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diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.0.4',
+    VERSION: '0.0.5',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/about.html b/docs/about.html
@@ -4,8 +4,9 @@
 <html lang="en">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>About BioSimulators-GINsim &#8212; BioSimulators-GINsim 0.0.4 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
+    <title>About BioSimulators-GINsim &#8212; BioSimulators-GINsim 0.0.5 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -112,21 +113,21 @@ <h3 id="searchlabel">Quick search</h3>
 
           <div class="body" role="main">
 
-  <div class="section" id="about-biosimulators-ginsim">
+  <section id="about-biosimulators-ginsim">
 <h1>About BioSimulators-GINsim<a class="headerlink" href="#about-biosimulators-ginsim" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="license">
+<section id="license">
 <h2>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h2>
 <p>This package is released under the <a class="reference external" href="https://github.com/biosimulators/Biosimulators_GINsim/blob/dev/LICENSE">MIT License</a>. GINsim is released under the <a class="reference external" href="https://spdx.org/licenses/GPL-3.0-only.html">GPL 3.0 License</a>.</p>
-</div>
-<div class="section" id="development-team">
+</section>
+<section id="development-team">
 <h2>Development team<a class="headerlink" href="#development-team" title="Permalink to this headline">¶</a></h2>
 <p>This package was developed by the <a class="reference external" href="https://www.karrlab.org">Karr Lab</a> at the Icahn School of Medicine at Mount Sinai and the <a class="reference external" href="https://reproduciblebiomodels.org/">Center for Reproducible Biomedical Modeling</a>. GINsim was developed at the <a class="reference external" href="https://gulbenkian.pt/ciencia/">Gulbenkian Institute of Science</a>.</p>
-</div>
-<div class="section" id="questions-and-comments">
+</section>
+<section id="questions-and-comments">
 <h2>Questions and comments<a class="headerlink" href="#questions-and-comments" title="Permalink to this headline">¶</a></h2>
 <p>Please contact the <a class="reference external" href="mailto:info&#37;&#52;&#48;biosimulators&#46;org">BioSimulators Team</a> with any questions or comments about the command-line program or Docker image. Please contact the <a class="reference external" href="mailto:support&#37;&#52;&#48;ginsim&#46;org">GINsim Team</a> with any questions or comments about GINsim.</p>
-</div>
-</div>
+</section>
+</section>
 
 
           </div>

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; BioSimulators-GINsim 0.0.4 documentation</title>
+    <title>Index &#8212; BioSimulators-GINsim 0.0.5 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>

diff --git a/docs/index.html b/docs/index.html
@@ -4,8 +4,9 @@
 <html lang="en">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>BioSimulators-GINsim documentation &#8212; BioSimulators-GINsim 0.0.4 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
+    <title>BioSimulators-GINsim documentation &#8212; BioSimulators-GINsim 0.0.5 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -105,13 +106,13 @@ <h3 id="searchlabel">Quick search</h3>
 
           <div class="body" role="main">
 
-  <div class="section" id="biosimulators-ginsim-documentation">
+  <section id="biosimulators-ginsim-documentation">
 <h1>BioSimulators-GINsim documentation<a class="headerlink" href="#biosimulators-ginsim-documentation" title="Permalink to this headline">¶</a></h1>
 <p>BioSimulators-GINsim provides a <a class="reference external" href="https://biosimulators.org">BioSimulators</a>-compliant command-line interface to the <a class="reference external" href="http://ginsim.org/">GINsim</a> biological simulation tool. A Docker image for this package is also available.</p>
 <p>This command-line interface and Docker image enable users to use GINsim to execute <a class="reference external" href="https://combinearchive.org/">COMBINE/OMEX archives</a> that describe one or more simulation experiments (in <a class="reference external" href="https://sed-ml.org">SED-ML format</a>) of one or more logical models (in <a class="reference external" href="http://sbml.org">SBML-qual format</a>).</p>
 <p>A list of the algorithms and algorithm parameters supported by GINsim is available at <a class="reference external" href="https://biosimulators.org/simulators/ginsim">BioSimulators</a>.</p>
 <p>A simple web application and web service for using GINsim to execute COMBINE/OMEX archives is also available at <a class="reference external" href="https://run.biosimulations.org">runBioSimulations</a>.</p>
-<div class="section" id="contents">
+<section id="contents">
 <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
@@ -142,8 +143,8 @@ <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this head
 <li class="toctree-l1"><a class="reference internal" href="genindex.html">Index</a></li>
 </ul>
 </div>
-</div>
-</div>
+</section>
+</section>
 
 
           </div>

diff --git a/docs/installation.html b/docs/installation.html
@@ -4,8 +4,9 @@
 <html lang="en">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Installation instructions &#8212; BioSimulators-GINsim 0.0.4 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
+    <title>Installation instructions &#8212; BioSimulators-GINsim 0.0.5 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -111,24 +112,24 @@ <h3 id="searchlabel">Quick search</h3>
 
           <div class="body" role="main">
 
-  <div class="section" id="installation-instructions">
+  <section id="installation-instructions">
 <h1>Installation instructions<a class="headerlink" href="#installation-instructions" title="Permalink to this headline">¶</a></h1>
 <p>BioSimulators-GINsim is available as a command-line program and as a command-line program encapsulated into a Docker image.</p>
-<div class="section" id="command-line-program">
+<section id="command-line-program">
 <h2>Command-line program<a class="headerlink" href="#command-line-program" title="Permalink to this headline">¶</a></h2>
 <p>After installing the <a class="reference external" href="https://www.java.com/en/">Java</a>, <a class="reference external" href="https://www.python.org/downloads/">Python</a> (&gt;= 3.7),`pip &lt;<a class="reference external" href="https://pip.pypa.io/">https://pip.pypa.io/</a>&gt;`_, and the <a class="reference external" href="https://github.com/GINsim/GINsim-python">GINsim Python API</a>, run the following command to install BioSimulators-GINsim:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>pip install biosimulators-ginsim
 </pre></div>
 </div>
-</div>
-<div class="section" id="docker-image-with-a-command-line-entrypoint">
+</section>
+<section id="docker-image-with-a-command-line-entrypoint">
 <h2>Docker image with a command-line entrypoint<a class="headerlink" href="#docker-image-with-a-command-line-entrypoint" title="Permalink to this headline">¶</a></h2>
 <p>After installing <a class="reference external" href="https://docs.docker.com/get-docker/">Docker</a>, run the following command to install the Docker image for BioSimulators-GINsim:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>docker pull ghcr.io/biosimulators/ginsim
 </pre></div>
 </div>
-</div>
-</div>
+</section>
+</section>
 
 
           </div>

diff --git a/docs/py-modindex.html b/docs/py-modindex.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Python Module Index &#8212; BioSimulators-GINsim 0.0.4 documentation</title>
+    <title>Python Module Index &#8212; BioSimulators-GINsim 0.0.5 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
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diff --git a/docs/search.html b/docs/search.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Search &#8212; BioSimulators-GINsim 0.0.4 documentation</title>
+    <title>Search &#8212; BioSimulators-GINsim 0.0.5 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
 

diff --git a/docs/source/biosimulators_ginsim.html b/docs/source/biosimulators_ginsim.html
@@ -4,8 +4,9 @@
 <html lang="en">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>biosimulators_ginsim package &#8212; BioSimulators-GINsim 0.0.4 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
+    <title>biosimulators_ginsim package &#8212; BioSimulators-GINsim 0.0.5 documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../_static/alabaster.css" />
     <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
@@ -113,7 +114,7 @@ <h3 id="searchlabel">Quick search</h3>
 
           <div class="body" role="main">
 
-  <div class="section" id="module-biosimulators_ginsim">
+  <section id="module-biosimulators_ginsim">
 <span id="biosimulators-ginsim-package"></span><h1>biosimulators_ginsim package<a class="headerlink" href="#module-biosimulators_ginsim" title="Permalink to this headline">¶</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="biosimulators_ginsim.exec_sed_task">
@@ -195,10 +196,10 @@ <h3 id="searchlabel">Quick search</h3>
 </dl>
 </dd></dl>
 
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-biosimulators_ginsim.core">
+</section>
+<section id="module-biosimulators_ginsim.core">
 <span id="biosimulators-ginsim-core-module"></span><h2>biosimulators_ginsim.core module<a class="headerlink" href="#module-biosimulators_ginsim.core" title="Permalink to this headline">¶</a></h2>
 <p>BioSimulators-compliant command-line interface to the <a class="reference external" href="http://ginsim.org/">GINsim</a> simulation program.</p>
 <dl class="field-list simple">
@@ -281,8 +282,8 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 </dl>
 </dd></dl>
 
-</div>
-<div class="section" id="module-biosimulators_ginsim.data_model">
+</section>
+<section id="module-biosimulators_ginsim.data_model">
 <span id="biosimulators-ginsim-data-model-module"></span><h2>biosimulators_ginsim.data_model module<a class="headerlink" href="#module-biosimulators_ginsim.data_model" title="Permalink to this headline">¶</a></h2>
 <p>Data model</p>
 <dl class="field-list simple">
@@ -326,8 +327,8 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-biosimulators_ginsim.utils">
+</section>
+<section id="module-biosimulators_ginsim.utils">
 <span id="biosimulators-ginsim-utils-module"></span><h2>biosimulators_ginsim.utils module<a class="headerlink" href="#module-biosimulators_ginsim.utils" title="Permalink to this headline">¶</a></h2>
 <p>Utility methods</p>
 <dl class="field-list simple">
@@ -494,8 +495,8 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 </dl>
 </dd></dl>
 
-</div>
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+</section>
 
 
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diff --git a/docs/tutorial.html b/docs/tutorial.html
@@ -4,8 +4,9 @@
 <html lang="en">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Tutorial &#8212; BioSimulators-GINsim 0.0.4 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
+    <title>Tutorial &#8212; BioSimulators-GINsim 0.0.5 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -112,27 +113,27 @@ <h3 id="searchlabel">Quick search</h3>
 
           <div class="body" role="main">
 
-  <div class="section" id="tutorial">
+  <section id="tutorial">
 <h1>Tutorial<a class="headerlink" href="#tutorial" title="Permalink to this headline">¶</a></h1>
 <p>BioSimulators-GINsim is available as a command-line program and as a command-line program encapsulated into a Docker image.</p>
-<div class="section" id="creating-combine-omex-archives-and-encoding-simulation-experiments-into-sed-ml">
+<section id="creating-combine-omex-archives-and-encoding-simulation-experiments-into-sed-ml">
 <h2>Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML<a class="headerlink" href="#creating-combine-omex-archives-and-encoding-simulation-experiments-into-sed-ml" title="Permalink to this headline">¶</a></h2>
 <p>Information about how to create COMBINE/OMEX archives which can be executed by BioSimulators-GINsim is available at <a class="reference external" href="https://biosimulators.org/help">BioSimulators</a>.</p>
 <p>A list of the algorithms and algorithm parameters supported by GINsim is available at <a class="reference external" href="https://biosimulators.org/simulators/ginsim">BioSimulators</a>.</p>
-<div class="section" id="models-sbml-qual">
+<section id="models-sbml-qual">
 <h3>Models (SBML-qual)<a class="headerlink" href="#models-sbml-qual" title="Permalink to this headline">¶</a></h3>
 <p>BioSimulators-GINsim can execute models encoded in the <code class="docutils literal notranslate"><span class="pre">qual</span></code> package of SBML and GINsim’s format (zginml).</p>
-</div>
-<div class="section" id="simulation-experiments-sed-ml-kisao">
+</section>
+<section id="simulation-experiments-sed-ml-kisao">
 <h3>Simulation experiments (SED-ML, KISAO)<a class="headerlink" href="#simulation-experiments-sed-ml-kisao" title="Permalink to this headline">¶</a></h3>
 <p>BioSimulators-GINsim can execute simulation experiments encoded in SED-ML, using KiSAO to indicate specific algorithms and their parameters. Information about the algorithms (KiSAO terms), algorithm parameters (KiSAO terms), and outputs (XML XPaths for variables) supported by BioSimulators-GINsim is available from the <a class="reference external" href="https://biosimulators.org/simulators/ginsim">BioSimulators registry</a>.</p>
-</div>
-<div class="section" id="example-combine-omex-archives">
+</section>
+<section id="example-combine-omex-archives">
 <h3>Example COMBINE/OMEX archives<a class="headerlink" href="#example-combine-omex-archives" title="Permalink to this headline">¶</a></h3>
 <p>Examples of COMBINE/OMEX archives for logical simulations which BioSimulators-GINsim can execute are available in the <a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/tree/deploy/examples">BioSimulators test suite</a>.</p>
-</div>
-</div>
-<div class="section" id="command-line-program">
+</section>
+</section>
+<section id="command-line-program">
 <h2>Command-line program<a class="headerlink" href="#command-line-program" title="Permalink to this headline">¶</a></h2>
 <p>The command-line program can be used to execute COMBINE/OMEX archives that describe simulations as illustrated below.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>usage: biosimulators-ginsim [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
@@ -155,8 +156,8 @@ <h2>Command-line program<a class="headerlink" href="#command-line-program" title
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>biosimulators-ginsim -i ./modeling-study.omex -o ./
 </pre></div>
 </div>
-</div>
-<div class="section" id="docker-image-with-a-command-line-entrypoint">
+</section>
+<section id="docker-image-with-a-command-line-entrypoint">
 <h2>Docker image with a command-line entrypoint<a class="headerlink" href="#docker-image-with-a-command-line-entrypoint" title="Permalink to this headline">¶</a></h2>
 <p>The entrypoint to the Docker image supports the same command-line interface described above.</p>
 <p>For example, the following command could be used to use the Docker image to execute the same simulations described in <code class="docutils literal notranslate"><span class="pre">./modeling-study.omex</span></code> and save their results to <code class="docutils literal notranslate"><span class="pre">./</span></code>:</p>
@@ -169,8 +170,8 @@ <h2>Docker image with a command-line entrypoint<a class="headerlink" href="#dock
         -o /tmp/working-dir
 </pre></div>
 </div>
-</div>
-</div>
+</section>
+</section>
 
 
           </div>