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SCN1A gain-of-function in early infantile encephalopathy (Berecki et al 2019)

Home Page: https://modeldb.science/264834

AMPL 5.41% AGS Script 93.42% Python 1.17%
neuron-simulator action-potentials-epilepsy-depolarization-block-de

264834's Introduction

<html>
<p><strong>*** README ***</strong>
</p>
<p>Optimised PV neuron with NaV1.1 conductance used in:
</p>
<p>Berecki G, Bryson A, Terhag J, Maljevic S, Gazina EV, Hill SL, Petrou S (2019) SCN1A gain of function in early infantile encephalopathy. Ann Neurol 85:514-525
<br/>doi: <a href="http://dx.doi.org/10.1002/ana.25438">10.1002/ana.25438</a>
</p>
<p>This model uses the NEURON simulation environment and was contributed by A Bryson.
</p>
<p>Model morphology and mechanisms taken from the BBP Neocortical Microcircuit Portal:
<br/><a href="https://bbp.epfl.ch/nmc-portal/welcome">https://bbp.epfl.ch/nmc-portal/welcome</a>
</p>
<p>The model was optimised using BluePyOpt:
</p>
<p>"Van Geit W, Gevaert M, Chindemi G, Rossert C, Courcol J, Muller EB, Schurmann F, Segev I and Markram H (2016).BluePyOpt: Leveraging open source software and cloud infrastructure to optimise model parameters in neuroscience. Front. Neuroinform. 10:17.
<br/>doi: <a href="https://doi.org/10.3389/fninf.2016.00017">10.3389/fninf.2016.00017</a>
</p>
<p>HOC template for PV model is found in 'PV_template.hoc'
</p>
<p>Morphology and mechanisms found under '/morphologies' and '/mechanisms'
</p>
<p>run.py contains a short script to generate the time-voltage traces and
the first part (it is easy to edit the code to provide more if
desired) of the IF curves found in Figures 4C and 4D/
</p>
<p>First compile the mod files with a command like
nrnivmodl mechanisms
</p>
<p>To generate figures, run with either 'if' or 'trace' as plot argument:
</p>
<p>python run.py --plot trace
</p>
<p>The above takes under 20 seconds to run and generates pdf's for these
in the save folder:
</p>
<p><img src="./save/screenshot_het.png" alt="screenshot het">
</p>
<p><img src="./save/screenshot_hom.png" alt="screenshot hom">
</p>
<p>The 'if' plot argument in the above command takes about 35 minutes and
produces a file save/if.pdf with these traces:
</p>
<p><img src="./save/screenshot_if_het.png" alt="screenshot if het">
</p>
<p><img src="./save/screenshot_if_hom.png" alt="screenshot if hom">
</p>
</html>

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