initCobraToolbox;
changeCobraSolver('gurobi5','LP');
% testAll();
model=readCbModel('LiverNew.xml');
%%%%%
writeCbModel(model,'xls');
%%%%%
model2 = changeRxnBounds(model, {'HMR_4394','HMR_4381'}, [500,800], 'u');
%%%%%
modelAdd=addReaction(model,'bio',{'MET1','MET2','MET3'},[-1,-2,1]);
% modelAdd2=addReaction(model,'bio2','MET4 + MET5 -> 4 MET6');
%%%%%
modelRem=removeRxns(model,{'HMR_4394','HMR_4381'});
%%%%%
modelchan = changeObjective(model, {'HMR_4394'}, [1]);
%%%%%
f=optimizeCbModel(modelchan);
%%%%%
[grRatio, grRateKO, grRateWT, hasEffect, delRxns, fluxSolution] = singleGeneDeletion(model,'FBA',{'ENSG00000000419','ENSG00000001630'});
%%%%%
[grRatioDble, grRateKO, grRateWT] = doubleGeneDeletion(model,'FBA', {'ENSG00000000419','ENSG00000001630'},{'ENSG00000004799','ENSG00000005381'});
%%%%%
[minFluxA,maxFluxA] = fluxVariability(model);
%%%%%
mapA=readCbMap();
drawFluxVariability(mapA,model,minFluxA,maxFluxA);
%%%%%
[sampleStructOut, mixedFrac] = gpSampler(model,100);
%%%%%
[modelSampling,samplesPre]=sampleCbModel(model,'modelsamples');
[setsSorted,setNoSorted,setSize] = identifyCorrelSets(model,samplesPre);
%%%%%
[controlFlux, objFlux] = robustnessAnalysis(model,'HMR_4381')