes
 .../test_00003/00003-sbml-l3v2-sedml.xml      |  66 ++++++++
 test_suite/test_00003/00003-sbml-l3v2.xml     |  52 +++++++
 .../tests/d1_plots_local/amici_plot_1.pdf     | Bin 0 -> 8638 bytes
 .../tests/d1_plots_local/bionetgen_plot_1.pdf | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/boolnet_plot_1.pdf   | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/cbmpy_plot_1.pdf     | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/cobrapy_plot_1.pdf   | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/copasi_plot_1.pdf    | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/gillespy2_plot_1.pdf | Bin 0 -> 8640 bytes
 .../tests/d1_plots_local/ginsim_plot_1.pdf    | Bin 0 -> 5948 bytes
 .../d1_plots_local/libsbmlsim_plot_1.pdf      | Bin 0 -> 8638 bytes
 .../tests/d1_plots_local/masspy_plot_1.pdf    | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/pysces_plot_1.pdf    | Bin 0 -> 8628 bytes
 .../tests/d1_plots_local/rbapy_plot_1.pdf     | Bin 0 -> 5948 bytes
 .../tests/d1_plots_local/tellurium_plot_1.pdf | Bin 0 -> 8640 bytes
 .../tests/d1_plots_remote/amici_plot_1.pdf    | Bin 0 -> 8644 bytes
 .../d1_plots_remote/bionetgen_plot_1.pdf      | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/boolnet_plot_1.pdf  | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/cbmpy_plot_1.pdf    | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/cobrapy_plot_1.pdf  | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/copasi_plot_1.pdf   | Bin 0 -> 5954 bytes
 .../d1_plots_remote/gillespy2_plot_1.pdf      | Bin 0 -> 8646 bytes
 .../tests/d1_plots_remote/ginsim_plot_1.pdf   | Bin 0 -> 5954 bytes
 .../d1_plots_remote/libsbmlsim_plot_1.pdf     | Bin 0 -> 8644 bytes
 .../tests/d1_plots_remote/masspy_plot_1.pdf   | Bin 0 -> 5954 bytes
 .../tests/d1_plots_remote/pysces_plot_1.pdf   | Bin 0 -> 8634 bytes
 .../tests/d1_plots_remote/rbapy_plot_1.pdf    | Bin 0 -> 5954 bytes
 .../d1_plots_remote/tellurium_plot_1.pdf      | Bin 0 -> 8646 bytes
 .../results_compatibility_biosimulators.md    |  23 +++
 ..._test_suite_compatibility_biosimulators.py | 144 ++++++++++++++++++
 utils/__init__.py                             |  87 ++++++-----
 93 files changed, 658 insertions(+), 61 deletions(-)
 create mode 100644 test_suite/test_00001/00001-sbml-l3v2-sedml.omex
 create mode 100644 test_suite/test_00001/00001-sbml-l3v2-sedml.xml
 create mode 100644 test_suite/test_00001/00001-sbml-l3v2.xml
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/bionetgen_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/boolnet_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/cbmpy_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/cobrapy_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/copasi_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/gillespy2_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/ginsim_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/libsbmlsim_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/masspy_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/pysces_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/rbapy_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_local/tellurium_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/amici_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/bionetgen_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/boolnet_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/cbmpy_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/cobrapy_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/copasi_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/gillespy2_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/ginsim_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/libsbmlsim_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/masspy_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/pysces_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/rbapy_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/d1_plots_remote/tellurium_plot_1.pdf
 create mode 100644 test_suite/test_00001/tests/results_compatibility_biosimulators.md
 create mode 100644 test_suite/test_00002/00002-sbml-l3v2-sedml.omex
 create mode 100644 test_suite/test_00002/00002-sbml-l3v2-sedml.xml
 create mode 100644 test_suite/test_00002/00002-sbml-l3v2.xml
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/amici_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/bionetgen_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/boolnet_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/cbmpy_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/cobrapy_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/copasi_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/gillespy2_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/ginsim_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/libsbmlsim_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/masspy_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/pysces_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/rbapy_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_local/tellurium_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/amici_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/bionetgen_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/boolnet_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/cbmpy_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/cobrapy_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/copasi_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/gillespy2_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/ginsim_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/libsbmlsim_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/masspy_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/pysces_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/rbapy_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/d1_plots_remote/tellurium_plot_1.pdf
 create mode 100644 test_suite/test_00002/tests/results_compatibility_biosimulators.md
 create mode 100644 test_suite/test_00003/00003-sbml-l3v2-sedml.omex
 create mode 100644 test_suite/test_00003/00003-sbml-l3v2-sedml.xml
 create mode 100644 test_suite/test_00003/00003-sbml-l3v2.xml
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/amici_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/bionetgen_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/boolnet_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/cbmpy_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/cobrapy_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/copasi_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/gillespy2_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/ginsim_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/libsbmlsim_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/masspy_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/pysces_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/rbapy_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_local/tellurium_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/amici_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/bionetgen_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/boolnet_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/cbmpy_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/cobrapy_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/copasi_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/gillespy2_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/ginsim_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/libsbmlsim_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/masspy_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/pysces_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/rbapy_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/d1_plots_remote/tellurium_plot_1.pdf
 create mode 100644 test_suite/test_00003/tests/results_compatibility_biosimulators.md
 create mode 100644 test_suite/test_test_suite_compatibility_biosimulators.py

diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index 995762c..f13856d 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                                              | Compat (L)                                                                                                                                                                                                                                                                                                                              | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                                                            | d1 (R)                                                     | d1 (L)                                                    |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|:----------------------------------------------------------|
-|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_d1.pdf">plot</a>      |
-|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']</details></span>            | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_d1.pdf">plot</a>  |
-|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_d1.pdf">plot</a>    |
-|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2</details>                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                            |                                                           |
-|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy</details>                                                                                                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_d1.pdf">plot</a>      |
-|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy</details>                                                                                                                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_d1.pdf">plot</a>    |
-|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_d1.pdf">plot</a>     |
-|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_d1.pdf">plot</a>  |
-|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']</details></span>          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_d1.pdf">plot</a>     |
-|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim</details>                                                                                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
-| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_d1.pdf">plot</a>     |
-| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne</details>                                                                                                                       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                            |                                                           |
-| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span>    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                            |                                                           |
-| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']</details></span>            | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                            |                                                           |
-| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                            |                                                           |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces</details>                                                                                                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmp36492nwm/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmp36492nwm/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_d1.pdf">plot</a>     |
-| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']</details></span>               | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_d1.pdf">plot</a>      |
-| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>smoldyn compatible file types unknown.</details></span>                                                                                                                                                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                            |                                                           |
-| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium</details>                                                                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_d1.pdf">plot</a>  |
-| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/><details><summary>pass</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell</details>                                                                                                                         |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                            |                                                           |
-| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']</details></span>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                            |                                                           |
\ No newline at end of file
+|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                           | Compat (L)                                                                                                                                                                                                                                                                                                           | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                                                            | d1 (R)                                                     | d1 (L)                                                    |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|:----------------------------------------------------------|
+|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici</details>                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici</details>                                                                      |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_d1.pdf">plot</a>      |
+|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details></span>                      | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details></span>                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_d1.pdf">plot</a>  |
+|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details></span>                     | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details></span>                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_d1.pdf">plot</a>    |
+|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details>                              | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details>                              | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                            |                                                           |
+|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_d1.pdf">plot</a>      |
+|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                                                    | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_d1.pdf">plot</a>    |
+|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_d1.pdf">plot</a>     |
+|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                                                  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_d1.pdf">plot</a>  |
+|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details></span>                       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details></span>                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_d1.pdf">plot</a>     |
+|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                                                 |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
+| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_d1.pdf">plot</a>     |
+| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                            |                                                           |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details></span>       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details></span>       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                            |                                                           |
+| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details></span>                        | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details></span>                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                            |                                                           |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                            |                                                           |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpquunm0rr/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpquunm0rr/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_d1.pdf">plot</a>     |
+| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details></span>                             | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details></span>                             | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_d1.pdf">plot</a>      |
+| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn</details></span>                                          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn</details></span>                                          | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                            |                                                           |
+| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                                                  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_d1.pdf">plot</a>  |
+| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                            |                                                           |
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                            |                                                           |
\ No newline at end of file
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HcmV?d00001

diff --git a/test_suite/test_00001/00001-sbml-l3v2-sedml.xml b/test_suite/test_00001/00001-sbml-l3v2-sedml.xml
new file mode 100644
index 0000000..799636d
--- /dev/null
+++ b/test_suite/test_00001/00001-sbml-l3v2-sedml.xml
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Written by libSedML v1.1.5419.25885 see http://libsedml.sf.net -->
+<sedML level="1" version="1" xmlns="http://sed-ml.org/">
+  <listOfSimulations>
+    <uniformTimeCourse id="simulation_1" initialTime="0" outputStartTime="0" outputEndTime="5" numberOfPoints="50">
+      <algorithm kisaoID="KISAO:0000019" />
+    </uniformTimeCourse>
+  </listOfSimulations>
+  <listOfModels>
+    <model id="model_1" language="urn:sedml:language:sbml" source="00001-sbml-l3v2.xml" />
+  </listOfModels>
+  <listOfTasks>
+    <task id="task_1" modelReference="model_1" simulationReference="simulation_1" />
+  </listOfTasks>
+  <listOfDataGenerators>
+    <dataGenerator id="time_1" name="time">
+      <listOfVariables>
+        <variable id="time" taskReference="task_1" symbol="urn:sedml:symbol:time" />
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> time </ci>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="S1_1" name="S1">
+      <listOfVariables>
+        <variable id="S1_1_s" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']" />
+        <variable id="S1_1_c" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']" />
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <apply>
+          <times />
+          <ci> S1_1_s </ci>
+          <ci> S1_1_c </ci>
+        </apply>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="S2_1" name="S2">
+      <listOfVariables>
+        <variable id="S2_1_s" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']" />
+        <variable id="S2_1_c" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']" />
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <apply>
+          <times />
+          <ci> S2_1_s </ci>
+          <ci> S2_1_c </ci>
+        </apply>
+      </math>
+    </dataGenerator>
+  </listOfDataGenerators>
+  <listOfOutputs>
+    <plot2D id="plot_1" name="Timecourse for test 00001">
+      <listOfCurves>
+        <curve id="c_S1_1" name="S1" logX="false" logY="false" xDataReference="time_1" yDataReference="S1_1" />
+        <curve id="c_S2_1" name="S2" logX="false" logY="false" xDataReference="time_1" yDataReference="S2_1" />
+      </listOfCurves>
+    </plot2D>
+    <report id="report_1" name="Report for test 00001">
+      <listOfDataSets>
+        <dataSet id="ds_time" dataReference="time_1" label="Time" />
+        <dataSet id="ds_S1_1" dataReference="S1_1" label="S1" />
+        <dataSet id="ds_S2_1" dataReference="S2_1" label="S2" />
+      </listOfDataSets>
+    </report>
+  </listOfOutputs>
+</sedML>
\ No newline at end of file
diff --git a/test_suite/test_00001/00001-sbml-l3v2.xml b/test_suite/test_00001/00001-sbml-l3v2.xml
new file mode 100644
index 0000000..23fbaac
--- /dev/null
+++ b/test_suite/test_00001/00001-sbml-l3v2.xml
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="_case00001" id="case00001" name="case00001" timeUnits="time">
+    <listOfUnitDefinitions>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" name="S1" compartment="compartment" initialAmount="0.00015" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" name="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="reaction1" name="reaction1" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..b1fe80088d06bfcd3121a6f34801b7b5cfda8055
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diff --git a/test_suite/test_00001/tests/d1_plots_remote/libsbmlsim_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/libsbmlsim_plot_1.pdf
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diff --git a/test_suite/test_00001/tests/d1_plots_remote/tellurium_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/tellurium_plot_1.pdf
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HcmV?d00001

diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md
new file mode 100644
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@@ -0,0 +1,23 @@
+|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                         | Compat (L)                                                                                                                                                                                                                         | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Error (L)                                                                                                                                                                                   | d1 (R)                                                         | d1 (L)                                                        |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------|
+|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\amici_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_plot_1.pdf">plot</a>      |
+|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>             | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_plot_1.pdf">plot</a>  |
+|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).</details>                                                                                                                 | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_plot_1.pdf">plot</a>    |
+|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                |                                                               |
+|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_plot_1.pdf">plot</a>      |
+|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_plot_1.pdf">plot</a>    |
+|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Compartments[compartment].Volume'</details>                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_plot_1.pdf">plot</a>     |
+|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\gillespy2_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_plot_1.pdf">plot</a>  |
+|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:<br>          Output start time: 0.0<br>          Output end time: 5.0<br>          Number of steps: 50</details> | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_plot_1.pdf">plot</a>     |
+|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\libsbmlsim_plot_1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_plot_1.pdf">plot</a> |
+| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_plot_1.pdf">plot</a>     |
+| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                |                                                               |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                |                                                               |
+| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                |                                                               |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                |                                                               |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\pysces_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_plot_1.pdf">plot</a>     |
+| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_plot_1.pdf">plot</a>      |
+| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                |                                                               |
+| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\tellurium_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_plot_1.pdf">plot</a>  |
+| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                                |                                                               |
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                |                                                               |
\ No newline at end of file
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diff --git a/test_suite/test_00002/00002-sbml-l3v2-sedml.xml b/test_suite/test_00002/00002-sbml-l3v2-sedml.xml
new file mode 100644
index 0000000..8d3b477
--- /dev/null
+++ b/test_suite/test_00002/00002-sbml-l3v2-sedml.xml
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Written by libSedML v1.1.5419.25885 see http://libsedml.sf.net -->
+<sedML level="1" version="1" xmlns="http://sed-ml.org/">
+  <listOfSimulations>
+    <uniformTimeCourse id="simulation_1" initialTime="0" outputStartTime="0" outputEndTime="5" numberOfPoints="50">
+      <algorithm kisaoID="KISAO:0000019" />
+    </uniformTimeCourse>
+  </listOfSimulations>
+  <listOfModels>
+    <model id="model_1" language="urn:sedml:language:sbml" source="00002-sbml-l3v2.xml" />
+  </listOfModels>
+  <listOfTasks>
+    <task id="task_1" modelReference="model_1" simulationReference="simulation_1" />
+  </listOfTasks>
+  <listOfDataGenerators>
+    <dataGenerator id="time_1" name="time">
+      <listOfVariables>
+        <variable id="time" taskReference="task_1" symbol="urn:sedml:symbol:time" />
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> time </ci>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="S1_1" name="S1">
+      <listOfVariables>
+        <variable id="S1_1_s" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']" />
+        <variable id="S1_1_c" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']" />
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <apply>
+          <times />
+          <ci> S1_1_s </ci>
+          <ci> S1_1_c </ci>
+        </apply>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="S2_1" name="S2">
+      <listOfVariables>
+        <variable id="S2_1_s" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']" />
+        <variable id="S2_1_c" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']" />
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <apply>
+          <times />
+          <ci> S2_1_s </ci>
+          <ci> S2_1_c </ci>
+        </apply>
+      </math>
+    </dataGenerator>
+  </listOfDataGenerators>
+  <listOfOutputs>
+    <plot2D id="plot_1" name="Timecourse for test 00002">
+      <listOfCurves>
+        <curve id="c_S1_1" name="S1" logX="false" logY="false" xDataReference="time_1" yDataReference="S1_1" />
+        <curve id="c_S2_1" name="S2" logX="false" logY="false" xDataReference="time_1" yDataReference="S2_1" />
+      </listOfCurves>
+    </plot2D>
+    <report id="report_1" name="Report for test 00002">
+      <listOfDataSets>
+        <dataSet id="ds_time" dataReference="time_1" label="Time" />
+        <dataSet id="ds_S1_1" dataReference="S1_1" label="S1" />
+        <dataSet id="ds_S2_1" dataReference="S2_1" label="S2" />
+      </listOfDataSets>
+    </report>
+  </listOfOutputs>
+</sedML>
\ No newline at end of file
diff --git a/test_suite/test_00002/00002-sbml-l3v2.xml b/test_suite/test_00002/00002-sbml-l3v2.xml
new file mode 100644
index 0000000..a7d7ff9
--- /dev/null
+++ b/test_suite/test_00002/00002-sbml-l3v2.xml
@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="_case00002" id="case00002" name="case00002" timeUnits="time">
+    <listOfUnitDefinitions>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" name="S1" compartment="compartment" initialAmount="0.0015" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" name="k1" value="1" constant="true"/>
+      <parameter id="k2" name="k2" value="0" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="reaction1" name="reaction1" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="reaction2" name="reaction2" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k2 </ci>
+              <ci> S2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/test_suite/test_00002/tests/d1_plots_local/amici_plot_1.pdf b/test_suite/test_00002/tests/d1_plots_local/amici_plot_1.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..52d790a9320c14245199c75b37ad5ac7f43d0c00
GIT binary patch
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diff --git a/test_suite/test_00002/tests/d1_plots_local/gillespy2_plot_1.pdf b/test_suite/test_00002/tests/d1_plots_local/gillespy2_plot_1.pdf
new file mode 100644
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HcmV?d00001

diff --git a/test_suite/test_00002/tests/results_compatibility_biosimulators.md b/test_suite/test_00002/tests/results_compatibility_biosimulators.md
new file mode 100644
index 0000000..332ba2b
--- /dev/null
+++ b/test_suite/test_00002/tests/results_compatibility_biosimulators.md
@@ -0,0 +1,23 @@
+|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                         | Compat (L)                                                                                                                                                                                                                         | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Error (L)                                                                                                                                                                                   | d1 (R)                                                         | d1 (L)                                                        |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------|
+|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\amici_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_plot_1.pdf">plot</a>      |
+|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>             | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_plot_1.pdf">plot</a>  |
+|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).</details>                                                                                                                 | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_plot_1.pdf">plot</a>    |
+|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                |                                                               |
+|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_plot_1.pdf">plot</a>      |
+|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_plot_1.pdf">plot</a>    |
+|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Compartments[compartment].Volume'</details>                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_plot_1.pdf">plot</a>     |
+|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\gillespy2_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_plot_1.pdf">plot</a>  |
+|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:<br>          Output start time: 0.0<br>          Output end time: 5.0<br>          Number of steps: 50</details> | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_plot_1.pdf">plot</a>     |
+|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\libsbmlsim_plot_1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_plot_1.pdf">plot</a> |
+| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_plot_1.pdf">plot</a>     |
+| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                |                                                               |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                |                                                               |
+| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                |                                                               |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                |                                                               |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\pysces_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_plot_1.pdf">plot</a>     |
+| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_plot_1.pdf">plot</a>      |
+| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                |                                                               |
+| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\tellurium_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_plot_1.pdf">plot</a>  |
+| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                                |                                                               |
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                |                                                               |
\ No newline at end of file
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diff --git a/test_suite/test_00003/00003-sbml-l3v2-sedml.xml b/test_suite/test_00003/00003-sbml-l3v2-sedml.xml
new file mode 100644
index 0000000..41ac28b
--- /dev/null
+++ b/test_suite/test_00003/00003-sbml-l3v2-sedml.xml
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Written by libSedML v1.1.5419.25885 see http://libsedml.sf.net -->
+<sedML level="1" version="1" xmlns="http://sed-ml.org/">
+  <listOfSimulations>
+    <uniformTimeCourse id="simulation_1" initialTime="0" outputStartTime="0" outputEndTime="5" numberOfPoints="50">
+      <algorithm kisaoID="KISAO:0000019" />
+    </uniformTimeCourse>
+  </listOfSimulations>
+  <listOfModels>
+    <model id="model_1" language="urn:sedml:language:sbml" source="00003-sbml-l3v2.xml" />
+  </listOfModels>
+  <listOfTasks>
+    <task id="task_1" modelReference="model_1" simulationReference="simulation_1" />
+  </listOfTasks>
+  <listOfDataGenerators>
+    <dataGenerator id="time_1" name="time">
+      <listOfVariables>
+        <variable id="time" taskReference="task_1" symbol="urn:sedml:symbol:time" />
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <ci> time </ci>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="S1_1" name="S1">
+      <listOfVariables>
+        <variable id="S1_1_s" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']" />
+        <variable id="S1_1_c" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']" />
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <apply>
+          <times />
+          <ci> S1_1_s </ci>
+          <ci> S1_1_c </ci>
+        </apply>
+      </math>
+    </dataGenerator>
+    <dataGenerator id="S2_1" name="S2">
+      <listOfVariables>
+        <variable id="S2_1_s" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']" />
+        <variable id="S2_1_c" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']" />
+      </listOfVariables>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+        <apply>
+          <times />
+          <ci> S2_1_s </ci>
+          <ci> S2_1_c </ci>
+        </apply>
+      </math>
+    </dataGenerator>
+  </listOfDataGenerators>
+  <listOfOutputs>
+    <plot2D id="plot_1" name="Timecourse for test 00003">
+      <listOfCurves>
+        <curve id="c_S1_1" name="S1" logX="false" logY="false" xDataReference="time_1" yDataReference="S1_1" />
+        <curve id="c_S2_1" name="S2" logX="false" logY="false" xDataReference="time_1" yDataReference="S2_1" />
+      </listOfCurves>
+    </plot2D>
+    <report id="report_1" name="Report for test 00003">
+      <listOfDataSets>
+        <dataSet id="ds_time" dataReference="time_1" label="Time" />
+        <dataSet id="ds_S1_1" dataReference="S1_1" label="S1" />
+        <dataSet id="ds_S2_1" dataReference="S2_1" label="S2" />
+      </listOfDataSets>
+    </report>
+  </listOfOutputs>
+</sedML>
\ No newline at end of file
diff --git a/test_suite/test_00003/00003-sbml-l3v2.xml b/test_suite/test_00003/00003-sbml-l3v2.xml
new file mode 100644
index 0000000..7b17b5e
--- /dev/null
+++ b/test_suite/test_00003/00003-sbml-l3v2.xml
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="_case00003" id="case00003" name="case00003" timeUnits="time">
+    <listOfUnitDefinitions>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" name="S1" compartment="compartment" initialAmount="0.015" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" name="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="reaction1" name="reaction1" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/test_suite/test_00003/tests/d1_plots_local/amici_plot_1.pdf b/test_suite/test_00003/tests/d1_plots_local/amici_plot_1.pdf
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diff --git a/test_suite/test_00003/tests/d1_plots_local/bionetgen_plot_1.pdf b/test_suite/test_00003/tests/d1_plots_local/bionetgen_plot_1.pdf
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HcmV?d00001

diff --git a/test_suite/test_00003/tests/results_compatibility_biosimulators.md b/test_suite/test_00003/tests/results_compatibility_biosimulators.md
new file mode 100644
index 0000000..7a0884e
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+++ b/test_suite/test_00003/tests/results_compatibility_biosimulators.md
@@ -0,0 +1,23 @@
+|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                         | Compat (L)                                                                                                                                                                                                                         | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Error (L)                                                                                                                                                                                   | d1 (R)                                                         | d1 (L)                                                        |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------|
+|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\amici_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_plot_1.pdf">plot</a>      |
+|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>             | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_plot_1.pdf">plot</a>  |
+|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).</details>                                                                                                                 | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_plot_1.pdf">plot</a>    |
+|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                |                                                               |
+|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_plot_1.pdf">plot</a>      |
+|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_plot_1.pdf">plot</a>    |
+|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Compartments[compartment].Volume'</details>                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_plot_1.pdf">plot</a>     |
+|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\gillespy2_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_plot_1.pdf">plot</a>  |
+|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:<br>          Output start time: 0.0<br>          Output end time: 5.0<br>          Number of steps: 50</details> | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_plot_1.pdf">plot</a>     |
+|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\libsbmlsim_plot_1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_plot_1.pdf">plot</a> |
+| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_plot_1.pdf">plot</a>     |
+| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                |                                                               |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                |                                                               |
+| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                |                                                               |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                |                                                               |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\pysces_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_plot_1.pdf">plot</a>     |
+| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_plot_1.pdf">plot</a>      |
+| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                |                                                               |
+| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\tellurium_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_plot_1.pdf">plot</a>  |
+| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                                |                                                               |
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                |                                                               |
\ No newline at end of file
diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py
new file mode 100644
index 0000000..1a1a590
--- /dev/null
+++ b/test_suite/test_test_suite_compatibility_biosimulators.py
@@ -0,0 +1,144 @@
+#!/usr/bin/env python3
+
+"""
+produce a markdown table of the results of running various tests on the SBML Test Suite
+
+get this version of the test suite that includes sedml versions or the sedml validation will fail:
+https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip
+"""
+
+import os
+import glob
+from pyneuroml.sbml import validate_sbml_files
+from pyneuroml.sedml import validate_sedml_files
+import sys
+import shutil
+sys.path.append("..")
+import utils
+engines = utils.engines
+
+
+md_description = \
+'''
+Markdown file description goes here.
+'''
+
+
+#suppress stdout output from validation functions to make progress counter readable
+suppress_stdout = True
+
+def parse_arguments():
+    "Parse command line arguments"
+
+    import argparse
+
+    parser = argparse.ArgumentParser(
+        description="Run various tests on the SBML Test Suite (or any similar set of SBML/SEDML files)"
+    )
+
+    parser.add_argument(
+        "--limit",
+        action="store",
+        type=int,
+        default=0,
+        help="Limit to the first n test cases, 0 means no limit",
+    )
+
+    parser.add_argument(
+        "--suite-path",
+        action="store",
+        type=str,
+        default=".",
+        help="Path to test suite directory, eg '~/repos/sbml-test-suite/cases/semantic'",
+    )
+
+    parser.add_argument(
+        "--sbml-level_version",
+        action="store",
+        type=str,
+        default="highest",
+        help="SBML level and version to test (e.g. 'l3v2'), default is '' which will try to find the highest level and version in the folder",
+    )
+
+    parser.add_argument(
+        "--suite-url-base",
+        action="store",
+        type=str,
+        default="https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic",
+        help="Base of the URL-to-suite-test-cases link to embed in results, use '' empty string to disable links",
+    )
+
+    return parser.parse_args()
+
+def process_cases(args):
+    """
+    process the test cases and write results out as a markdown table
+    with links to the test case files online (as noted above the sedml files are actually in a zip file)
+    with a summary of how many cases were tested and how many tests failed
+
+    examples of command line instructions
+
+    To test all the cases in the test suite:
+    python test_test_suite_compatibility_biosimulators.py --limit 0 --suite-path /path/to/sbml-test-suite/cases/semantic --sbml-level_version l3v2
+
+    To test the first 10 cases in the test suite:
+    python test_test_suite_compatibility_biosimulators.py --limit 10 --suite-path /path/to/sbml-test-suite/cases/semantic --sbml-level_version l3v2
+
+    To test the highest level and version of SBML of the first 5 cases in the test suite:
+    python test_test_suite_compatibility_biosimulators.py --limit 5 --suite-path /path/to/sbml-test-suite/cases/semantic --sbml-level_version highest
+    """
+
+    starting_dir = os.getcwd() # where results will be written
+
+    os.chdir(args.suite_path) # change to test suite directory
+    suite_path_abs = os.getcwd() # absolute path to test suite
+
+    subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit]   
+    print(f"Processing {len(subfolders)} subfolders in {args.suite_path}") 
+    test_folder = 'tests'
+
+    for subfolder in subfolders:
+        # create an equivalently named folder in the starting directory
+        os.chdir(args.suite_path)
+        print(f"Processing {subfolder}")
+
+        # if sbml_level_version is empty string (default), find the highest level and version in the folder
+        if args.sbml_level_version == "highest":
+            sedml_file_paths = glob.glob(os.path.join(subfolder, "*-sbml-*sedml.xml"))
+            # get last entry in list of sedml_file_paths (because it has the highest level and version number considering the alphabetical order and naming convention)
+            sedml_file_path = sedml_file_paths[-1] if sedml_file_paths != [] else []
+            sbml_file_path = sedml_file_path.replace("-sedml.xml",".xml") if sedml_file_path != [] else []
+        else:
+            sbml_file_name = f"*-sbml-{args.sbml_level_version}.xml"
+            sedml_file_name = f"*-sbml-{args.sbml_level_version}-sedml.xml"
+            sbml_file_path = glob.glob(os.path.join(subfolder, sbml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sbml_file_name))) > 0 else []
+            sedml_file_path = glob.glob(os.path.join(subfolder, sedml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sedml_file_name))) > 0 else []
+        
+        if sbml_file_path == [] or sedml_file_path == []:
+            print(f"Folder {subfolder} has no SBML or SED-ML files {args.sbml_level_version}")
+            continue
+
+        new_subfolder = "test_" + subfolder
+        new_directory = os.path.join(starting_dir, new_subfolder)
+        os.makedirs(new_directory, exist_ok=True)
+        print (f"Copying {sbml_file_path} and {sedml_file_path} to {starting_dir}/{subfolder}")
+        new_sbml_file_path = os.path.join(new_directory, os.path.basename(sbml_file_path))
+        new_sedml_file_path = os.path.join(new_directory, os.path.basename(sedml_file_path))
+        shutil.copy(sbml_file_path, new_sbml_file_path)
+        shutil.copy(sedml_file_path, new_sedml_file_path)
+
+        os.chdir(new_directory)
+        print(f"Changed to {new_directory}")
+        
+        utils.run_biosimulators_remotely_and_locally(os.path.basename(sedml_file_path), 
+                                 os.path.basename(sbml_file_path),
+                                 os.path.join(test_folder,'d1_plots_remote'), 
+                                 os.path.join(test_folder,'d1_plots_local'),
+                                 engines=engines, test_folder=test_folder)
+
+
+if __name__ == "__main__":
+    args = parse_arguments()
+
+    process_cases(args)
+
diff --git a/utils/__init__.py b/utils/__init__.py
index af152b1..79bf4bb 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -23,7 +23,7 @@
 
 engines = {
     'amici': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_AMICI/',
         'status': ""
     },
@@ -33,52 +33,52 @@
         'status': ""
     },
     'bionetgen': {
-        'formats': ('bngl', 'sedml'),
+        'formats': [('bngl', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_BioNetGen/',
         'status': ""
     },
     'boolnet': {
-        'formats': ('sbmlqual', 'sedml'),
+        'formats': [('sbmlqual', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_BoolNet/',
         'status': ""
     },
     'cbmpy': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_CBMPy/',
         'status': ""
     },
     'cobrapy': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_COBRApy/',
         'status': "Only allows steady state simulations"
     },
     'copasi': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_COPASI/',
         'status': ""
     },
     'gillespy2': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_GillesPy2/',
         'status': ""
     },
     'ginsim': {
-        'formats': ('sbmlqual', 'sedml'),
+        'formats': [('sbmlqual', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_GINsim/',
         'status': ""
     },
     'libsbmlsim': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_LibSBMLSim/',
         'status': ""
     },
     'masspy': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_MASSpy/',
         'status': ""
     },
     'netpyne': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
         'status': ""
     },
@@ -88,7 +88,7 @@
         'status': ""
     },
     'opencor': {
-        'formats': ('cellml', 'sedml'),
+        'formats': [('cellml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_OpenCOR/',
         'status': ""
     },
@@ -98,22 +98,22 @@
         'status': ""
     },
     'pysces': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_PySCeS/',
         'status': ""
     },
     'rbapy': {
-        'formats': ('rbapy', 'sedml'),
+        'formats': [('rbapy', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_RBApy/',
         'status': ""
     },
     'smoldyn': {
-        'formats': None,
+        'formats': ['unclear'],
         'url': 'https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api',
         'status': ""
     },
     'tellurium': {
-        'formats': ('sbml', 'sedml'),
+        'formats': [('sbml', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_tellurium/',
         'status': ""
     },
@@ -123,7 +123,7 @@
         'status': ""
     },
     'xpp': {
-        'formats': ('xpp', 'sedml'),
+        'formats': [('xpp', 'sedml')],
         'url': 'https://docs.biosimulators.org/Biosimulators_XPP/',
         'status': ""
     }
@@ -140,7 +140,8 @@
                 'rbapy':'RBApy',\
                 'xpp':'XPP',\
                 'smoldyn':'Smoldyn',\
-                'cellml':'CellML'\
+                'cellml':'CellML',\
+                'xml':'XML'\
              }
 
 
@@ -430,25 +431,28 @@ def display_error_message(error_message):
 
 def check_file_compatibility_test(engine, types_dict, model_filepath, experiment_filepath):
     '''
-    Check if the file extensions suggest the file types are compatible with the engine
+    Check if the file extensions suggest the file types are compatible with the engine.
+    This is done by comparing the file extensions of the model and experiment files with the file types supported by the engine.
+    For SED-ML files, the expected file extension is '.sedml'. For SBML files, the expected file extension is '.sbml'.
     '''
-    input_filetypes = set(get_filetypes(model_filepath, experiment_filepath))
-    input_file_types_text = [types_dict[i] for i in input_filetypes]
-
-
-    engine_filetypes = engines[engine]['formats']
-    if engine_filetypes is not None:
-        # Flatten the list if the engine_filetypes is a list of tuples
-        if all(isinstance(i, tuple) for i in engine_filetypes):
-            engine_filetypes = {item for sublist in engine_filetypes for item in sublist}
-        engine_file_types_text = [types_dict[i] for i in engine_filetypes if i in types_dict]
-        if input_filetypes.issubset(engine_filetypes):
-            return 'pass', (f"The file extensions suggest the input file types are '{input_file_types_text}'. These are compatible with {engine}")
-        else:
-            return 'FAIL', (f"The file extensions suggest the input file types are '{input_file_types_text}'. These are not compatible with {engine}. The following file types will be compatible {engine_file_types_text}")
+    input_filetypes_tuple = get_filetypes(model_filepath, experiment_filepath)
+    print('input filetypes:', input_filetypes_tuple)
+    engine_filetypes_tuple_list = engines[engine]['formats']
+    print('engine filetypes:', engine_filetypes_tuple_list)
+    flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist] if \
+        engine_filetypes_tuple_list != 'unclear' else engine_filetypes_tuple_list
+    print('flat list:', flat_engine_filetypes_tuple_list)
+    compatible_filetypes = [types_dict[i] for i in flat_engine_filetypes_tuple_list if i in list(types_dict.keys())]
+    print('compatible filetypes:', compatible_filetypes)
+
+    if input_filetypes_tuple in engine_filetypes_tuple_list:
+        file_types = [types_dict[i] for i in input_filetypes_tuple]
+        return 'pass', (f"The file extensions {input_filetypes_tuple} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}")
+    if 'xml' in input_filetypes_tuple:
+        return 'unsure', (f"The file extensions of the input files are '{input_filetypes_tuple}'. These may be compatible with {engine}. {compatible_filetypes} are compatible with {engine}")
     else:
-        return 'FAIL', (f"{engine} compatible file types unknown.")
-
+        return 'FAIL', (f"The file extensions {input_filetypes_tuple} suggest the input file types are not compatibe with {engine}. {compatible_filetypes} are compatible with {engine}")
+    
 
 def collapsible_content(content, title='Details'):
     """
@@ -470,6 +474,12 @@ def get_filetypes(model_filepath, simulation_filepath):
     """
     if model_filepath.endswith(".sbml") and simulation_filepath.endswith(".sedml"):
         filetypes = ('sbml', 'sedml')
+    elif model_filepath.endswith(".xml") and simulation_filepath.endswith(".xml"):
+        filetypes = ('xml', 'xml')
+    elif model_filepath.endswith(".xml") and simulation_filepath.endswith(".sedml"):
+        filetypes = ('xml', 'sedml')
+    elif model_filepath.endswith(".sbml") and simulation_filepath.endswith(".xml"):
+        filetypes = ('sbml', 'xml')
     else:
         filetypes = "other"
     return filetypes
@@ -1095,9 +1105,10 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng
     # compatibility_message
     results_table['Compat'] = results_table['Engine'].apply(lambda x: check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath))
     results_table['Compat'] = results_table['Compat'].apply(lambda x: collapsible_content(x[1], title=x[0]))
-    results_table['Compat'] = results_table['Compat'].apply(lambda x: f'<span style="color:darkred;"><img src={link_red_square}/> {x}</span>'\
-                                                             if 'FAIL' in x else f'<img src={link_green_square}/>{x}')
-
+    results_table['Compat'] = results_table['Compat'].apply(lambda x: 
+                                                        f'<span style="color:darkred;"><img src={link_red_square}/> {x}</span>' if 'FAIL' in x else 
+                                                        f'{x}' if 'xml' in x or 'unsure' in x else 
+                                                        f'<img src={link_green_square}/> {x}' if 'pass' in x else x)
     # pass / FAIL
     results_table['pass / FAIL'] = results_table['pass / FAIL'].apply(lambda x: f'<span style="color:darkred;">\
                                                                       <img src={link_red_square}/> {x}</span>' if x == 'FAIL' \

From 421b2651457893d5126822e5276734bd7f9461b2 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Mon, 2 Sep 2024 09:30:14 +0100
Subject: [PATCH 52/71] Test on py 3.11 as brian gives errors on py 3.9 now...

---
 .github/workflows/non-omv.yml | 2 +-
 regenerate.sh                 | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index de3a9b4..1f41f49 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9, "3.10" ]
+        python-version: [ "3.10", "3.11" ]
 
     steps:
     - uses: actions/checkout@v4
diff --git a/regenerate.sh b/regenerate.sh
index b31a2b0..99add05 100755
--- a/regenerate.sh
+++ b/regenerate.sh
@@ -34,7 +34,9 @@ jnml LEMS_Regular_HindmarshRose.xml -sbml-sedml
 mv *sedml ../SBML
 mv *sbml ../SBML
 
-cd ../SBML
+cd ../SBML/tests
 ./validateAll.sh
 python test_tellurium.py LEMS_Regular_HindmarshRose.sedml -nogui
 python test_tellurium.py LEMS_NML2_Ex9_FN.sedml -nogui
+
+echo "Finished all tests!"

From e6f6f71f6983f976b01dcf614de566ceb5ead5fc Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Mon, 2 Sep 2024 09:34:52 +0100
Subject: [PATCH 53/71] Update other workfow file

---
 .github/workflows/omv-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
index 7b00762..8819ba6 100644
--- a/.github/workflows/omv-ci.yml
+++ b/.github/workflows/omv-ci.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9, "3.10" ]
+        python-version: [ "3.10", "3.11" ]
         engine: [ jLEMS, jNeuroML, jNeuroML_NEURON, jNeuroML_validate, PyLEMS, PyLEMS_NeuroML2, jNeuroML_Brian2, Brian2, pyNeuroML_validate_sbml ]
 
     steps:

From 85ab845936c9c2e704a5387f8371026d336e2660 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 23 Sep 2024 14:10:12 +0100
Subject: [PATCH 54/71] fix broken d1 plot links results_table SBML folder

Co-authored-by: Robert Vickerstaff <robert.vickerstaff@gmail.com>
---
 .../results_compatibility_biosimulators.md    | 46 +++++++++----------
 .../tests/test_compatibility_biosimulators.py |  4 +-
 utils/__init__.py                             |  3 +-
 3 files changed, 26 insertions(+), 27 deletions(-)

diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index f13856d..689549c 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                           | Compat (L)                                                                                                                                                                                                                                                                                                           | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                                                            | d1 (R)                                                     | d1 (L)                                                    |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|:----------------------------------------------------------|
-|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici</details>                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici</details>                                                                      |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_d1.pdf">plot</a>      |
-|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details></span>                      | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details></span>                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_d1.pdf">plot</a>  |
-|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details></span>                     | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details></span>                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_d1.pdf">plot</a>    |
-|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details>                              | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details>                              | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                            |                                                           |
-|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_d1.pdf">plot</a>      |
-|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                                                    | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_d1.pdf">plot</a>    |
-|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Values[V]'</details>                                                                                                                                                                                                                           | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_d1.pdf">plot</a>     |
-|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                                                  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_d1.pdf">plot</a>  |
-|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details></span>                       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details></span>                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_d1.pdf">plot</a>     |
-|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                                                 |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
-| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_d1.pdf">plot</a>     |
-| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                            |                                                           |
-| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details></span>       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details></span>       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                            |                                                           |
-| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details></span>                        | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details></span>                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                            |                                                           |
-| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                            |                                                           |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpquunm0rr/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpquunm0rr/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_d1.pdf">plot</a>     |
-| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details></span>                             | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details></span>                             | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_d1.pdf">plot</a>      |
-| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn</details></span>                                          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn</details></span>                                          | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                            |                                                           |
-| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                                                  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="tests\d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_d1.pdf">plot</a>  |
-| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                            |                                                           |
-| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                            |                                                           |
\ No newline at end of file
+|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                                                                                                           | Compat (L)                                                                                                                                                                                                                                                                                                           | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Error (L)                                                                                                                                                                                            | d1 (R)                                               | d1 (L)                                              |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
+|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici</details>                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici</details>                                                                      |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\amici_d1.pdf">plot</a>      | <a href="d1_plots_local\amici_d1.pdf">plot</a>      |
+|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details></span>                      | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details></span>                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>              | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="d1_plots_remote\bionetgen_d1.pdf">plot</a>  | <a href="d1_plots_local\bionetgen_d1.pdf">plot</a>  |
+|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details></span>                     | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details></span>                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).</details>                                                                                                                  | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\boolnet_d1.pdf">plot</a>    | <a href="d1_plots_local\boolnet_d1.pdf">plot</a>    |
+|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details>                              | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details>                              | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                      |                                                     |
+|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                                                      | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\cbmpy_d1.pdf">plot</a>      | <a href="d1_plots_local\cbmpy_d1.pdf">plot</a>      |
+|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                                                    | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `sim1` is not supported.<br>      - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                                     | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\cobrapy_d1.pdf">plot</a>    | <a href="d1_plots_local\cobrapy_d1.pdf">plot</a>    |
+|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi</details>                                                                     |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\copasi_d1.pdf">plot</a>     | <a href="d1_plots_local\copasi_d1.pdf">plot</a>     |
+|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                                                  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\gillespy2_d1.pdf">plot</a>  | <a href="d1_plots_local\gillespy2_d1.pdf">plot</a>  |
+|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details></span>                       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details></span>                       | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `sim1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:<br>          Output start time: 0.0<br>          Output end time: 200.0<br>          Number of steps: 20000</details> | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\ginsim_d1.pdf">plot</a>     | <a href="d1_plots_local\ginsim_d1.pdf">plot</a>     |
+|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                                                 |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\libsbmlsim_d1.pdf">plot</a> | <a href="d1_plots_local\libsbmlsim_d1.pdf">plot</a> |
+| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\masspy_d1.pdf">plot</a>     | <a href="d1_plots_local\masspy_d1.pdf">plot</a>     |
+| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                      |                                                     |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details></span>       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details></span>       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                      |                                                     |
+| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details></span>                        | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details></span>                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                      |                                                     |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                      |                                                     |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpv03zz6ui/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpv03zz6ui/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
+| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details></span>                             | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details></span>                             | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_d1.pdf">plot</a>      |
+| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn</details></span>                                          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn</details></span>                                          | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                      |                                                     |
+| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                                                  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_d1.pdf">plot</a>  |
+| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> None                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                      |                                                     |
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```(109, 'GetOverlappedResult', 'The pipe has been ended.')```</details>                                                                                          |                                                      |                                                     |
\ No newline at end of file
diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py
index c801471..40b7710 100644
--- a/SBML/tests/test_compatibility_biosimulators.py
+++ b/SBML/tests/test_compatibility_biosimulators.py
@@ -37,8 +37,8 @@
 
 test_folder = 'tests'
 
-d1_plots_remote_dir = os.path.join(test_folder, args.output_dir + '_remote')
-d1_plots_local_dir = os.path.join(test_folder, args.output_dir + '_local')
+d1_plots_remote_dir = os.path.join(args.output_dir + '_remote')
+d1_plots_local_dir = os.path.join(args.output_dir + '_local')
 
 print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir)
 
diff --git a/utils/__init__.py b/utils/__init__.py
index 79bf4bb..ca146c3 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -439,8 +439,7 @@ def check_file_compatibility_test(engine, types_dict, model_filepath, experiment
     print('input filetypes:', input_filetypes_tuple)
     engine_filetypes_tuple_list = engines[engine]['formats']
     print('engine filetypes:', engine_filetypes_tuple_list)
-    flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist] if \
-        engine_filetypes_tuple_list != 'unclear' else engine_filetypes_tuple_list
+    flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist if sublist != 'unclear']
     print('flat list:', flat_engine_filetypes_tuple_list)
     compatible_filetypes = [types_dict[i] for i in flat_engine_filetypes_tuple_list if i in list(types_dict.keys())]
     print('compatible filetypes:', compatible_filetypes)

From 6c2a07c2ffbd5afec8d7af254fa8e4577a3f2f64 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 23 Sep 2024 15:48:41 +0100
Subject: [PATCH 55/71] fix broken d1_plots_path in a different way to avoid
 problems with folder structure

---
 SBML/tests/results_compatibility_biosimulators.md | 4 ++--
 SBML/tests/test_compatibility_biosimulators.py    | 6 +++---
 utils/__init__.py                                 | 7 +++----
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index 689549c..c558ced 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -15,9 +15,9 @@
 | 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details></span>       | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details></span>       | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                      |                                                     |
 | 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details></span>                        | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details></span>                        | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                      |                                                     |
 | 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details></span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details></span> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                      |                                                     |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpv03zz6ui/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpv03zz6ui/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces</details>                                                                     | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Model at /tmp/tmpod71_ka_/./LEMS_NML2_Ex9_FN.sbml could not be imported:<br>      <br>      File /tmp/tmpod71_ka_/./LEMS_NML2_Ex9_FN.sbml.xml does not exist</details>                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\pysces_d1.pdf">plot</a>     | <a href="d1_plots_local\pysces_d1.pdf">plot</a>     |
 | 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details></span>                             | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details></span>                             | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `net1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                 | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\rbapy_d1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_d1.pdf">plot</a>      |
 | 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn</details></span>                                          | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn</details></span>                                          | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                      |                                                     |
 | 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                                                  | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                      | <a href="d1_plots_remote\tellurium_d1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_d1.pdf">plot</a>  |
 | 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> None                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                                                    | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> <details><summary>pass</summary>The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                                                    |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                      |                                                     |
-| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```(109, 'GetOverlappedResult', 'The pipe has been ended.')```</details>                                                                                          |                                                      |                                                     |
\ No newline at end of file
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <span style="color:darkred;"><img src=https://via.placeholder.com/15/dd0000/dd0000.png/> <details><summary>FAIL</summary>The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details></span>                                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                             | <details><summary>Details</summary>```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                      |                                                     |
\ No newline at end of file
diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py
index 40b7710..83ce930 100644
--- a/SBML/tests/test_compatibility_biosimulators.py
+++ b/SBML/tests/test_compatibility_biosimulators.py
@@ -37,8 +37,8 @@
 
 test_folder = 'tests'
 
-d1_plots_remote_dir = os.path.join(args.output_dir + '_remote')
-d1_plots_local_dir = os.path.join(args.output_dir + '_local')
+d1_plots_remote_dir = os.path.join(test_folder, args.output_dir + '_remote')
+d1_plots_local_dir = os.path.join(test_folder, args.output_dir + '_local')
 
 print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir)
 
@@ -46,4 +46,4 @@
                                  sbml_file_name,
                                  d1_plots_remote_dir, 
                                  d1_plots_local_dir,
-                                 engines=engines, test_folder='tests')
\ No newline at end of file
+                                 engines=engines, test_folder=test_folder)
\ No newline at end of file
diff --git a/utils/__init__.py b/utils/__init__.py
index ca146c3..12bd767 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -365,7 +365,10 @@ def d1_plots_dict(engines=engines, d1_plots_path='d1_plots'):
     Create a dictionary with engine names as keys and d1 plot paths as values.
     """
     d1_plots = find_files(d1_plots_path, '.pdf')
+    # to fix broken links in output table after changing the file structure, remove the first two parts of the path
+    d1_plots = [os.path.join(*Path(d1_plot).parts[1:]) for d1_plot in d1_plots]
     d1_plots_dict = {e: d1_plot for e in engines.keys() for d1_plot in d1_plots if e in d1_plot}
+    
     return d1_plots_dict
 
 
@@ -436,13 +439,9 @@ def check_file_compatibility_test(engine, types_dict, model_filepath, experiment
     For SED-ML files, the expected file extension is '.sedml'. For SBML files, the expected file extension is '.sbml'.
     '''
     input_filetypes_tuple = get_filetypes(model_filepath, experiment_filepath)
-    print('input filetypes:', input_filetypes_tuple)
     engine_filetypes_tuple_list = engines[engine]['formats']
-    print('engine filetypes:', engine_filetypes_tuple_list)
     flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist if sublist != 'unclear']
-    print('flat list:', flat_engine_filetypes_tuple_list)
     compatible_filetypes = [types_dict[i] for i in flat_engine_filetypes_tuple_list if i in list(types_dict.keys())]
-    print('compatible filetypes:', compatible_filetypes)
 
     if input_filetypes_tuple in engine_filetypes_tuple_list:
         file_types = [types_dict[i] for i in input_filetypes_tuple]

From ab238ee01b38a0a7ff8c65171957de89da783377 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 23 Sep 2024 17:40:06 +0100
Subject: [PATCH 56/71] update results table with correct plot links

---
 .../results_compatibility_biosimulators.md    | 46 +++++++++----------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md
index e35c5d1..1fd797f 100644
--- a/test_suite/test_00001/tests/results_compatibility_biosimulators.md
+++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                         | Compat (L)                                                                                                                                                                                                                         | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Error (L)                                                                                                                                                                                   | d1 (R)                                                         | d1 (L)                                                        |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------|
-|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\amici_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_plot_1.pdf">plot</a>      |
-|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>             | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_plot_1.pdf">plot</a>  |
-|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).</details>                                                                                                                 | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_plot_1.pdf">plot</a>    |
-|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                |                                                               |
-|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_plot_1.pdf">plot</a>      |
-|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_plot_1.pdf">plot</a>    |
-|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Compartments[compartment].Volume'</details>                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_plot_1.pdf">plot</a>     |
-|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\gillespy2_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_plot_1.pdf">plot</a>  |
-|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:<br>          Output start time: 0.0<br>          Output end time: 5.0<br>          Number of steps: 50</details> | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_plot_1.pdf">plot</a>     |
-|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\libsbmlsim_plot_1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_plot_1.pdf">plot</a> |
-| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_plot_1.pdf">plot</a>     |
-| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                |                                                               |
-| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                |                                                               |
-| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                |                                                               |
-| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                |                                                               |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\pysces_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_plot_1.pdf">plot</a>     |
-| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_plot_1.pdf">plot</a>      |
-| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                |                                                               |
-| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\tellurium_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_plot_1.pdf">plot</a>  |
-| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                                |                                                               |
-| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                |                                                               |
\ No newline at end of file
+|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                         | Compat (L)                                                                                                                                                                                                                         | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Error (L)                                                                                                                                                                                   | d1 (R)                                                   | d1 (L)                                                  |
+|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------|
+|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="d1_plots_remote\amici_plot_1.pdf">plot</a>      | <a href="d1_plots_local\amici_plot_1.pdf">plot</a>      |
+|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>             | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="d1_plots_remote\bionetgen_plot_1.pdf">plot</a>  | <a href="d1_plots_local\bionetgen_plot_1.pdf">plot</a>  |
+|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).</details>                                                                                                                 | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\boolnet_plot_1.pdf">plot</a>    | <a href="d1_plots_local\boolnet_plot_1.pdf">plot</a>    |
+|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                          |                                                         |
+|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\cbmpy_plot_1.pdf">plot</a>      | <a href="d1_plots_local\cbmpy_plot_1.pdf">plot</a>      |
+|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="d1_plots_remote\cobrapy_plot_1.pdf">plot</a>    | <a href="d1_plots_local\cobrapy_plot_1.pdf">plot</a>    |
+|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="d1_plots_remote\copasi_plot_1.pdf">plot</a>     | <a href="d1_plots_local\copasi_plot_1.pdf">plot</a>     |
+|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="d1_plots_remote\gillespy2_plot_1.pdf">plot</a>  | <a href="d1_plots_local\gillespy2_plot_1.pdf">plot</a>  |
+|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:<br>          Output start time: 0.0<br>          Output end time: 5.0<br>          Number of steps: 50</details> | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\ginsim_plot_1.pdf">plot</a>     | <a href="d1_plots_local\ginsim_plot_1.pdf">plot</a>     |
+|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="d1_plots_remote\libsbmlsim_plot_1.pdf">plot</a> | <a href="d1_plots_local\libsbmlsim_plot_1.pdf">plot</a> |
+| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="d1_plots_remote\masspy_plot_1.pdf">plot</a>     | <a href="d1_plots_local\masspy_plot_1.pdf">plot</a>     |
+| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                          |                                                         |
+| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                          |                                                         |
+| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                          |                                                         |
+| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                          |                                                         |
+| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="d1_plots_remote\pysces_plot_1.pdf">plot</a>     | <a href="d1_plots_local\pysces_plot_1.pdf">plot</a>     |
+| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="d1_plots_remote\rbapy_plot_1.pdf">plot</a>      | <a href="d1_plots_local\rbapy_plot_1.pdf">plot</a>      |
+| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                          |                                                         |
+| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="d1_plots_remote\tellurium_plot_1.pdf">plot</a>  | <a href="d1_plots_local\tellurium_plot_1.pdf">plot</a>  |
+| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> None                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                          |                                                         |
+| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                          |                                                         |
\ No newline at end of file

From c5ebf65d2a8654b0e71351d1559ffc1ed7bf4bce Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 23 Sep 2024 17:41:04 +0100
Subject: [PATCH 57/71]  remove test_00002 and test_00003 folders before
 merging

---
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index 8d3b477..0000000
--- a/test_suite/test_00002/00002-sbml-l3v2-sedml.xml
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index a7d7ff9..0000000
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diff --git a/test_suite/test_00002/tests/results_compatibility_biosimulators.md b/test_suite/test_00002/tests/results_compatibility_biosimulators.md
deleted file mode 100644
index 332ba2b..0000000
--- a/test_suite/test_00002/tests/results_compatibility_biosimulators.md
+++ /dev/null
@@ -1,23 +0,0 @@
-|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                         | Compat (L)                                                                                                                                                                                                                         | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Error (L)                                                                                                                                                                                   | d1 (R)                                                         | d1 (L)                                                        |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------|
-|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\amici_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_plot_1.pdf">plot</a>      |
-|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>             | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_plot_1.pdf">plot</a>  |
-|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).</details>                                                                                                                 | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_plot_1.pdf">plot</a>    |
-|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                |                                                               |
-|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_plot_1.pdf">plot</a>      |
-|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_plot_1.pdf">plot</a>    |
-|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Compartments[compartment].Volume'</details>                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_plot_1.pdf">plot</a>     |
-|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\gillespy2_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_plot_1.pdf">plot</a>  |
-|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:<br>          Output start time: 0.0<br>          Output end time: 5.0<br>          Number of steps: 50</details> | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_plot_1.pdf">plot</a>     |
-|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\libsbmlsim_plot_1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_plot_1.pdf">plot</a> |
-| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_plot_1.pdf">plot</a>     |
-| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                |                                                               |
-| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                |                                                               |
-| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                |                                                               |
-| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                |                                                               |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\pysces_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_plot_1.pdf">plot</a>     |
-| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_plot_1.pdf">plot</a>      |
-| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                |                                                               |
-| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\tellurium_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_plot_1.pdf">plot</a>  |
-| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                                |                                                               |
-| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                |                                                               |
\ No newline at end of file
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diff --git a/test_suite/test_00003/00003-sbml-l3v2-sedml.xml b/test_suite/test_00003/00003-sbml-l3v2-sedml.xml
deleted file mode 100644
index 41ac28b..0000000
--- a/test_suite/test_00003/00003-sbml-l3v2-sedml.xml
+++ /dev/null
@@ -1,66 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!-- Written by libSedML v1.1.5419.25885 see http://libsedml.sf.net -->
-<sedML level="1" version="1" xmlns="http://sed-ml.org/">
-  <listOfSimulations>
-    <uniformTimeCourse id="simulation_1" initialTime="0" outputStartTime="0" outputEndTime="5" numberOfPoints="50">
-      <algorithm kisaoID="KISAO:0000019" />
-    </uniformTimeCourse>
-  </listOfSimulations>
-  <listOfModels>
-    <model id="model_1" language="urn:sedml:language:sbml" source="00003-sbml-l3v2.xml" />
-  </listOfModels>
-  <listOfTasks>
-    <task id="task_1" modelReference="model_1" simulationReference="simulation_1" />
-  </listOfTasks>
-  <listOfDataGenerators>
-    <dataGenerator id="time_1" name="time">
-      <listOfVariables>
-        <variable id="time" taskReference="task_1" symbol="urn:sedml:symbol:time" />
-      </listOfVariables>
-      <math xmlns="http://www.w3.org/1998/Math/MathML">
-        <ci> time </ci>
-      </math>
-    </dataGenerator>
-    <dataGenerator id="S1_1" name="S1">
-      <listOfVariables>
-        <variable id="S1_1_s" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']" />
-        <variable id="S1_1_c" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']" />
-      </listOfVariables>
-      <math xmlns="http://www.w3.org/1998/Math/MathML">
-        <apply>
-          <times />
-          <ci> S1_1_s </ci>
-          <ci> S1_1_c </ci>
-        </apply>
-      </math>
-    </dataGenerator>
-    <dataGenerator id="S2_1" name="S2">
-      <listOfVariables>
-        <variable id="S2_1_s" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']" />
-        <variable id="S2_1_c" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']" />
-      </listOfVariables>
-      <math xmlns="http://www.w3.org/1998/Math/MathML">
-        <apply>
-          <times />
-          <ci> S2_1_s </ci>
-          <ci> S2_1_c </ci>
-        </apply>
-      </math>
-    </dataGenerator>
-  </listOfDataGenerators>
-  <listOfOutputs>
-    <plot2D id="plot_1" name="Timecourse for test 00003">
-      <listOfCurves>
-        <curve id="c_S1_1" name="S1" logX="false" logY="false" xDataReference="time_1" yDataReference="S1_1" />
-        <curve id="c_S2_1" name="S2" logX="false" logY="false" xDataReference="time_1" yDataReference="S2_1" />
-      </listOfCurves>
-    </plot2D>
-    <report id="report_1" name="Report for test 00003">
-      <listOfDataSets>
-        <dataSet id="ds_time" dataReference="time_1" label="Time" />
-        <dataSet id="ds_S1_1" dataReference="S1_1" label="S1" />
-        <dataSet id="ds_S2_1" dataReference="S2_1" label="S2" />
-      </listOfDataSets>
-    </report>
-  </listOfOutputs>
-</sedML>
\ No newline at end of file
diff --git a/test_suite/test_00003/00003-sbml-l3v2.xml b/test_suite/test_00003/00003-sbml-l3v2.xml
deleted file mode 100644
index 7b17b5e..0000000
--- a/test_suite/test_00003/00003-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
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-    <listOfUnitDefinitions>
-      <unitDefinition id="volume">
-        <listOfUnits>
-          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
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-      </unitDefinition>
-      <unitDefinition id="time">
-        <listOfUnits>
-          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
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-      </unitDefinition>
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-      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
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-    <listOfSpecies>
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-    <listOfParameters>
-      <parameter id="k1" name="k1" value="1" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="reaction1" name="reaction1" reversible="false">
-        <listOfReactants>
-          <speciesReference species="S1" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="S2" stoichiometry="2" constant="true"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> compartment </ci>
-              <ci> k1 </ci>
-              <ci> S1 </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/test_suite/test_00003/tests/d1_plots_local/amici_plot_1.pdf b/test_suite/test_00003/tests/d1_plots_local/amici_plot_1.pdf
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diff --git a/test_suite/test_00003/tests/results_compatibility_biosimulators.md b/test_suite/test_00003/tests/results_compatibility_biosimulators.md
deleted file mode 100644
index 7a0884e..0000000
--- a/test_suite/test_00003/tests/results_compatibility_biosimulators.md
+++ /dev/null
@@ -1,23 +0,0 @@
-|    | Engine                                                                                                                                     | pass / FAIL (R)                                                                                                                                                            | pass / FAIL (L)                                                                                                                                                            | Compat (R)                                                                                                                                                                                                                         | Compat (L)                                                                                                                                                                                                                         | Type (R)                                                               | Error (R)                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Error (L)                                                                                                                                                                                   | d1 (R)                                                         | d1 (L)                                                        |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------|
-|  0 | <details><summary>amici</summary>https://docs.biosimulators.org/Biosimulators_AMICI/<br></details>                                         | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici</details>                                          |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\amici_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\amici_plot_1.pdf">plot</a>      |
-|  1 | <details><summary>bionetgen</summary>https://docs.biosimulators.org/Biosimulators_BioNetGen/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen</details>                                  | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).</details>             | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```</details> | <a href="tests\d1_plots_remote\bionetgen_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\bionetgen_plot_1.pdf">plot</a>  |
-|  2 | <details><summary>boolnet</summary>https://docs.biosimulators.org/Biosimulators_BoolNet/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet</details>                                 | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).</details>                                                                                                                 | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\boolnet_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\boolnet_plot_1.pdf">plot</a>    |
-|  3 | <details><summary>brian2</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2</details> | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```</details>    |                                                                |                                                               |
-|  4 | <details><summary>cbmpy</summary>https://docs.biosimulators.org/Biosimulators_CBMPy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy</details>                                          | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\cbmpy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\cbmpy_plot_1.pdf">plot</a>      |
-|  5 | <details><summary>cobrapy</summary>https://docs.biosimulators.org/Biosimulators_COBRApy/<br>Only allows steady state simulations</details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy</details>                                      | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    UniformTimeCourseSimulation `simulation_1` is not supported.<br>      - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:<br>          - SteadyStateSimulation</details>                       | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```</details>   | <a href="tests\d1_plots_remote\cobrapy_plot_1.pdf">plot</a>    | <a href="tests\d1_plots_local\cobrapy_plot_1.pdf">plot</a>    |
-|  6 | <details><summary>copasi</summary>https://docs.biosimulators.org/Biosimulators_COPASI/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    could not convert string to float: 'Compartments[compartment].Volume'</details>                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\copasi_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\copasi_plot_1.pdf">plot</a>     |
-|  7 | <details><summary>gillespy2</summary>https://docs.biosimulators.org/Biosimulators_GillesPy2/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\gillespy2_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\gillespy2_plot_1.pdf">plot</a>  |
-|  8 | <details><summary>ginsim</summary>https://docs.biosimulators.org/Biosimulators_GINsim/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim</details>                                   | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Simulation `simulation_1` is invalid.<br>      - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:<br>          Output start time: 0.0<br>          Output end time: 5.0<br>          Number of steps: 50</details> | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\ginsim_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\ginsim_plot_1.pdf">plot</a>     |
-|  9 | <details><summary>libsbmlsim</summary>https://docs.biosimulators.org/Biosimulators_LibSBMLSim/<br></details>                               | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim</details>                                |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\libsbmlsim_plot_1.pdf">plot</a> | <a href="tests\d1_plots_local\libsbmlsim_plot_1.pdf">plot</a> |
-| 10 | <details><summary>masspy</summary>https://docs.biosimulators.org/Biosimulators_MASSpy/<br></details>                                       | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy</details>                                        | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .<br>    	`(model, errors) = validate_sbml_model(filename)`<br>    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .</details>                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```</details>    | <a href="tests\d1_plots_remote\masspy_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\masspy_plot_1.pdf">plot</a>     |
-| 11 | <details><summary>netpyne</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                   | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne</details>                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```</details>   |                                                                |                                                               |
-| 12 | <details><summary>neuron</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                    | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron</details>                   | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```</details>    |                                                                |                                                               |
-| 13 | <details><summary>opencor</summary>https://docs.biosimulators.org/Biosimulators_OpenCOR/<br></details>                                     | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor</details>                                    | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```</details>   |                                                                |                                                               |
-| 14 | <details><summary>pyneuroml</summary>https://docs.biosimulators.org/Biosimulators_pyNeuroML/<br></details>                                 | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml</details>             | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```</details> |                                                                |                                                               |
-| 15 | <details><summary>pysces</summary>https://docs.biosimulators.org/Biosimulators_PySCeS/<br></details>                                       | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces</details>                                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\pysces_plot_1.pdf">plot</a>     | <a href="tests\d1_plots_local\pysces_plot_1.pdf">plot</a>     |
-| 16 | <details><summary>rbapy</summary>https://docs.biosimulators.org/Biosimulators_RBApy/<br></details>                                         | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy</details>                                         | <details><summary>CAEE</summary>CombineArchiveExecutionError</details> | <details><summary>Details</summary><span style="color:red;">The COMBINE/OMEX did not execute successfully:<br><br>  The SED document did not execute successfully:<br>  <br>    Language for model `model_1` is not supported.<br>      - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).</details>                | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```</details>     | <a href="tests\d1_plots_remote\rbapy_plot_1.pdf">plot</a>      | <a href="tests\d1_plots_local\rbapy_plot_1.pdf">plot</a>      |
-| 17 | <details><summary>smoldyn</summary>https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api<br></details> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn</details>                                                      | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```</details>   |                                                                |                                                               |
-| 18 | <details><summary>tellurium</summary>https://docs.biosimulators.org/Biosimulators_tellurium/<br></details>                                 | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium</details>                                  |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                             | <a href="tests\d1_plots_remote\tellurium_plot_1.pdf">plot</a>  | <a href="tests\d1_plots_local\tellurium_plot_1.pdf">plot</a>  |
-| 19 | <details><summary>vcell</summary>https://github.com/virtualcell/vcell<br></details>                                                        | <img src=https://via.placeholder.com/15/00dd00/00dd00.png/> pass                                                                                                           | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell</details>                        |                                                                        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```</details>     |                                                                |                                                               |
-| 20 | <details><summary>xpp</summary>https://docs.biosimulators.org/Biosimulators_XPP/<br></details>                                             | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <span style="color:darkred;">                                                                      <img src=https://via.placeholder.com/15/dd0000/dd0000.png/> FAIL</span> | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>unsure</summary>The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp</details>                                               | <details><summary>MNFE</summary>ModuleNotFoundError</details>          | <details><summary>Details</summary>No module named 'libsbml'</details>                                                                                                                                                                                                                                                                                                                                                                                               | <details><summary>Details</summary>```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```</details>       |                                                                |                                                               |
\ No newline at end of file

From 86052129376a4650ae54c9a8d1a16888b0113fe4 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 23 Sep 2024 18:12:00 +0100
Subject: [PATCH 58/71] add  non-omv-remote.yml  and  non-omv-local.yml

---
 .github/workflows/non-omv-local.yml     | 40 +++++++++++++++++++++
 .github/workflows/non-omv-remote.yml    | 40 +++++++++++++++++++++
 SBML/tests/test_biosimulators_local.py  | 48 +++++++++++++++++++++++++
 SBML/tests/test_biosimulators_remote.py | 48 +++++++++++++++++++++++++
 4 files changed, 176 insertions(+)
 create mode 100644 .github/workflows/non-omv-local.yml
 create mode 100644 .github/workflows/non-omv-remote.yml
 create mode 100644 SBML/tests/test_biosimulators_local.py
 create mode 100644 SBML/tests/test_biosimulators_remote.py

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
new file mode 100644
index 0000000..9742918
--- /dev/null
+++ b/.github/workflows/non-omv-local.yml
@@ -0,0 +1,40 @@
+
+name: Testing non OMV scripts for remote biosimulators testing
+
+on:
+  push:
+    branches: [ master, development, experimental, test*, feature/* ]
+  pull_request:
+    branches: [ master, development, experimental, test*, feature/* ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ 3.9, "3.10" ]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version:  ${{ matrix.python-version }}
+
+    # - name: Install OMV
+    #   run: |
+    #     pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+
+    # - name: Run tests
+    #   run: |
+    #     omv install jneuroml
+
+    - name: Test remote biosimulators compatibility table creation
+      run: |
+        cd SBML/tests
+        sudo rm -rf output
+        python ./test_biosimulators_remote.py --output-dir=tmp_plots
+
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
new file mode 100644
index 0000000..9742918
--- /dev/null
+++ b/.github/workflows/non-omv-remote.yml
@@ -0,0 +1,40 @@
+
+name: Testing non OMV scripts for remote biosimulators testing
+
+on:
+  push:
+    branches: [ master, development, experimental, test*, feature/* ]
+  pull_request:
+    branches: [ master, development, experimental, test*, feature/* ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ 3.9, "3.10" ]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version:  ${{ matrix.python-version }}
+
+    # - name: Install OMV
+    #   run: |
+    #     pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+
+    # - name: Run tests
+    #   run: |
+    #     omv install jneuroml
+
+    - name: Test remote biosimulators compatibility table creation
+      run: |
+        cd SBML/tests
+        sudo rm -rf output
+        python ./test_biosimulators_remote.py --output-dir=tmp_plots
+
diff --git a/SBML/tests/test_biosimulators_local.py b/SBML/tests/test_biosimulators_local.py
new file mode 100644
index 0000000..982efd5
--- /dev/null
+++ b/SBML/tests/test_biosimulators_local.py
@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+"""
+This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file.
+It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation.
+The results are then displayed in a table and saved to a markdown file.
+"""
+
+import sys
+import os
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils
+import utils
+import argparse
+
+engines = utils.engines
+types_dict = utils.types_dict
+
+# Save the current working directory
+cwd = os.getcwd()
+print('Current working directory:', cwd)
+
+# SBML folder is one folder up relative to cwd
+path_to_sbml_folder = os.path.abspath(os.path.join(cwd, os.pardir))
+print('Path to SBML folder:', path_to_sbml_folder)
+
+# change the working directory to the SBML folder (because here the SBML and SED-ML files are located)
+os.chdir(path_to_sbml_folder)
+print('Changed working directory to:', os.getcwd())
+
+sbml_file_name = 'LEMS_NML2_Ex9_FN.sbml'
+sedml_file_name = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
+
+# output_dir is set to 'd1_plots' by default but can be changed using the --output-dir argument (required to deal with GitHub Actions permission issues)
+parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines')
+parser.add_argument('--output-dir',action='store',default='d1_plots',help='prefix of the output directory where the d1 plots will be saved')
+args = parser.parse_args()
+
+test_folder = 'tests'
+
+d1_plots_local_dir = os.path.join(test_folder, args.output_dir + '_local')
+
+print('d1 plots will be saved in:', d1_plots_local_dir)
+
+results_remote = utils.run_biosimulators_locally(sedml_file_name=sedml_file_name, 
+                                    sbml_file_name=sbml_file_name,
+                                    d1_plots_remote_dir=d1_plots_local_dir, 
+                                    engines=engines, test_folder=test_folder)
+    
\ No newline at end of file
diff --git a/SBML/tests/test_biosimulators_remote.py b/SBML/tests/test_biosimulators_remote.py
new file mode 100644
index 0000000..75b2b3b
--- /dev/null
+++ b/SBML/tests/test_biosimulators_remote.py
@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+"""
+This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file.
+It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation.
+The results are then displayed in a table and saved to a markdown file.
+"""
+
+import sys
+import os
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils
+import utils
+import argparse
+
+engines = utils.engines
+types_dict = utils.types_dict
+
+# Save the current working directory
+cwd = os.getcwd()
+print('Current working directory:', cwd)
+
+# SBML folder is one folder up relative to cwd
+path_to_sbml_folder = os.path.abspath(os.path.join(cwd, os.pardir))
+print('Path to SBML folder:', path_to_sbml_folder)
+
+# change the working directory to the SBML folder (because here the SBML and SED-ML files are located)
+os.chdir(path_to_sbml_folder)
+print('Changed working directory to:', os.getcwd())
+
+sbml_file_name = 'LEMS_NML2_Ex9_FN.sbml'
+sedml_file_name = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
+
+# output_dir is set to 'd1_plots' by default but can be changed using the --output-dir argument (required to deal with GitHub Actions permission issues)
+parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines')
+parser.add_argument('--output-dir',action='store',default='d1_plots',help='prefix of the output directory where the d1 plots will be saved')
+args = parser.parse_args()
+
+test_folder = 'tests'
+
+d1_plots_remote_dir = os.path.join(test_folder, args.output_dir + '_remote')
+
+print('d1 plots will be saved in:', d1_plots_remote_dir)
+
+results_remote = utils.run_biosimulators_remotely(sedml_file_name=sedml_file_name, 
+                                    sbml_file_name=sbml_file_name,
+                                    d1_plots_remote_dir=d1_plots_remote_dir, 
+                                    engines=engines, test_folder=test_folder)
+    
\ No newline at end of file

From 7cd27107a18e5f465d32d163285f3d94e7baf325 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 10:43:32 +0100
Subject: [PATCH 59/71] add installation command for jneuroml in
 non-omv-local.yml and non-omv-remote.yml

---
 .github/workflows/non-omv-local.yml  | 6 +++---
 .github/workflows/non-omv-remote.yml | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
index 9742918..be18dcf 100644
--- a/.github/workflows/non-omv-local.yml
+++ b/.github/workflows/non-omv-local.yml
@@ -28,9 +28,9 @@ jobs:
     #   run: |
     #     pip install git+https://github.com/OpenSourceBrain/osb-model-validation
 
-    # - name: Run tests
-    #   run: |
-    #     omv install jneuroml
+    - name: Run tests
+      run: |
+        omv install jneuroml
 
     - name: Test remote biosimulators compatibility table creation
       run: |
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
index 9742918..be18dcf 100644
--- a/.github/workflows/non-omv-remote.yml
+++ b/.github/workflows/non-omv-remote.yml
@@ -28,9 +28,9 @@ jobs:
     #   run: |
     #     pip install git+https://github.com/OpenSourceBrain/osb-model-validation
 
-    # - name: Run tests
-    #   run: |
-    #     omv install jneuroml
+    - name: Run tests
+      run: |
+        omv install jneuroml
 
     - name: Test remote biosimulators compatibility table creation
       run: |

From 0612b6d4eb8419aa0d661bbd89e297328b7b5075 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 10:44:50 +0100
Subject: [PATCH 60/71] add installation command for OMV in non-omv-local.yml
 and non-omv-remote.yml

---
 .github/workflows/non-omv-local.yml  | 6 +++---
 .github/workflows/non-omv-remote.yml | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
index be18dcf..75b74c1 100644
--- a/.github/workflows/non-omv-local.yml
+++ b/.github/workflows/non-omv-local.yml
@@ -24,9 +24,9 @@ jobs:
       with:
         python-version:  ${{ matrix.python-version }}
 
-    # - name: Install OMV
-    #   run: |
-    #     pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+    - name: Install OMV
+      run: |
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
 
     - name: Run tests
       run: |
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
index be18dcf..75b74c1 100644
--- a/.github/workflows/non-omv-remote.yml
+++ b/.github/workflows/non-omv-remote.yml
@@ -24,9 +24,9 @@ jobs:
       with:
         python-version:  ${{ matrix.python-version }}
 
-    # - name: Install OMV
-    #   run: |
-    #     pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+    - name: Install OMV
+      run: |
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
 
     - name: Run tests
       run: |

From c4d0073c74210fc88c8cdb404f32a8806d802f9d Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 10:52:35 +0100
Subject: [PATCH 61/71] remove non-omv-local.yml and non-omv-remote.yml and add
 workflows to non-omv.yml

---
 .github/workflows/non-omv-local.yml  | 40 ----------------------------
 .github/workflows/non-omv-remote.yml | 40 ----------------------------
 .github/workflows/non-omv.yml        | 15 +++++++++++
 3 files changed, 15 insertions(+), 80 deletions(-)
 delete mode 100644 .github/workflows/non-omv-local.yml
 delete mode 100644 .github/workflows/non-omv-remote.yml

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
deleted file mode 100644
index 75b74c1..0000000
--- a/.github/workflows/non-omv-local.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-
-name: Testing non OMV scripts for remote biosimulators testing
-
-on:
-  push:
-    branches: [ master, development, experimental, test*, feature/* ]
-  pull_request:
-    branches: [ master, development, experimental, test*, feature/* ]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: [ 3.9, "3.10" ]
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version:  ${{ matrix.python-version }}
-
-    - name: Install OMV
-      run: |
-        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
-
-    - name: Run tests
-      run: |
-        omv install jneuroml
-
-    - name: Test remote biosimulators compatibility table creation
-      run: |
-        cd SBML/tests
-        sudo rm -rf output
-        python ./test_biosimulators_remote.py --output-dir=tmp_plots
-
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
deleted file mode 100644
index 75b74c1..0000000
--- a/.github/workflows/non-omv-remote.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-
-name: Testing non OMV scripts for remote biosimulators testing
-
-on:
-  push:
-    branches: [ master, development, experimental, test*, feature/* ]
-  pull_request:
-    branches: [ master, development, experimental, test*, feature/* ]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: [ 3.9, "3.10" ]
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version:  ${{ matrix.python-version }}
-
-    - name: Install OMV
-      run: |
-        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
-
-    - name: Run tests
-      run: |
-        omv install jneuroml
-
-    - name: Test remote biosimulators compatibility table creation
-      run: |
-        cd SBML/tests
-        sudo rm -rf output
-        python ./test_biosimulators_remote.py --output-dir=tmp_plots
-
diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index de3a9b4..97922da 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -73,3 +73,18 @@ jobs:
         omv list -V # list installed engines
         pip list
         env
+
+    - name: Test remote biosimulators compatibility table creation
+      run: |
+        cd SBML/tests
+        sudo rm -rf output
+        python ./test_biosimulators_remote.py --output-dir=tmp_plots
+
+
+    - name: Test local biosimulators compatibility table creation
+        run: |
+          cd SBML/tests
+          sudo rm -rf output
+          python ./test_biosimulators_local.py --output-dir=tmp_plots
+  
+  
\ No newline at end of file

From 6a8a02567e1c7d62d2923a781e4bf3f1afcc1d6c Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 11:07:46 +0100
Subject: [PATCH 62/71] add non-omv-local.yml and non-omv-remote.yml

---
 .github/workflows/non-omv-local.yml  | 47 ++++++++++++++++++++++++++++
 .github/workflows/non-omv-remote.yml | 47 ++++++++++++++++++++++++++++
 .github/workflows/non-omv.yml        |  2 +-
 3 files changed, 95 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/non-omv-local.yml
 create mode 100644 .github/workflows/non-omv-remote.yml

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
new file mode 100644
index 0000000..a34eda0
--- /dev/null
+++ b/.github/workflows/non-omv-local.yml
@@ -0,0 +1,47 @@
+
+name: Testing non OMV scripts
+
+on:
+  push:
+    branches: [ master, development, experimental, test*, feature/* ]
+  pull_request:
+    branches: [ master, development, experimental, test*, feature/* ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ 3.9, "3.10" ]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version:  ${{ matrix.python-version }}
+
+    - name: Install OMV
+      run: |
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+
+    - name: Run tests
+      run: |
+        omv install jneuroml
+
+    - name: Final version info
+      run: |
+        omv list -V # list installed engines
+        pip list
+        env
+
+    - name: Test local biosimulators compatibility table creation
+      run: |
+          cd SBML/tests
+          sudo rm -rf output
+          python ./test_biosimulators_local.py --output-dir=tmp_plots
+  
+  
\ No newline at end of file
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
new file mode 100644
index 0000000..3d8ba21
--- /dev/null
+++ b/.github/workflows/non-omv-remote.yml
@@ -0,0 +1,47 @@
+
+name: Testing non OMV scripts
+
+on:
+  push:
+    branches: [ master, development, experimental, test*, feature/* ]
+  pull_request:
+    branches: [ master, development, experimental, test*, feature/* ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ 3.9, "3.10" ]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version:  ${{ matrix.python-version }}
+
+    - name: Install OMV
+      run: |
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+
+    - name: Run tests
+      run: |
+        omv install jneuroml
+
+    - name: Final version info
+      run: |
+        omv list -V # list installed engines
+        pip list
+        env
+
+    - name: Test remote biosimulators compatibility table creation
+      run: |
+        cd SBML/tests
+        sudo rm -rf output
+        python ./test_biosimulators_remote.py --output-dir=tmp_plots
+  
+  
\ No newline at end of file
diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index 97922da..c5fea53 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -82,7 +82,7 @@ jobs:
 
 
     - name: Test local biosimulators compatibility table creation
-        run: |
+      run: |
           cd SBML/tests
           sudo rm -rf output
           python ./test_biosimulators_local.py --output-dir=tmp_plots

From 9a4710d67b9a5fca63dc738c9da6f1b64dd7125f Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 11:31:19 +0100
Subject: [PATCH 63/71] add pyneuroml installation to non-omv local and remote
 ymls

---
 .github/workflows/non-omv-local.yml  | 4 ++++
 .github/workflows/non-omv-remote.yml | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
index a34eda0..235ae71 100644
--- a/.github/workflows/non-omv-local.yml
+++ b/.github/workflows/non-omv-local.yml
@@ -28,6 +28,10 @@ jobs:
       run: |
         pip install git+https://github.com/OpenSourceBrain/osb-model-validation
 
+    - name: Install pyNeuroML
+      run: |
+        pip install pyNeuroML pyNeuroML[annotations]
+
     - name: Run tests
       run: |
         omv install jneuroml
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
index 3d8ba21..ef3d879 100644
--- a/.github/workflows/non-omv-remote.yml
+++ b/.github/workflows/non-omv-remote.yml
@@ -27,6 +27,10 @@ jobs:
     - name: Install OMV
       run: |
         pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+        
+    - name: Install pyNeuroML
+      run: |
+        pip install pyNeuroML pyNeuroML[annotations]
 
     - name: Run tests
       run: |

From d4681fca1520f8d93400ed4eb2b61238845703ec Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 11:34:24 +0100
Subject: [PATCH 64/71] add libsedml installation to non-omv local and remote
 ymls

---
 .github/workflows/non-omv-local.yml  | 4 ++++
 .github/workflows/non-omv-remote.yml | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
index 235ae71..79fc4d6 100644
--- a/.github/workflows/non-omv-local.yml
+++ b/.github/workflows/non-omv-local.yml
@@ -32,6 +32,10 @@ jobs:
       run: |
         pip install pyNeuroML pyNeuroML[annotations]
 
+    - name: Install libsedml
+      run: |
+          pip install python-libsedml
+
     - name: Run tests
       run: |
         omv install jneuroml
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
index ef3d879..4877102 100644
--- a/.github/workflows/non-omv-remote.yml
+++ b/.github/workflows/non-omv-remote.yml
@@ -32,6 +32,10 @@ jobs:
       run: |
         pip install pyNeuroML pyNeuroML[annotations]
 
+    - name: Install libsedml
+      run: |
+        pip install python-libsedml
+
     - name: Run tests
       run: |
         omv install jneuroml

From bc2fc7c4e6f4f7fd248c7acd96331f5300ec9a3e Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 11:41:55 +0100
Subject: [PATCH 65/71] add tellurium and sudo libncurses5 installation to
 non-omv local and remote ymls

---
 .github/workflows/non-omv-local.yml  | 5 +++++
 .github/workflows/non-omv-remote.yml | 5 +++++
 2 files changed, 10 insertions(+)

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
index 79fc4d6..ee15fc5 100644
--- a/.github/workflows/non-omv-local.yml
+++ b/.github/workflows/non-omv-local.yml
@@ -36,6 +36,11 @@ jobs:
       run: |
           pip install python-libsedml
 
+    - name: Install Tellurium
+      run: |
+          pip install tellurium
+          sudo apt-get install libncurses5 --fix-missing
+
     - name: Run tests
       run: |
         omv install jneuroml
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
index 4877102..34f0ae6 100644
--- a/.github/workflows/non-omv-remote.yml
+++ b/.github/workflows/non-omv-remote.yml
@@ -36,6 +36,11 @@ jobs:
       run: |
         pip install python-libsedml
 
+    - name: Install Tellurium and libncurses5
+      run: |
+          pip install tellurium
+          sudo apt-get install libncurses5 --fix-missing
+
     - name: Run tests
       run: |
         omv install jneuroml

From 650ab28ba7bb544e624e8618e49846f7bd0c5014 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 11:46:57 +0100
Subject: [PATCH 66/71] add pymetadata installation to non-omv local and remote
 ymls and add all required modules to "Install dependencies"

---
 .github/workflows/non-omv-local.yml  | 21 +++++----------------
 .github/workflows/non-omv-remote.yml | 19 ++++---------------
 2 files changed, 9 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
index ee15fc5..135b829 100644
--- a/.github/workflows/non-omv-local.yml
+++ b/.github/workflows/non-omv-local.yml
@@ -24,26 +24,15 @@ jobs:
       with:
         python-version:  ${{ matrix.python-version }}
 
-    - name: Install OMV
-      run: |
-        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
-
-    - name: Install pyNeuroML
-      run: |
-        pip install pyNeuroML pyNeuroML[annotations]
-
-    - name: Install libsedml
+    - name: Install dependencies
       run: |
+          pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+          pip install pyNeuroML pyNeuroML[annotations]
           pip install python-libsedml
-
-    - name: Install Tellurium
-      run: |
           pip install tellurium
           sudo apt-get install libncurses5 --fix-missing
-
-    - name: Run tests
-      run: |
-        omv install jneuroml
+          omv install jneuroml
+          pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
 
     - name: Final version info
       run: |
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
index 34f0ae6..fc92b2e 100644
--- a/.github/workflows/non-omv-remote.yml
+++ b/.github/workflows/non-omv-remote.yml
@@ -24,26 +24,15 @@ jobs:
       with:
         python-version:  ${{ matrix.python-version }}
 
-    - name: Install OMV
+    - name: Install dependencies
       run: |
         pip install git+https://github.com/OpenSourceBrain/osb-model-validation
-        
-    - name: Install pyNeuroML
-      run: |
         pip install pyNeuroML pyNeuroML[annotations]
-
-    - name: Install libsedml
-      run: |
         pip install python-libsedml
-
-    - name: Install Tellurium and libncurses5
-      run: |
-          pip install tellurium
-          sudo apt-get install libncurses5 --fix-missing
-
-    - name: Run tests
-      run: |
+        pip install tellurium
+        sudo apt-get install libncurses5 --fix-missing
         omv install jneuroml
+        pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
 
     - name: Final version info
       run: |

From 8480395b2ee8e8c52305cec95a4ace3fe0fa4c74 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 12:11:02 +0100
Subject: [PATCH 67/71] fix indentation test_biosimulators_local.py script in
 non-omv.yml

---
 .github/workflows/non-omv.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index c5fea53..de8ff58 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -83,8 +83,8 @@ jobs:
 
     - name: Test local biosimulators compatibility table creation
       run: |
-          cd SBML/tests
-          sudo rm -rf output
-          python ./test_biosimulators_local.py --output-dir=tmp_plots
+        cd SBML/tests
+        sudo rm -rf output
+        python ./test_biosimulators_local.py --output-dir=tmp_plots
   
   
\ No newline at end of file

From 2138f9145bbf6b1b322ef8af29d7848a587d4aec Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 12:15:59 +0100
Subject: [PATCH 68/71] fix typos (remote --> local)

---
 SBML/tests/test_biosimulators_local.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/SBML/tests/test_biosimulators_local.py b/SBML/tests/test_biosimulators_local.py
index 982efd5..d3ddf1e 100644
--- a/SBML/tests/test_biosimulators_local.py
+++ b/SBML/tests/test_biosimulators_local.py
@@ -41,8 +41,8 @@
 
 print('d1 plots will be saved in:', d1_plots_local_dir)
 
-results_remote = utils.run_biosimulators_locally(sedml_file_name=sedml_file_name, 
+results_local = utils.run_biosimulators_locally(sedml_file_name=sedml_file_name, 
                                     sbml_file_name=sbml_file_name,
-                                    d1_plots_remote_dir=d1_plots_local_dir, 
+                                    d1_plots_local_dir=d1_plots_local_dir, 
                                     engines=engines, test_folder=test_folder)
     
\ No newline at end of file

From f75db3a238ccd0d581d7c8b41e06ed608e876811 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 24 Sep 2024 16:25:39 +0100
Subject: [PATCH 69/71] remove remote and local (docker) related tests from
 non-omv.yml

---
 .github/workflows/non-omv.yml | 25 +------------------------
 1 file changed, 1 insertion(+), 24 deletions(-)

diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
index de8ff58..94f51e2 100644
--- a/.github/workflows/non-omv.yml
+++ b/.github/workflows/non-omv.yml
@@ -55,36 +55,13 @@ jobs:
         cd SBML/tests    
         python ./test_biosimulators_docker.py
 
-    - name: Test biosimulators compatibility table creation
-      run: |
-        cd SBML/tests
-        sudo rm -rf output
-        python ./test_compatibility_biosimulators.py --output-dir=tmp_plots
-
-
     - name: Test test_suite output regeneration
       run: |
         cd test_suite        
         ./test_results_regeneration.sh
 
-
     - name: Final version info
       run: |
         omv list -V # list installed engines
         pip list
-        env
-
-    - name: Test remote biosimulators compatibility table creation
-      run: |
-        cd SBML/tests
-        sudo rm -rf output
-        python ./test_biosimulators_remote.py --output-dir=tmp_plots
-
-
-    - name: Test local biosimulators compatibility table creation
-      run: |
-        cd SBML/tests
-        sudo rm -rf output
-        python ./test_biosimulators_local.py --output-dir=tmp_plots
-  
-  
\ No newline at end of file
+        env
\ No newline at end of file

From 0f8917fe09a4310d2f7745b28743bfc71e70d875 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 25 Sep 2024 10:40:57 +0100
Subject: [PATCH 70/71] add description to local and remote non omv github
 action workflows

---
 .github/workflows/non-omv-local.yml  | 2 +-
 .github/workflows/non-omv-remote.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
index 135b829..8f3ab6c 100644
--- a/.github/workflows/non-omv-local.yml
+++ b/.github/workflows/non-omv-local.yml
@@ -1,5 +1,5 @@
 
-name: Testing non OMV scripts
+name: Testing non OMV scripts (locally using docker)
 
 on:
   push:
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
index fc92b2e..602fbf2 100644
--- a/.github/workflows/non-omv-remote.yml
+++ b/.github/workflows/non-omv-remote.yml
@@ -1,5 +1,5 @@
 
-name: Testing non OMV scripts
+name: Testing non OMV scripts (remotely via URLs)
 
 on:
   push:

From bbdc6227ab494e13df5b99ba18b86ab17828bce5 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 26 Sep 2024 07:58:50 +0100
Subject: [PATCH 71/71] Raise HTTPError when downloading of engine results via
 URL fails and fix pyneuroml import to correct branch (for accessing correct
 version of biosimulations.submit_simulation_archive)

Co-authored-by: Robert Vickerstaff <robert.vickerstaff@gmail.com>
---
 .github/workflows/non-omv-local.yml  |  2 +-
 .github/workflows/non-omv-remote.yml |  2 +-
 utils/__init__.py                    | 11 ++++++++---
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
index 8f3ab6c..fb60d8b 100644
--- a/.github/workflows/non-omv-local.yml
+++ b/.github/workflows/non-omv-local.yml
@@ -27,7 +27,7 @@ jobs:
     - name: Install dependencies
       run: |
           pip install git+https://github.com/OpenSourceBrain/osb-model-validation
-          pip install pyNeuroML pyNeuroML[annotations]
+          pip install pyNeuroML[annotations]
           pip install python-libsedml
           pip install tellurium
           sudo apt-get install libncurses5 --fix-missing
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
index 602fbf2..2a3541b 100644
--- a/.github/workflows/non-omv-remote.yml
+++ b/.github/workflows/non-omv-remote.yml
@@ -27,7 +27,7 @@ jobs:
     - name: Install dependencies
       run: |
         pip install git+https://github.com/OpenSourceBrain/osb-model-validation
-        pip install pyNeuroML pyNeuroML[annotations]
+        pip install pyNeuroML[annotations]
         pip install python-libsedml
         pip install tellurium
         sudo apt-get install libncurses5 --fix-missing
diff --git a/utils/__init__.py b/utils/__init__.py
index 12bd767..ec35c6d 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -20,6 +20,7 @@
 import glob
 from pyneuroml import biosimulations
 import pandas as pd
+from requests.exceptions import HTTPError 
 
 engines = {
     'amici': {
@@ -1033,7 +1034,7 @@ def download_file_from_link(engine, download_link, output_file='results.zip', ma
         return filepath
     else:
         print(f'Failed to download {engine} results.')
-        return False
+        raise HTTPError(f'Failed to download {engine} results.') 
 
 # unzip the file in file_path if it is a zip file and remove the zip file, replace with the unzipped folder
 def unzip_file(file_path, output_dir=None):
@@ -1144,11 +1145,15 @@ def run_biosimulators_remotely(sedml_file_name,
         download_links_dict[e] = download_link
 
     extract_dir_dict = dict()
+    results_remote = dict()
     for e, link in download_links_dict.items():
-        extract_dir = get_remote_results(e, link, remote_output_dir)
+        try:
+            extract_dir = get_remote_results(e, link, remote_output_dir)
+        except HTTPError as emessage:
+            results_remote[e] = ["FAIL", str(emessage), type(emessage).__name__]
+            continue
         extract_dir_dict[e] = extract_dir
 
-    results_remote = dict()
     for e, extract_dir in extract_dir_dict.items():
         status = ""
         error_message = ""