This directory includes NEURON and MATLAB files to generate figure 3
and supplementary figures S3 and S4 of the paper:

"Opposing effects on NaV1.2 function underlie differences between
SCN2A variants observed in individuals with autism spectrum disorder
or infantile seizures". Biological Psychiatry (2017) DOI:
http://dx.doi.org/10.1016/j.biopsych.2017.01.009

This model is based on the model that accompanied the paper "State and
location dependence of action potential metabolic cost (Hallermann et
al., 2012)" model.  (model=144526 at ModelDB)

The root directory includes 2 sub-folders, "ActInact" includes the
VClamp simulations (Figure S3). And "Excitability" includes the single
neuron simulations.

VCalmp - "ActInact" folder
This folder holds the different .mod files for the Nav1.2 variantns
and Nav1.6 (nax). These mod files are variations on the original ones
which were published at: "Fast sodium channel gating supports
localized and efficient" Schmidt-Hieber C, Bischofberger J. (2010)
(see 144526 at ModelDB)
To run VClamp simulations: 
compile the .mod files 
In sodiumTrialsNa.hoc replace occurences of "na" with the suffix at
the .mod file e.g. nad82g at lines: 17,18,176,178.
After generating the recording files using sodiumTrialsNa.hoc you can
use the matlab script VClamp.m to create figure s3.

Single neuron models - "Excitability" folder
This folder holds subfolders for each condition that we ran in fig 3
and S4.

How to run simulations:
(see https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.html
for more detailed help)
change directory to Excitability/AdultD12N/
Compile .mod files 
run mosinit.hoc
Wait for it to load 
in the terminal run: runSCN2A()
which will run all the simulations neccessary for that condition, and
will generate output (Vms) .csv files.  Then run the matlab script
YoungModel.m or AdultModel.m to plot the figures from the data
produced by the NEURON simulations.
For this example cut and paste the matlab commands in AdultModel.m that
contain D12N to generate this trace which is similar to the D12N trace
in Fig3A (change the paths with "\"s (windows) to "/"s if on unix or mac).



Please refer any questions to:
Roy Ben-Shalom
bens.roy at gmail.com