tutorial4

 tutorial4
   This script contains the list of functions necessary for running
   Tutorial 4, see Tutorial 4 in "RAVEN tutorials.docx" for more details.
   Several key stages may be missing, try to fill these gaps before
   checking the solutions in tutorial4_solutions. It is assumed that the
   user is somewhat familiar with linear programming.

   It is assumed that the user has already completed Tutorials 2-3

0001 % tutorial4
0002 %   This script contains the list of functions necessary for running
0003 %   Tutorial 4, see Tutorial 4 in "RAVEN tutorials.docx" for more details.
0004 %   Several key stages may be missing, try to fill these gaps before
0005 %   checking the solutions in tutorial4_solutions. It is assumed that the
0006 %   user is somewhat familiar with linear programming.
0007 %
0008 %   It is assumed that the user has already completed Tutorials 2-3
0009 
0010 %Import the Excel model
0011 model=importExcelModel('smallYeastBad.xlsx');
0012 model.b=[model.b inf(numel(model.b),1)];
0013 sol=solveLP(model,1);
0014 printFluxes(model,sol.x,false,10^-5,[],'%rxnID (%rxnName):\n\t%eqn\n\t%flux\n');
0015 I=canConsume(model);
0016 disp(model.mets(I));
0017 gapReport(model,{refModel});
0018 
0019 model=importExcelModel('smallYeastBad2.xlsx');
0020 [reducedModel, deletedReactions, deletedMetabolites]=simplifyModel(model,false,false,false,true);
0021 disp(deletedReactions);
0022 disp(deletedMetabolites);
0023 [notProducedMets, ~, neededForProductionMat, minToConnect]=checkProduction(model,true,model.comps,false);
0024 disp(minToConnect);
0025 
0026 refModel=importExcelModel('smallYeast.xlsx');
0027 [newConnected, cannotConnect, addedRxns, newModel]=fillGaps(model,{refModel},false);
0028 disp(addedRxns);
0029 disp(newConnected);
0030 disp(cannotConnect);