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michaeldeistler committed Aug 22, 2024
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9 changes: 7 additions & 2 deletions faq/index.html
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<h1 id="frequently-asked-questions">Frequently asked questions<a class="headerlink" href="#frequently-asked-questions" title="Permanent link">&para;</a></h1>
<p><a href="question_01/">What units does <code>Jaxley</code> use?</a>
<a href="question_02/">How can I save and load cells and networks?</a></p>
<ul>
<li><a href="question_01/">What units does <code>Jaxley</code> use?</a> </li>
<li><a href="question_02/">How can I save and load cells and networks?</a> </li>
</ul>
<p>See also the <a href="https://github.com/jaxleyverse/jaxley/discussions">discussion page</a> and the <a href="https://github.com/jaxleyverse/jaxley/issues">issue
tracker</a> on the <code>Jaxley</code> GitHub repository for
recent questions and problems.</p>



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6 changes: 3 additions & 3 deletions index.html
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<li>elegant mechanisms for parameter sharing</li>
</ul>
<h2 id="getting-started">Getting started<a class="headerlink" href="#getting-started" title="Permanent link">&para;</a></h2>
<p><code>Jaxley</code> allows to simulate biophysical neuron models on CPU or GPU:
<p><code>Jaxley</code> allows to simulate biophysical neuron models on CPU, GPU, or TPU:
<div class="highlight"><pre><span></span><code><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">from</span> <span class="nn">jax</span> <span class="kn">import</span> <span class="n">config</span>

<span class="kn">import</span> <span class="nn">jaxley</span> <span class="k">as</span> <span class="nn">jx</span>
<span class="kn">from</span> <span class="nn">jaxley.channels</span> <span class="kn">import</span> <span class="n">HH</span>

<span class="n">config</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="s2">&quot;jax_platform_name&quot;</span><span class="p">,</span> <span class="s2">&quot;cpu&quot;</span><span class="p">)</span> <span class="c1"># or &quot;gpu&quot;.</span>
<span class="n">config</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="s2">&quot;jax_platform_name&quot;</span><span class="p">,</span> <span class="s2">&quot;cpu&quot;</span><span class="p">)</span> <span class="c1"># Or &quot;gpu&quot; / &quot;tpu&quot;.</span>

<span class="n">cell</span> <span class="o">=</span> <span class="n">jx</span><span class="o">.</span><span class="n">Cell</span><span class="p">()</span> <span class="c1"># Define cell.</span>
<span class="n">cell</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="n">HH</span><span class="p">())</span> <span class="c1"># Insert channels.</span>

<span class="n">current</span> <span class="o">=</span> <span class="n">jx</span><span class="o">.</span><span class="n">step_current</span><span class="p">(</span><span class="n">i_delay</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">i_dur</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">i_amp</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">dt</span><span class="o">=</span><span class="mf">0.025</span><span class="p">,</span> <span class="n">t_max</span><span class="o">=</span><span class="mf">10.0</span><span class="p">)</span>
<span class="n">current</span> <span class="o">=</span> <span class="n">jx</span><span class="o">.</span><span class="n">step_current</span><span class="p">(</span><span class="n">i_delay</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">i_dur</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">i_amp</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">delta_t</span><span class="o">=</span><span class="mf">0.025</span><span class="p">,</span> <span class="n">t_max</span><span class="o">=</span><span class="mf">10.0</span><span class="p">)</span>
<span class="n">cell</span><span class="o">.</span><span class="n">stimulate</span><span class="p">(</span><span class="n">current</span><span class="p">)</span> <span class="c1"># Stimulate with step current.</span>
<span class="n">cell</span><span class="o">.</span><span class="n">record</span><span class="p">(</span><span class="s2">&quot;v&quot;</span><span class="p">)</span> <span class="c1"># Record voltage.</span>

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