Added references

bioexcel · Mar 12, 2024 · 696289a · 696289a
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diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ This tutorial aims to illustrate the process of **setting up a simulation** syst
 * [biobb_gromacs](https://github.com/bioexcel/biobb_gromacs): Tools to setup and run Molecular Dynamics simulations.
 * [biobb_analysis](https://github.com/bioexcel/biobb_analysis): Tools to analyse Molecular Dynamics trajectories.
 
-### Auxiliar libraries used
+### Auxiliary libraries used
 
 * [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.
 * [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.

diff --git a/biobb_wf_md_setup/docs/source/readme.md b/biobb_wf_md_setup/docs/source/readme.md
@@ -20,7 +20,7 @@ This tutorial aims to illustrate the process of **setting up a simulation** syst
 * [biobb_gromacs](https://github.com/bioexcel/biobb_gromacs): Tools to setup and run Molecular Dynamics simulations.
 * [biobb_analysis](https://github.com/bioexcel/biobb_analysis): Tools to analyse Molecular Dynamics trajectories.
 
-### Auxiliar libraries used
+### Auxiliary libraries used
 
 * [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.
 * [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.

diff --git a/biobb_wf_md_setup/docs/source/tutorial.md b/biobb_wf_md_setup/docs/source/tutorial.md
@@ -13,7 +13,7 @@ This tutorial aims to illustrate the process of **setting up a simulation system
  - [biobb_gromacs](https://github.com/bioexcel/biobb_gromacs): Tools to setup and run Molecular Dynamics simulations.
  - [biobb_analysis](https://github.com/bioexcel/biobb_analysis): Tools to analyse Molecular Dynamics trajectories.
 
-### Auxiliar libraries used
+### Auxiliary libraries used
 
 * [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.
 * [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
@@ -1064,7 +1064,7 @@ Important **Output files** generated:
  - 1AKI_md.trr: **Final trajectory** of the MD setup protocol.
  - 1AKI_md.cpt: **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.
  - 1AKI_gppmd.tpr: **Final tpr file**, GROMACS portable binary run input file. This file contains the starting structure of the **MD setup free MD simulation step**, together with the molecular topology and all the simulation parameters. It can be used to **extend** the simulation.
- - 1AKI_genion_top.zip: **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliar **include topology** files (.itp).
+ - 1AKI_genion_top.zip: **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliary **include topology** files (.itp).
 
 **Analysis** (MD setup check) output files generated:
  - 1AKI_rms_first.xvg: **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.

diff --git a/biobb_wf_md_setup/html/biobb_MDsetup_tutorial.web.html b/biobb_wf_md_setup/html/biobb_MDsetup_tutorial.web.html
@@ -13087,7 +13087,7 @@ <h2 id="Settings">Settings<a class="anchor-link" href="#Settings">&#182;</a></h2
 <li><a href="https://github.com/bioexcel/biobb_gromacs">biobb_gromacs</a>: Tools to setup and run Molecular Dynamics simulations.</li>
 <li><a href="https://github.com/bioexcel/biobb_analysis">biobb_analysis</a>: Tools to analyse Molecular Dynamics trajectories.</li>
 </ul>
-<h3 id="Auxiliar-libraries-used">Auxiliar libraries used<a class="anchor-link" href="#Auxiliar-libraries-used">&#182;</a></h3><ul>
+<h3 id="Auxiliar-libraries-used">Auxiliary libraries used<a class="anchor-link" href="#Auxiliar-libraries-used">&#182;</a></h3><ul>
 <li><a href="https://jupyter.org/">jupyter</a>: Free software, open standards, and web services for interactive computing across all programming languages.</li>
 <li><a href="http://nglviewer.org/#nglview">nglview</a>: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.</li>
 <li><a href="https://plot.ly/python/offline/">plotly</a>: Python interactive graphing library integrated in Jupyter notebooks.</li>
@@ -15086,7 +15086,7 @@ <h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">&#
 <li>1AKI_md.trr: <strong>Final trajectory</strong> of the MD setup protocol.</li>
 <li>1AKI_md.cpt: <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
 <li>1AKI_gppmd.tpr: <strong>Final tpr file</strong>, GROMACS portable binary run input file. This file contains the starting structure of the <strong>MD setup free MD simulation step</strong>, together with the molecular topology and all the simulation parameters. It can be used to <strong>extend</strong> the simulation.</li>
-<li>1AKI_genion_top.zip: <strong>Final topology</strong> of the MD system. It is a compressed zip file including a <strong>topology file</strong> (.top) and a set of auxiliar <strong>include topology</strong> files (.itp).</li>
+<li>1AKI_genion_top.zip: <strong>Final topology</strong> of the MD system. It is a compressed zip file including a <strong>topology file</strong> (.top) and a set of auxiliary <strong>include topology</strong> files (.itp).</li>
 </ul>
 <p><strong>Analysis</strong> (MD setup check) output files generated:</p>
 <ul>

diff --git a/biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb b/biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
@@ -19,7 +19,7 @@
     " - [biobb_gromacs](https://github.com/bioexcel/biobb_gromacs): Tools to setup and run Molecular Dynamics simulations.\n",
     " - [biobb_analysis](https://github.com/bioexcel/biobb_analysis): Tools to analyse Molecular Dynamics trajectories.\n",
     " \n",
-    "### Auxiliar libraries used\n",
+    "### Auxiliary libraries used\n",
     "\n",
     "* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.\n",
     "* [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.\n",
@@ -1384,7 +1384,7 @@
     " - {{output_md_trr}}: **Final trajectory** of the MD setup protocol.\n",
     " - {{output_md_cpt}}: **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.\n",
     " - {{output_gppmd_tpr}}: **Final tpr file**, GROMACS portable binary run input file. This file contains the starting structure of the **MD setup free MD simulation step**, together with the molecular topology and all the simulation parameters. It can be used to **extend** the simulation.\n",
-    " - {{output_genion_top_zip}}: **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliar **include topology** files (.itp).\n",
+    " - {{output_genion_top_zip}}: **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliary **include topology** files (.itp).\n",
     "\n",
     "**Analysis** (MD setup check) output files generated:\n",
     " - {{output_rms_first}}: **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.\n",

diff --git a/references.html b/references.html
@@ -0,0 +1,26 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <title>Workflow references</title>
+</head>
+<body>
+
+  <div id="content"></div>
+
+  <script>
+    const packages = ['biobb_io', 'biobb_model', 'biobb_gromacs', 'biobb_analysis']
+
+    let targetElement = document.getElementById('content');
+
+    packages.forEach(pckg => {
+      fetch(`https://raw.githubusercontent.com/bioexcel/${pckg}/master/references.html`)
+          .then(response => response.text())
+          .then(data => {
+              targetElement.innerHTML += data;
+          })
+          .catch(error => console.error(error));
+    })
+  </script>
+
+</body>
+</html>