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installation.html
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<section id="installation-instructions">
<h1>Installation instructions<a class="headerlink" href="#installation-instructions" title="Permalink to this headline">¶</a></h1>
<p>BioSimulators-pyNeuroML is available as four command-line programs and four command-line programs encapsulated into four Docker images.</p>
<section id="command-line-program">
<h2>Command-line program<a class="headerlink" href="#command-line-program" title="Permalink to this headline">¶</a></h2>
<p>First, install <a class="reference external" href="https://www.python.org/downloads/">Python</a> (>= 3.7), <a class="reference external" href="https://pip.pypa.io/">pip</a>, and <a class="reference external" href="https://java.com/">Java</a>.</p>
<p>Second, install the following additional programs to use NetPyNe and NEURON:</p>
<ul>
<li><p>NEURON</p>
<blockquote>
<div><ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">gcc</span></code></p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">g++</span></code></p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">make</span></code></p></li>
</ul>
</div></blockquote>
</li>
<li><p>NetPyNe</p>
<blockquote>
<div><ul class="simple">
<li><p>All of the above</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">libmpich-dev</span></code></p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">mpi</span></code></p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">mpi-default-bin</span></code></p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">mpich</span></code></p></li>
</ul>
</div></blockquote>
</li>
</ul>
<p>Third, set <code class="docutils literal notranslate"><span class="pre">NEURON_HOME</span></code> to the parent directory of the <code class="docutils literal notranslate"><span class="pre">nrniv</span></code> executable, up to but not including <code class="docutils literal notranslate"><span class="pre">bin</span></code> (e.g., <code class="docutils literal notranslate"><span class="pre">NEURON_HOME=$(which</span> <span class="pre">nrniv</span> <span class="pre">|</span> <span class="pre">rev</span> <span class="pre">|</span> <span class="pre">cut</span> <span class="pre">-d</span> <span class="pre">'/'</span> <span class="pre">-f</span> <span class="pre">3-</span> <span class="pre">|</span> <span class="pre">rev)</span></code>).</p>
<p>Third, run the following command to install BioSimulators-pyNeuroML:</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>pip install biosimulators-pyneuroml
</pre></div>
</div>
<p>Add the <code class="docutils literal notranslate"><span class="pre">brian2</span></code> option to install support for Brian 2.</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>pip install biosimulators-pyneuroml[brian2]
</pre></div>
</div>
<p>Add the <code class="docutils literal notranslate"><span class="pre">netpyne</span></code> option to install support for NetPyNe.</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>pip install biosimulators-pyneuroml[netpyne]
</pre></div>
</div>
<p>Add the <code class="docutils literal notranslate"><span class="pre">neuron</span></code> option to install support for NEURON.</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>pip install biosimulators-pyneuroml[neuron]
</pre></div>
</div>
</section>
<section id="docker-images-with-command-line-entrypoints">
<h2>Docker images with command-line entrypoints<a class="headerlink" href="#docker-images-with-command-line-entrypoints" 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 commands to install the Docker images for jNeuroML/pyNeuroML, NetPyNe, and NEURON:</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>docker pull ghcr.io/biosimulators/brian2
docker pull ghcr.io/biosimulators/netpyne
docker pull ghcr.io/biosimulators/neuron
docker pull ghcr.io/biosimulators/pyneuroml
</pre></div>
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