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applyPaperValues.m
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function output = applyPaperValues(krishnanSpecification)
%APPLYPAPERVALUES - Apply values of model from paper, not code
%
% applyPaperValues takes a (Krishnan et al., 2016)-type DynaSim model
% specification and applies the values given in the original paper, which are
% not necessarily the same values as that seen in the source code. The default
% values of this overall model (dynasim-krishnan-2016-model) are based on the
% values seen in the source code, not the paper.
%
% 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 the paper's values applied
%
% 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. Combine all the changes to make
% ------------------------------------------
modifications = {...
'PYdr', 'gKLeak', 0.007;
'PYdr', 'gLeak', 0.023;
'PYdr', 'gNaP', 2.0;
'PYdr', 'gNa', 0.8;
'PYdr', 'gHVA', 0.012;
'PYdr', 'gKCa', 0.015;
'PYso', 'gNa', 3000;
'PYso', 'gK', 200;
'PYso', 'gNaP', 15;
'INdr', 'gKLeak', 0.034;
'INdr', 'gLeak', 0.006;
'INdr', 'gNa', 0.8;
'INdr', 'gHVA', 0.012;
'INdr', 'gKCa', 0.015;
'INso', 'gNa', 2500;
'INso', 'gK', 200;
'TC', 'gKLeak', 0.007;
'TC', 'gLeak', 0.01;
'TC', 'gNa', 90;
'TC', 'gK', 10;
'TC', 'gT', 2.5;
'TC', 'gH', 0.015;
'TRN', 'gKLeak', 0.016;
'TRN', 'gLeak', 0.05;
'TRN', 'gNa', 100;
'TRN', 'gK', 10;
'TRN', 'gT', 2.2;
% 0.024 uS * (1 mS / 1000 uS) * (1 / (165*1e-6 cm^2)) = 0.15 mS/cm^2
'PYdr<-PYso', 'gAMPA', 0.15;
% 0.033 uS * (1 mS / 1000 uS) * (1 / (165*1e-6 cm^2)) = 0.2 mS/cm^2
'PYdr<-PYso', 'gMiniAMPA', 0.2;
% 0.001 uS * (1 mS / 1000 uS) * (1 / (165*1e-6 cm^2)) = 0.006 mS/cm^2
'PYdr<-PYso', 'gNMDA', 0.006;
% 0.012 uS * (1 mS / 1000 uS) * (1 / (50*1e-6 cm^2)) = 0.24 mS/cm^2
'INdr<-PYso', 'gAMPA', 0.24;
% 0.02 uS * (1 mS / 1000 uS) * (1 / (50*1e-6 cm^2)) = 0.4 mS/cm^2
'INdr<-PYso', 'gMiniAMPA', 0.4;
% 0.001 uS * (1 mS / 1000 uS) * (1 / (50*1e-6 cm^2)) = 0.02 mS/cm^2
'INdr<-PYso', 'gNMDA', 0.02;
% 0.024 uS * (1 mS / 1000 uS) * (1 / (165*1e-6 cm^2)) = 0.15 mS/cm^2
'PYdr<-INso', 'gGABAA', 0.15;
% 0.02 uS * (1 mS / 1000 uS) * (1 / (165*1e-6 cm^2)) = 0.12 mS/cm^2
'PYdr<-INso', 'gMiniGABAA', 0.12;
% 0.05 uS * (1 mS / 1000 uS) * (1 / (2.9e-4 cm^2)) = 0.172 mS/cm^2
'TC<-TRN', 'gGABAA', 0.172;
% 0.02 uS * (1 mS / 1000 uS) * (1 / (2.9e-4 cm^2)) = 0.07 mS/cm^2
'TC<-TRN', 'gGABAB', 0.07;
% 0.05 uS * (1 mS / 1000 uS) * (1 / (1.43e-4 cm^2)) = 0.35 mS/cm^2
'TRN<-TRN', 'gGABAA', 0.35;
% 0.05 uS * (1 mS / 1000 uS) * (1 / (1.43e-4 cm^2)) = 0.35 mS/cm^2
'TRN<-TC', 'gAMPA', 0.35;
% 0.02 uS * (1 mS / 1000 uS) * (1 / (165*1e-6 cm^2)) = 0.12 mS/cm^2
'PYdr<-TC', 'gAMPA', 0.12;
% 0.02 uS * (1 mS / 1000 uS) * (1 / (50*1e-6 cm^2)) = 0.4 mS/cm^2
'INdr<-TC', 'gAMPA', 0.4;
% 0.005 uS * (1 mS / 1000 uS) * (1 / (2.9e-4 cm^2)) = 0.0172 mS/cm^2
'TC<-PYso', 'gAMPA', 0.0172;
% 0.015 uS * (1 mS / 1000 uS) * (1 / (1.43e-4 cm^2)) = 0.105 mS/cm^2
'TRN<-PYso', 'gAMPA', 0.105;
};
% ------------------------------------------
%% 2. Apply the changes to the model
% ------------------------------------------
output = dsApplyModifications(krishnanSpecification, modifications);