%{
p25d19: (for p25d1w3, RR 2.2.4.4) simple bigger param sweep
%}
% -------------------------------------------------------------------
%% 0. Random seed wrapper
% -------------------------------------------------------------------
% % Use this block below for single sims with identical seed
% seed_list = 1121149;
% % % Use this block below for many sims with different seeds
number_sims = 50;
% number_sims = 10;
% % number_sims = 3;
rng('shuffle')
seed_list = randi(9999999, number_sims, 1);
% -------------------------------------------------------------------
%% 1. Define simulation parameters
% -------------------------------------------------------------------
modifications = {
'PYdr', 'gext', 0.004;
'TC', 'gext', 0.004;
'TRN', 'gext', 0.004;
'PYdr', 'gLeak', 0.005;
'PYdr', 'baseline', 40.0;
'TC', 'baseline', 40.0;
'TRN', 'baseline', 40.0;
'PYdr', 'DC', 0.0;
'TC', 'DC', 0.0;
'TRN', 'DC', 0.0;
'PYdr<-PYso', 'gNMDA', 0.00257;
'IN<-PYso', 'gNMDA', 0.0025 ;
'PYso<-PYdr', 'gKNa', 1.33;
'IN<-PYso', 'gAMPA', 1.0;
'IN<-TC', 'gAMPA', 0.1;
'PYso<-IN', 'gGABAA', 0.1;
'TC', 'gH', 0.005;
'PYdr', 'appliedStim', 0;
'TRN', 'appliedStim', 0;
'TC', 'appliedStim', 0;
'PYso<-IN', 'propoCondMult', 3;
'PYso<-IN', 'propoTauMult', 3;
'IN<-IN', 'propoCondMult', 3;
'IN<-IN', 'propoTauMult', 3;
'TC<-TRN', 'propoCondMult', 3;
'TC<-TRN', 'propoTauMult', 3;
'TRN<-TRN', 'propoCondMult', 3;
'TRN<-TRN', 'propoTauMult', 3;
};
vary={...
'PYdr<-PYso', 'gAMPA', [0.004, 0.006, 0.008, 0.01];
'PYdr<-TC', 'gAMPA', [0.004, 0.006, 0.008, 0.01];
};
% Where the simulation output files (excluding data) will go.
output_dir = '/example-output-directory/x7-scc-data/p25-thalcort-data/';
% output_dir = '/example-output-directory/x7-scc-data/p25-thalcort-data/p025-thalcort-modeling/p25d1w3code-revisions/';
% This is where you set the length of your simulation
time_end = 30000; % in milliseconds
% time_end = 15000; % in milliseconds
% time_end = 5000; % in milliseconds
% time_end = 4000; % in milliseconds
% time_end = 1000; % in milliseconds
% The time step/"resolution" used for the simulation. By default, DynaSim
% uses 0.01 milliseconds.
dt = 0.01; % in milliseconds
% Global scaling factor by which to multiple the number of cells in each
% population. The default scaling is 1, meaning 100 PYdr, 100 PYso, 20 IN,
% 20 TC, and 20 TRN. Changing the scale changes the population sizes
% proportionally, meaning a scaling of 0.5 would simulate a network using
% 50 PYdr, 50 PYso, 10 IN, 10 TC, and 10 TRN. Use this to decrease (< 1) or
% increase (> 1) the number of cells modeled in each population,
% proportionally.
numCellsScaleFactor = 1;
% numCellsScaleFactor = 0.2;
% default was 0.0667
% Options that affect the simulation properties without affecting the data;
% configuration rather than scientific options.
% -------------------------------------------------------------------
%% 2. Assemble and customize the model
% -------------------------------------------------------------------
spec = assembleFullSpec(numCellsScaleFactor);
% Apply local non-vary modifications to spec
spec = dsApplyModifications(spec, modifications);
iteration_number = 0;
for random_seed_index = 1:length(seed_list)
iteration_number = iteration_number + 1;
study_dir = strcat(output_dir, mfilename, '_i', num2str(iteration_number, '%.3d'));
simulator_options={
'cluster_flag', 1,... % Whether to submit simulation jobs to a cluster, 0 or 1
'cluster_matlab_version','2022a',...
'compile_flag', 0,... % Whether to compile simulation using MEX, 0 or 1
'cpu_architecture', 'skylake',...
'disk_flag', 0,... % Not implemented, ignore
'downsample_factor', 10,... % How much to downsample data, proportionally {integer}
'dt', dt,... % Fixed time step, in milliseconds
'memory_limit', '64G',... % Memory limit for use on cluster
'mex_flag', 0,... % Flag for MEX compilation, not recommended
'num_cores', 1,... % Number of CPU cores to use, including on cluster
'overwrite_flag', 1,... % Whether to overwrite simulation raw data, 0 or 1
'parfor_flag', 0,... % Whether to use parfor if running multiple local sims, 0 or 1
'plot_functions', {@dsPlot, @dsPlot, @dsPlot, @dsPlot, @dsPlot,...
...
@dsPlot, @dsPlot, @dsPlot, @dsPlot, @dsPlot,...
@dsPlot},...
'plot_options', {{'plot_type', 'waveform', 'format', 'png'},... % Arguments to pass to each of those plot functions
{'plot_type', 'rastergram', 'format', 'png','plot_time_axis_sec_flag',0},...
{'plot_type', 'power', 'format', 'png'},...
{'plot_type', 'comodulograms','format','png',...
'variable', 'PYdr_PYso_iAMPA_PYdr_PYso_JB12_IAMPA_PYdr_PYso_JB12',...
'max_num_rows',1},...
{'plot_type', 'comodulograms','format','png',...
'variable', 'PYdr_TC_iAMPA_PYdr_TC_IAMPA_PYdr_TC',...
'max_num_rows',1},...
...
{'plot_type', 'waveform', ...
'variable', {'TC_iH_TC_AS17_Open',...
'TC_iH_TC_AS17_Pone',...
'TC_iH_TC_AS17_OpenLocked',...
'TC_iH_TC_AS17_iH_TC_AS17'}, ...
'max_num_rows', 4},...
{'plot_type', 'waveform', ...
'variable', {...
'PYdr_PYso_iAMPA_PYdr_PYso_JB12_IAMPA_PYdr_PYso_JB12',...
'PYdr_PYso_iAMPA_PYdr_PYso_JB12_res',...
},...
'max_num_rows', 2},...
{'plot_type', 'power', ...
'variable', {...
'PYdr_PYso_iAMPA_PYdr_PYso_JB12_IAMPA_PYdr_PYso_JB12',...
'PYdr_PYso_iAMPA_PYdr_PYso_JB12_res',...
},...
'max_num_rows', 2},...
{'plot_type', 'waveform', ...
'variable', {...
'TC_PYso_iAMPA_TC_PYso_IAMPA_TC_PYso',...
'TC_PYso_iAMPA_TC_PYso_sAMPA',...
},...
'max_num_rows', 2},...
{'plot_type', 'waveform', ...
'variable', {...
'PYdr_TC_iAMPA_PYdr_TC_IAMPA_PYdr_TC',...
'PYdr_TC_iAMPA_PYdr_TC_sAMPA',...
},...
'max_num_rows', 2},...
{'plot_type', 'power', ...
'variable', {...
'PYdr_TC_iAMPA_PYdr_TC_IAMPA_PYdr_TC',...
'PYdr_TC_iAMPA_PYdr_TC_sAMPA',...
},...
'max_num_rows', 2},...
},...
'random_seed', seed_list(random_seed_index),... % What seed to use; use value 'shuffle' to randomize
'save_data_flag', 0,... % Whether to save raw output data, 0 or 1
'save_results_flag', 1,... % Whether to save output plots and analyses, 0 or 1
'solver', 'euler',... % Numerical integration method {'euler','rk1','rk2','rk4'}
'study_dir', study_dir,... % Where to save simulation results and code
'tspan', [0 time_end],... % Time vector of simulation, [beg end], in milliseconds
'verbose_flag', 1,... % Whether to display process info, 0 or 1
};
% -------------------------------------------------------------------
%% 3. Run the simulation
% -------------------------------------------------------------------
data = dsSimulate(spec,'vary',vary,simulator_options{:});
end
exit