diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml new file mode 100644 index 0000000..fb60d8b --- /dev/null +++ b/.github/workflows/non-omv-local.yml @@ -0,0 +1,49 @@ + +name: Testing non OMV scripts (locally using docker) + +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 dependencies + run: | + pip install git+https://github.com/OpenSourceBrain/osb-model-validation + pip install pyNeuroML[annotations] + pip install python-libsedml + 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: | + 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..2a3541b --- /dev/null +++ b/.github/workflows/non-omv-remote.yml @@ -0,0 +1,49 @@ + +name: Testing non OMV scripts (remotely via URLs) + +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 dependencies + run: | + pip install git+https://github.com/OpenSourceBrain/osb-model-validation + pip install pyNeuroML[annotations] + pip install python-libsedml + 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: | + 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 6c69b90..e6c2c56 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 @@ -39,37 +39,29 @@ jobs: cd tellurium python simple.py -nogui - cd ../SBML + cd ../SBML/tests pip install python-libsedml - python test_tellurium.py + python ./test_tellurium.py - name: Test validity of files run: | - pip install pyNeuroML - cd SBML + pip install pyNeuroML pyNeuroML[annotations] + 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 - ./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 - + cd SBML/tests + python ./test_biosimulators_docker.py - 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 + env \ No newline at end of file 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: 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 @@ @@ -197,7 +197,7 @@ - + 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 @@ 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 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 @@ - - - - - - - - - - - -2020-01-21T10:03:15Z - - - - - - - v - - - - - - - - - - - - - - - -Mass action rate law for irreversible reactions -

-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. -

- - - - k1*PRODUCT<substrate_i> - - - - - - - - - - - - -2020-01-21T10:03:58Z - - - - - - - ER*4*vM3*k_CaA^n*(X^n/((X^n+k_CaA^n)*(X^n+k_CaI^n)))*(Z^m/(Z^m+kip3^m))*(Y-X) - - - - - - - - - - - - - - - - - - - - -2020-01-21T10:03:58Z - - - - - - - compartment*vM2*X^2/(X^2+k2^2) - - - - - - - - - - - - - - -2020-01-21T10:03:58Z - - - - - - - ER*kf*(Y-X) - - - - - - - - - - - - - - -2020-01-21T10:03:58Z - - - - - - - vp*X^2/(X^2+kp^2) - - - - - - - - - - - - - - - - - - - - - - - - 2008-08-21T11:36:22Z - - - - - 2009-09-17T15:58:46Z - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

The model reproduces the time profile of cytoplasmic Calcium as depicted in Fig 3 of the paper. Model successfully reproduced using Jarnac and MathSBML

-

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

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