Readme

OBS, the acronym DATASTUDY includes DREW/Uhlirova/Desjardins/Shmuel/Huber data and will be used to avoid repeating descriptions

To execute the code, the following is required

• Matlab R2017b, with add ons:

  • mex compiler (preferably MinGw-64): https://www.mathworks.com/matlabcentral/fileexchange/52848-matlab-support-for-mingw-w64-c-c-compiler
  • Symbolic Math Toolbox: https://www.mathworks.com/products/symbolic.html

• Advanced Multilanguage Interface to CVODES and IDAS https://github.com/AMICI-dev/AMICI under "tools" folder a slightly altered version is available, where issues related to the compilation of events are fixed. The mex compilation of models can cause error is the dictionary is to long, if that is the case, try moving the AMICI folder further up in the dictionary tree.

• PESTO: Parameter EStimation TOolbox https://github.com/ICB-DCM/PESTO

Furthermore, to run the optimization (OptDATASTUDY) the MEIGO toolbox in needed: https://bitbucket.org/jrbanga_/meigo64/src/master/

Before being able to run the code, SetUp.m must be executed, to generate the executable model simulation files (this requires the AMICI toolbox) and add needed folders to MATLAB path.

The following scripts are included: SetUp.m - calls GenerateModels.m to generates the executable model files, sets up MATLAB path and add a new folder named "mex and sim files".

GenerateModels.m - is called by SetUp.m and is the file that generates the executable model files and store the executable model files "mex and sim files/".

PlotArticleFigures.m - plots all model estimation figures from the article (Figure 3,5,6,7,S2,S4).

OptDATASTUDY - ESS Optimization script for each data set.

MCMC_DATASTUDY - Rampart algorithm for each data set.

Costfunctions/ - Model evaluation function for Chi2 to every data set.

Datamatrixes/ - Contain files with raw data from each study. Not formatted in the right way to be directly used.

functions/ - functions used by various scripts. Needs to be on path. functions/optsetupfunction - loads best objective function, data structure, simulation constants, end time for stimulation and parameters for each study by user input [1-Drew, 2-Uhlirova, 3-Desjardins, 4-Shmuel, 5-Huber, 6-DrewTimeVariant].

GenerateData/ - functions that create data field structure (Data) containing the experimental data to each data set/study from the raw data in /Datamatrixes

MCMC/ - functions called during MCMCDATASTUDY is stored here (GenerateUncertaintyDATASTUDY and SimulateDATASTUDYAll). Also, the results from the MCMC run is directed here.

Model files (_syms)/ - includes .m files ending with _syms --> model structure information that is used to build the executable model files.

OptimizedParameters/ - best parameter sets found.

Plotfunctions/ - the script that generates the figures presented in the article is stored here.