tutorial.m

rootDir = pwd;

%% Starts the cobratoolbox
initCobraToolbox

%% Change solver
solverOK=changeCobraSolver('ibm_cplex','LP');


websave('AGORA-master.zip','https://github.com/VirtualMetabolicHuman/AGORA/archive/master.zip')
unzip('AGORA-master')

modPath = [rootDir filesep 'AGORA-master' filesep 'CurrentVersion' filesep 'AGORA_1_03' filesep' 'AGORA_1_03_mat'];

abunFilePath = [rootDir filesep 'IBD_study_abundances.csv'];
computeProfiles = true;

dietFilePath = 'AverageEuropeanDiet';
infoFilePath = [rootDir filesep 'IBD_study_samples.csv'];

resPath = [rootDir filesep 'MicrobiomeModels'];
numWorkers = 4;

[init, netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary] = initMgPipe(modPath, abunFilePath, computeProfiles, 'dietFilePath', dietFilePath, 'infoFilePath', infoFilePath, 'resPath', resPath, 'numWorkers', numWorkers);