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View Code? Open in Web Editor NEWSCN1A gain-of-function in early infantile encephalopathy (Berecki et al 2019)
Home Page: https://modeldb.science/264834
SCN1A gain-of-function in early infantile encephalopathy (Berecki et al 2019)
Home Page: https://modeldb.science/264834
<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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