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Brain networks simulators - a comparative study (Tikidji-Hamburyan et al 2017)
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<meta name="changedby" content="Ruben Tikidji-Hamburyan"/>
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<meta name="changedby" content="Ruben Tikidji-Hamburyan">
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<h4 class="western"><i>These BRIAN/NEST/NEURON</i> <i>scripts
associated with paper (manuscript):</i></h4>
<h3 class="western"><br/>
Ruben A. Tikidji-Hamburyan, Vikram
Narayana, Zeki Bozkus, and Tarek A. El-Ghazawi</h3>
<h2 class="western">Software for Brain Network Simulations: A
Comparative Study</h2>
<h4 class="western" style="font-weight: normal"><i>We deeply appreciate the comments of reviewer Marcel Stimberg, which allowed us to significantly improve the quality of the code.</i></h4>
<hr/>
<p>To use theses scripts you need python libraries:
</p>
<ol>
<li/>
<p style="margin-bottom: 0in"><a href="http://www.numpy.org/">numpy</a>
</p>
<li/>
<p style="margin-bottom: 0in"><a href="http://www.scipy.org/">scipy</a>
</p>
<li/>
<p style="margin-bottom: 0in"><a href="http://matplotlib.org/">matplotlib</a>
and LaTeX for correct graphical interface
</p>
</ol>
<p style="margin-bottom: 0in"><br/>
</p>
<p style="margin-bottom: 0in">and simulators:</p>
<ol start="4">
<li/>
<p>NEURON Release 7.4 (1370:16a7055d4a86) 2015-11-09</p>
<li/>
<p>NEST version 2.12.0.</p>
<li/>
<p>BRIAN version 2.0.1</p>
</ol>
<p>Under <u>Ubuntu</u> or any other <u>Debian</u> based Linux, run
<br/>
<b>sudo apt-get install python-numpy python-scipy
python-matplotlib texlive-full cython</b>.</p>
<p>You can use <b>yum</b> or <b>zymm</b> under <u>RadHad</u> or <u>SUSE</u>
based Linux distributions.
</p>
<p>You may also use <b>sudo pip install numpu scipy matloblib cython</b>
in any distribution.
</p>
<p>Follow instructions for installation NEURON, NEST and BRIAN
simulators.</p>
<hr/>
<h2 class="western">Case Study 1</h2>
<p>To obtain results of the Case Study 1, cd into directory
CaseStudy1-5000LIF
</p>
<p><b>cd CaseStudy1-5000LIF </b>
</p>
<p>and run simulations</p>
<p><b>./Benchmark.sh</b></p>
<p>The raster diagrams for each software will be shown.</p>
<p><br/>
<br/>
</p>
<table width="100%" cellpadding="4" cellspacing="0" style="page-break-inside: avoid">
<col width="85*">
<col width="85*">
<col width="85*">
<tr valign="top">
<td width="33%" style="border: none; padding: 0in">
<p align="center"><b>BRIAN</b></p>
<p align="center"><img src="CaseStudy1-5000LIF/CaseStudy1-BRIAN.jpg" name="Image4" align="bottom" width="617" height="479" border="0"/>
</p>
</td>
<td width="33%" style="border: none; padding: 0in">
<p align="center"><b>NEST</b></p>
<p align="center"><img src="CaseStudy1-5000LIF/CaseStudy1-NEST.jpg" name="Image5" align="bottom" width="614" height="479" border="0"/>
</p>
</td>
<td width="33%" style="border: none; padding: 0in">
<p align="center"><b>NEURON</b></p>
<p align="center"><img src="CaseStudy1-5000LIF/CaseStudy1-NEURON.jpg" name="Image6" align="bottom" width="617" height="479" border="0"/>
</p>
</td>
</tr>
</table>
<p><br/>
<br/>
</p>
<p>Statistics of software performance and number of lines and
characters in corresponding modules and scripts will printed out in
standard output. This statistics was used to obtained results of the
case study.
</p>
<h4 class="western">Files in this directory:</h4>
<address style="text-indent: 0.25in; page-break-before: auto; page-break-after: auto">
Benchmark.sh – script helper</address>
<address style="text-indent: 0.25in"><i>BenchmarkAndMemory.sh</i> –
same as Benchmark.sh but with memory usage estimation.
</address>
<address style="text-indent: 0.25in">ee.ssv - E-E neuron connectivity</address>
<address style="text-indent: 0.25in">ei.ssv - E-I neuron connectivity</address>
<address style="text-indent: 0.25in">ie.ssv - I-E neuron connectivity</address>
<address style="text-indent: 0.25in">ii.ssv - I-I neuron connectivity</address>
<address style="text-indent: 0.25in">se.ssv - S-E neuron connectivity</address>
<address style="text-indent: 0.25in">input.ssv - input pattern</address>
<address style="text-indent: 0.25in">./BRIAN/example.py – script
for BRIAN</address>
<address style="text-indent: 0.25in">./NEST/example.py – script for
NEST</address>
<address style="text-indent: 0.25in">./NEST/iaf_psc_delta.h –
module of LIAF, header (*)</address>
<address style="text-indent: 0.25in">./NEST/iaf_psc_delta.cpp –
module of LIAF, c++ code (*)</address>
<address style="text-indent: 0.25in">./NEURON/example.py – script
for NEURON</address>
<address style="text-indent: 0.25in">./NEURON/intfire1.mod – module
of LIAF (*)</address>
<address style="text-indent: 0.25in; margin-bottom: 0.2in">./NEURON/vecevent.mod
– module for input generator</address>
<h2 class="western">Case Study 2</h2>
<div class="boxed" >
<h3 class="note">Note.</h3><p class="note">
NEST module hh_psc_alpha does NOT completely implement the system of differential equations (2) in the paper. This module has a synaptic model with an injected current instead of a model with reversal potential and conductance. The difference slightly reduces the computational load for the NEST benchmark and does not affect any results of Case Study 2. This inaccuracy was found after the publication. The authors have posted this note to prevent further confusion.
</p>
</div>
<p>To obtain results of the Case Study 2, cd into directory
CaseStudy2-400HH
</p>
<p><b>cd CaseStudy2-400HH </b>
</p>
<p>and run simulations</p>
<p><b>./Benchmark.sh</b></p>
<p>The raster diagrams for each software will be shown.</p>
<p><br/>
<br/>
</p>
<table width="100%" cellpadding="4" cellspacing="0" style="page-break-inside: avoid">
<col width="85*">
<col width="85*">
<col width="85*">
<tr valign="top">
<td width="33%" style="border: none; padding: 0in">
<p align="center"><b>BRIAN</b></p>
<p align="center"><img src="CaseStudy2-400HH/CaseStudy2-Brian.jpg" name="Image7" align="bottom" width="616" height="482" border="0"/>
</p>
</td>
<td width="33%" style="border: none; padding: 0in">
<p align="center"><b>NEST</b></p>
<p align="center"><img src="CaseStudy2-400HH/CaseStudy2-NEST.jpg" name="Image8" align="bottom" width="616" height="482" border="0"/>
</p>
</td>
<td width="33%" style="border: none; padding: 0in">
<p align="center"><b>NEURON</b></p>
<p align="center"><img src="CaseStudy2-400HH/CaseStudy2-NEURON.jpg" name="Image9" align="bottom" width="616" height="482" border="0"/>
</p>
</td>
</tr>
</table>
<p><br/>
<br/>
</p>
<p>Statistics of software performance and number of lines and
characters in corresponding modules and scripts will printed out in
standard output. This statistics was used to obtained results of the
case study.
</p>
<h4 class="western">Files in this directory:</h4>
<address style="text-indent: 0.25in; page-break-before: auto; page-break-after: auto">
<br/>
</address>
<address style="text-indent: 0.25in">Benchmark.sh – script helper</address>
<address style="text-indent: 0.25in"><i>BenchmarkAndMemory.sh</i> –
same as Benchmark.sh but with memory usage estimation.
</address>
<address style="text-indent: 0.25in">connections.ssv - network
connectivity</address>
<address style="text-indent: 0.25in">volt.ssv – voltage initial
condition</address>
<address style="text-indent: 0.25in">./BRIAN/example.py – script
for BIRAK</address>
<address style="text-indent: 0.25in">./NEST/example.py – script for
NEST</address>
<address style="text-indent: 0.25in">./NEST/hh_psc_alpha.h – module
of HH, header (*)</address>
<address style="text-indent: 0.25in">./NEST/hh_psc_alpha.cppmodule of
HH, c++ code (*)</address>
<address style="text-indent: 0.25in">./NEURON/example.py – script
for NEURON</address>
<address style="text-indent: 0.25in">./NEURON/expsyn.mod – module
of double exponential synapses (*)</address>
<address style="text-indent: 0.25in">./NEURON/exp2syn.mod – module
of double exponential synapses (*)</address>
<address style="text-indent: 0.25in">./NEURON/hh.mod – module for
HH currents (*)</address>
<address style="text-indent: 0.25in"><br/>
</address>
<address style="text-indent: 0.25in; margin-bottom: 0.2in">(*)<span style="font-variant: normal">
</span><span style="font-variant: normal"><span style="font-style: normal">files
are not required for simulation, but used for code complexity study.
These files were copied from NEURON/NEST source code and cleaned from
comments, empty lines etc.</span></span></address>
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