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Potjans-Diesmann cortical microcircuit model in NetPyNE (Romaro et al 2021)

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<p class=MsoNormal style='margin-bottom:12.0pt;mso-outline-level:1'><span
class=SpellE><b><span style='font-size:24.0pt;font-family:"Segoe UI",sans-serif;
mso-fareast-font-family:"Times New Roman";color:#24292F;mso-font-kerning:18.0pt'>NetPyNE</span></b></span><b><span
style='font-size:24.0pt;font-family:"Segoe UI",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#24292F;mso-font-kerning:18.0pt'> implementation of the
<span class=SpellE>Potjans</span> and <span class=SpellE>Diesmann</span>
cortical microcircuit (PDCM) model with scaling option<o:p></o:p></span></b></p>

<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-family:"Segoe UI",sans-serif;
mso-fareast-font-family:"Times New Roman";color:#24292F'>This code reproduces
the simulations for the following paper:<o:p></o:p></span></p>

<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-family:"Segoe UI",sans-serif;
mso-fareast-font-family:"Times New Roman";color:#24292F'>Cecilia <span
class=SpellE>Romaro</span>, Fernando Araujo <span class=SpellE>Najman</span>,
William W. Lytton, Antonio C. Roque, Salvador Dura-Bernal.&nbsp;<span
class=SpellE><b>NetPyNE</b></span><b> Implementation and Scaling of the <span
class=SpellE>Potjans-Diesmann</span> Cortical Microcircuit Model</b>. Neural <span
class=SpellE>Comput</span> 2021; 33 (7): 1993–2032. <span class=SpellE>doi</span>:&nbsp;<a
href="https://doi.org/10.1162/neco_a_01400">https://doi.org/10.1162/neco_a_01400</a><o:p></o:p></span></p>

<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-family:"Segoe UI",sans-serif;
mso-fareast-font-family:"Times New Roman";color:#24292F'>The <span
class=SpellE>Potjans-Diesmann</span> cortical microcircuit model is a widely
used model originally implemented in NEST. Here, we reimplemented the model
using <span class=SpellE>NetPyNE</span>, a high-level Python interface to the
NEURON simulator, and reproduced the findings of the original publication. We
also implemented a method for scaling the network size that preserves first-
and second-order statistics, building on existing work on network theory. Our
new implementation enabled the use of more detailed neuron models with
multicompartmental morphologies and multiple biophysically realistic ion
channels. This opens the model to new research, including the study of dendritic
processing, the influence of individual channel parameters, the relation to
local field potentials, and other multiscale interactions. The scaling method
we used provides flexibility to increase or decrease the network size as needed
when running these CPU-intensive detailed simulations. Finally, <span
class=SpellE>NetPyNE</span> facilitates modifying or extending the model using
its declarative language; optimizing model parameters; running efficient,
large-scale parallelized simulations; and analyzing the model through built-in
methods, including local field potential calculation and information flow
measures.<o:p></o:p></span></p>

<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-family:"Segoe UI",sans-serif;
mso-fareast-font-family:"Times New Roman";color:#24292F'>The code requires
NEURON (&gt; v7.8) and Python (&gt;v3.5) and has been tested on Linux machines
(CentOS and Ubuntu) and Mac OS X. To run the <span class=GramE>model</span>
follow these steps:<o:p></o:p></span></p>

<ol start=1 type=1>
 <li class=MsoNormal style='color:#24292F;mso-margin-top-alt:auto;mso-margin-bottom-alt:
     auto;mso-list:l1 level1 lfo1;tab-stops:list .5in'><span style='font-family:
     "Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>Unzip all
     files.<o:p></o:p></span></li>
 <li class=MsoNormal style='color:#24292F;margin-top:3.0pt;mso-margin-bottom-alt:
     auto;mso-list:l1 level1 lfo1;tab-stops:list .5in'><span style='font-family:
     "Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>Change to
     model folder and compile the IntFire_PD.mod file via &quot;<span
     class=SpellE><span class=GramE>nrnivmodl</span></span><span class=GramE> .</span>&quot;.
     This should create a directory called either i686 or x86_64, depending on
     your computer's architecture.<o:p></o:p></span></li>
 <li class=MsoNormal style='color:#24292F;mso-margin-bottom-alt:auto;
     mso-list:l1 level1 lfo1;tab-stops:list .5in'><span style='font-family:
     "Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>Run the
     init.py file. This can be done directly via&nbsp;</span><span
     style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>python
     -<span class=SpellE>i</span> init.py</span><span style='font-family:"Segoe UI",sans-serif;
     mso-fareast-font-family:"Times New Roman"'>&nbsp;or using MPI, <span
     class=GramE>e.g.</span>&nbsp;</span><span class=SpellE><span
     style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>mpiexec</span></span><span
     style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>
     -np 4 <span class=SpellE>nrniv</span> -<span class=SpellE>mpi</span>
     init.py</span><span style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:
     "Times New Roman"'>. Alternatively, if running in an HPC via SLURM you can
     adapt and run&nbsp;</span><span class=SpellE><span style='font-size:10.0pt;
     font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>sbatch</span></span><span
     style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>
     <span class=SpellE><span class=GramE>pd.sbatch</span></span></span><span
     style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></li>
</ol>

<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-family:"Segoe UI",sans-serif;
mso-fareast-font-family:"Times New Roman";color:#24292F'>List of files:<o:p></o:p></span></p>

<ul style='margin-top:0in' type=disc>
 <li class=MsoNormal style='color:#24292F;mso-list:l0 level1 lfo2;tab-stops:
     list .5in'><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
     "Times New Roman"'>netParams.py</span><span style='font-family:"Segoe UI",sans-serif;
     mso-fareast-font-family:"Times New Roman"'>: High-level specifications of
     the network parameters. Includes the definition of the populations (</span><span
     class=SpellE><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
     "Times New Roman"'>popParams</span></span><span style='font-family:"Segoe UI",sans-serif;
     mso-fareast-font-family:"Times New Roman"'>) and connectivity (</span><span
     class=SpellE><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
     "Times New Roman"'>connParams</span></span><span style='font-family:"Segoe UI",sans-serif;
     mso-fareast-font-family:"Times New Roman"'>). Note the external inputs are
     also implemented as populations of <span class=SpellE>NetStims</span>.
     This file also contains the function to scale the connections and inputs (</span><span
     class=SpellE><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
     "Times New Roman"'>Reescale</span></span><span style='font-family:"Segoe UI",sans-serif;
     mso-fareast-font-family:"Times New Roman"'>) based on the&nbsp;</span><span
     class=SpellE><span class=GramE><span style='font-size:10.0pt;font-family:
     Menlo;mso-fareast-font-family:"Times New Roman"'>cfg.ScaleFactor</span></span></span><span
     style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></li>
 <li class=MsoNormal style='color:#24292F;mso-list:l0 level1 lfo2;tab-stops:
     list .5in'><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
     "Times New Roman"'>cfg.py</span><span style='font-family:"Segoe UI",sans-serif;
     mso-fareast-font-family:"Times New Roman"'>: Simulation configuration
     options, including the simulation duration (</span><span class=SpellE><span
     class=GramE><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
     "Times New Roman"'>cfg.duration</span></span></span><span
     style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>)
     and the network scale factor (</span><span class=SpellE><span
     style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>cfg.ScaleFactor</span></span><span
     style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>).
     This file also contains the flags to reproduce the different conditions
     shown in the paper:&nbsp;</span><span class=SpellE><span class=GramE><span
     style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>cfg.DC</span></span></span><span
     style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>,&nbsp;</span><span
     style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>cfg.TH</span><span
     style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>&nbsp;and&nbsp;</span><span
     class=SpellE><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
     "Times New Roman"'>cfg.Balanced</span></span><span style='font-family:
     "Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>. Additionally,
     the user can select different recording, <span class=GramE>saving</span>
     and plotting options.<o:p></o:p></span></li>
 <li class=MsoNormal style='color:#24292F;mso-list:l0 level1 lfo2;tab-stops:
     list .5in'><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
     "Times New Roman"'>init.py</span><span style='font-family:"Segoe UI",sans-serif;
     mso-fareast-font-family:"Times New Roman"'>: File to run the simulation;
     also includes the function calls for creating the network, saving <span
     class=GramE>data</span> and analyzing results.<o:p></o:p></span></li>
 <li class=MsoNormal style='color:#24292F;mso-list:l0 level1 lfo2;tab-stops:
     list .5in'><span class=SpellE><span class=GramE><span style='font-size:
     10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>pd.sbatch</span></span></span><span
     style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>&nbsp;and&nbsp;</span><span
     style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman"'>pd_128.sbatch</span><span
     style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman"'>&nbsp;<span
     class=SpellE>etc</span>: Script files to run on HPCs via SLURM workload
     manager using different number of cores.<o:p></o:p></span></li>
 <li class=MsoNormal style='color:#24292F;mso-list:l0 level1 lfo2;tab-stops:
     list .5in'><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
     "Times New Roman"'>IntFire_PD.mod</span><span style='font-family:"Segoe UI",sans-serif;
     mso-fareast-font-family:"Times New Roman"'>: NMODL file for he <span
     class=GramE>integrate</span> and fire artificial cell used in this
     network.<o:p></o:p></span></li>
</ul>

<p class=MsoNormal><span style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#24292F'>To run the multicompartment neuron version of
the network use the files in the&nbsp;</span><span style='font-size:10.0pt;
font-family:Menlo;mso-fareast-font-family:"Times New Roman";color:#24292F'>/multicompartment</span><span
style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:"Times New Roman";
color:#24292F'>&nbsp;folder. The running instructions and file description is
the same as above, except that you need to compile the&nbsp;</span><span
style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman";
color:#24292F'>mod</span><span style='font-family:"Segoe UI",sans-serif;
mso-fareast-font-family:"Times New Roman";color:#24292F'>&nbsp;folder via&nbsp;</span><span
class=SpellE><span style='font-size:10.0pt;font-family:Menlo;mso-fareast-font-family:
"Times New Roman";color:#24292F'>nrnivmodl</span></span><span style='font-size:
10.0pt;font-family:Menlo;mso-fareast-font-family:"Times New Roman";color:#24292F'>
mod</span><span style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#24292F'>.<o:p></o:p></span></p>

<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-family:"Segoe UI",sans-serif;
mso-fareast-font-family:"Times New Roman";color:#24292F'>The model is also
available in Github:&nbsp;<a
href="https://github.com/suny-downstate-medical-center/PDCM_NetPyNE">https://github.com/suny-downstate-medical-center/PDCM_NetPyNE</a>&nbsp;;
and the multicompartment version is available in the
&quot;multicompartment&quot; branch:&nbsp;<a
href="https://github.com/suny-downstate-medical-center/PDCM_NetPyNE/tree/multicompartment">https://github.com/suny-downstate-medical-center/PDCM_NetPyNE/tree/multicompartment</a><o:p></o:p></span></p>

<p class=MsoNormal><span style='font-family:"Segoe UI",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#24292F'>For any questions or further assistance please
contact: <span class=SpellE>salvadordura</span> at gmail.com<o:p></o:p></span></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

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Potjans-Diesmann cortical microcircuit model in NetPyNE (Romaro et al 2021)

modeldb.science/266872

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python neuron-simulator netpyne abstract-integrate-and-fire-leaky-neuron-abstract- detailed-neuronal-models-simplified-models

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