Anaconda allensdk NEURON model
<p>I've download Allen neuron model:
Nr5a1-Cre VISp layer 2/3 473862496</p>

<p>Installed Anaconda with all the required packages, have the NEURON:
<a href="https://alleninstitute.github.io/AllenSDK/install.html" rel="nofollow">https://alleninstitute.github.io/AllenSDK/install.html</a></p>

<p>now how do I use allensdk package to run their model through the NEURON,</p>

<p>they have a sort of explanation:
<a href="http://alleninstitute.github.io/AllenSDK/biophysical_models.html" rel="nofollow">http://alleninstitute.github.io/AllenSDK/biophysical_models.html</a></p>

<p>but where exactly do I write this code? Python? Anaconda promt? Spider?</p>

<p>Not python not Anaconda accept the code as is, so I guess I need to access the allensdk package first, how do I do that?</p>

<p>Thank you.</p>

<p>Thanks for the question.  The first example in your documentation link shows how to download a model, as you've probably done.  I do this by writing a python script and running it from the command prompt.</p>

<p>The script looks like this:</p>

<pre class="lang-py prettyprint-override"><code>from allensdk.api.queries.biophysical_api import BiophysicalApi

bp = BiophysicalApi() 
bp.cache_stimulus = True # change to False to not download the large stimulus NWB file
neuronal_model_id = 473862496    # here's your model
bp.cache_data(neuronal_model_id, working_directory='neuronal_model')
</code></pre>

<p>You can run this from the command prompt (Anaconda command prompt is fine) as follows:</p>

<pre><code>$ python &lt;your_script_name.py&gt;
</code></pre>

<p>Moving down the documentation, the next step to running the model is to run the following on the command prompt:</p>

<pre><code>$ cd neuronal_model
$ nrnivmodl ./modfiles   # compile the model (only needs to be done once)
$ python -m allensdk.model.biophysical.runner manifest.json
</code></pre>

<p>First you step into the working directory you specified in the first script.  </p>

<p>Next you run a NEURON binary (nrnivmodl), which compiles your modfiles.    You'll need to have NEURON with python bindings installed and on your PATH to run this.  I'm not sure about this, but I think compiling modfiles in Windows requires a different command/workflow.  If that's your operating system, I'll have to refer you here since I'm not too familiar with NEURON on Windows:</p>

<p><a href="https://www.neuron.yale.edu/neuron/static/docs/nmodl/mswin.html" rel="nofollow">https://www.neuron.yale.edu/neuron/static/docs/nmodl/mswin.html</a></p>

<p>Next you are calling an script packaged with the allensdk for running models based on one of the files we downloaded in the first script (manifest.json).</p>

python neuron-simulator