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removeCorticalNoiseIC.m
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removeCorticalNoiseIC.m
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function output = removeCorticalNoiseIC(krishnanSpecification)
%REMOVECORTICALNOISEIC - Set all initial condition noise to 0 for cortex portion of (Krishnan et al., 2016) models
%
% For a (Krishnan et al., 2016)-style DynaSim specification, this function
% simply sets all the initial condition noise terms to 0, so that every
% simulation using this has the same starting conditions. This is useful for
% both reproducibility and debugging.
%
% Inputs:
% 'krishnanSpecification': DynaSim specification structure for the (Krishnan
% et al., 2016) model
% - see dsCheckModel and dsCheckSpecification for details
%
% Outputs:
% 'output': DynaSim specification structure for the (Krishnan
% et al., 2016) model with all initial condition noise removed.
%
% Dependencies:
% - This has only been tested on MATLAB version 2017a.
%
% References:
% - Krishnan GP, Chauvette S, Shamie I, Soltani S, Timofeev I, Cash SS, et
% al. Cellular and neurochemical basis of sleep stages in the
% thalamocortical network. eLife. 2016;5: e18607.
%
% Author: Austin E. Soplata <[email protected]>
% Copyright (C) 2018 Austin E. Soplata, Boston University, USA
% ------------------------------------------
%% 1. Set all NoiseIC terms to 0
% ------------------------------------------
modifications = {...
'INdr', 'CaBufferNoiseIC' , 0;
'PYdr', 'CaBufferNoiseIC' , 0;
'INdr<-PYso', 'sAMPANoiseIC' , 0;
'INdr<-PYso', 'deprAMPANoiseIC' , 0;
'PYdr<-PYso', 'sAMPANoiseIC' , 0;
'PYdr<-PYso', 'deprAMPANoiseIC' , 0;
'PYdr<-INso', 'sGABAANoiseIC' , 0;
'PYdr<-INso', 'deprGABAANoiseIC' , 0;
'INdr', 'mHVANoiseIC' , 0;
'INdr', 'hHVANoiseIC' , 0;
'PYdr', 'mHVANoiseIC' , 0;
'PYdr', 'hHVANoiseIC' , 0;
'INdr', 'mKCaNoiseIC' , 0;
'PYdr', 'mKCaNoiseIC' , 0;
'INso', 'nKNoiseIC' , 0;
'PYso', 'nKNoiseIC' , 0;
'INdr', 'mMNoiseIC' , 0;
'INdr<-PYso', 'neMiniNoiseIC' , 0;
'INdr<-PYso', 'laMiniNoiseIC' , 0;
'PYdr<-PYso', 'neMiniNoiseIC' , 0;
'PYdr<-PYso', 'laMiniNoiseIC' , 0;
'PYdr<-INso', 'neMiniNoiseIC' , 0;
'PYdr<-INso', 'laMiniNoiseIC' , 0;
'PYdr', 'mMNoiseIC' , 0;
'INdr', 'mNaNoiseIC' , 0;
'INdr', 'hNaNoiseIC' , 0;
'INso', 'mNaNoiseIC' , 0;
'INso', 'hNaNoiseIC' , 0;
'PYdr', 'mNaPNoiseIC' , 0;
'PYso', 'mNaPNoiseIC' , 0;
'PYdr', 'mNaNoiseIC' , 0;
'PYdr', 'hNaNoiseIC' , 0;
'PYso', 'mNaNoiseIC' , 0;
'PYso', 'hNaNoiseIC' , 0;
'INdr<-PYso', 'sNMDANoiseIC' , 0;
'PYdr<-PYso', 'sNMDANoiseIC' , 0;
'INdr', 'vNoiseIC' , 0;
'INso', 'vNoiseIC' , 0;
'PYdr', 'vNoiseIC' , 0;
'PYso', 'vNoiseIC' , 0;
};
% ------------------------------------------
%% 2. Apply the changes to the model
% ------------------------------------------
output = dsApplyModifications(krishnanSpecification, modifications);