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Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML
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<section id="tutorial">
<h1>Tutorial<a class="headerlink" href="#tutorial" title="Permalink to this headline">¶</a></h1>
<p>BioSimulators-pyNeuroML is available as three command-line programs and as a command-line programs encapsulated into three Docker images.</p>
<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-pyNeuroML is available <a class="reference external" href="https://docs.biosimulations.org/users/creating-projects/">here</a>.</p>
<p>A list of the algorithms and algorithm parameters supported by jNeuroML/pyNeuroML, NetPyNe, and NEURON is available at <a class="reference external" href="https://biosimulators.org/simulators/">BioSimulators</a>.</p>
</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 programs 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-pyneuroml [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulators-compliant command-line interface to the pyNeuroML <https://github.com/NeuroML/pyNeuroML> simulation program.
optional arguments:
-h, --help show this help message and exit
-d, --debug full application debug mode
-q, --quiet suppress all console output
-i ARCHIVE, --archive ARCHIVE
Path to OMEX file which contains one or more SED-ML-
encoded simulation experiments
-o OUT_DIR, --out-dir OUT_DIR
Directory to save outputs
-v, --version show program's version number and exit
</pre></div>
</div>
<p>For example, the following commands could be used to execute the 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>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>biosimulators-netpyne -i ./modeling-study.omex -o ./
biosimulators-neuron -i ./modeling-study.omex -o ./
biosimulators-pyneuroml -i ./modeling-study.omex -o ./
</pre></div>
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</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>The entrypoints to the Docker images support the same command-line interface described above.</p>
<p>For example, the following command could be used to use the jNeuroML/pyNeuroML 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>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>docker run \
--tty \
--rm \
--mount type=bind,source="$(pwd),target=/tmp/working-dir \
ghcr.io/biosimulators/pyneuroml:latest \
-i /tmp/working-dir/modeling-study.omex \
-o /tmp/working-dir
</pre></div>
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