Scripts

This is the entry point for our code, it calls all other relevant functions.

Run_main

Code

% Script to import sbtab and run the analyis
% clear functions

%Get the date and time
date_stamp = string(year(datetime)) + "_" + ...
    string(month(datetime)) + "_" + string(day(datetime))...
    + "__" + string(hour(datetime)) + "_" + string(minute(datetime))...
    + "_" + string(round(second(datetime)));

% Get the folder where the MATLAB code and models are located
Matlab_main_folder = fileparts(mfilename('fullpath'))+"/";
Matlab_main_folder = strrep(Matlab_main_folder,"\","/");
addpath(genpath(Matlab_main_folder));
mmf.main = Matlab_main_folder;

% Name of the various analysis that can be run with this code
analysis_options = ["Diagnostics","Parameter Estimation",...
    "Global Sensitivity Analysis","Reproduce a previous analysis",...
    "Reproduce the plots of a previous analysis","Import model files"];

% Code for choosing the model and loading the settings files
[stg,rst,sb] = f_user_input(mmf,analysis_options);

% Get the folder structure used for the model files
[mmf] = default_folders(stg,mmf,date_stamp);

% Runs the import scripts if chosen in settings
if stg.import
    [stg,sb] = f_import(stg,mmf);
else
    % Creates a struct based on the sbtab that is used elswhere in the code
    % and also adds the number of experiments and outputs to the settings
    % variable
    if isempty(sb)% check needed for plot reproduction
        [stg,sb] = f_generate_sbtab_struct(stg,mmf);
    end
end

% Runs the Analysis chosen in settings
if any(contains(analysis_options(1:3),stg.analysis))
    rst = f_analysis(stg,stg.analysis,mmf,analysis_options);
end
% Save Analysis results if chosen in settings
if stg.save_results
    f_save_analysis(stg,sb,rst,mmf)
end

% Plots the results of the analysis, this can be done independently after
% loading the results of a previously run analysis
if stg.plot
    f_plot(rst,stg,mmf)
    % Save plots results if chosen in settings
    if stg.save_results
        f_save_plots(mmf)
    end
end

This is the main script from the MATLAB® portion of the workflow. Depending on the configurations on the settings file and choices on the user facing prompts it can call functions to:

• Perform conversions of the SBtab:

  • SBtab( .xlsx) to SBtab (.tsv)

  • SBtab (.xlsx) to MATLAB® SimBiology® (.m, .sbproj)

  • MATLAB® SimBiology® to SBML (.xml)

• Perform analysis on the model:

  • Diagnostics

  • Parameter Estimation

  • Global Sensitivity Analysis

• Saving results from analysis

• Plotting relevant results

• Saving plots

It can also reproduce a the calculations of a previous analysis or just its plots.