%Simulation PDH activity using FBA %Requirements: %COBRA Toolbox (https://opencobra.github.io/cobratoolbox/latest/) fid = fopen('Simulation_PDH.txt', 'w+'); fprintf(fid, '%s\t%s\t%s\t%s\n','Normoxia','Hypoxia','Hypoxa+Glm','Hypoxia (additional AA)'); % header initCobraToolbox %initialise cobra toolbox changeCobraSolver('glpk'); model=readCbModel('SupplementaryS1.xml'); % read SBML file, Supplementary File S1, must be in the same folder or an alternative folder must be included in the path to the file %[nrows,ncols]=size(model.rxns); %for row = 1:nrows; % fprintf(fid,'%s\t%s\t','RxnID',model.rxns{row,:}); % rxn=model.rxns{row,:} %end % Similation normoxia %oxygenUptake=[19.8,1.98] model=changeObjective(model,'BioMass5',1); % maximise ATP production solution=optimizeCbModel(model,'max',0,true); x=solution.x; %Simulation hypoxia model=changeRxnBounds(model,'Boundary2',1.98,'u'); %Change uptake of oxygen (1.98 = 10%) y=solution.x; %Simualtion with Glutamine model=changeRxnBounds(model,'Boundray22',0,'u'); %uptake of glucose momel=changeRxnBounds(model,'Boundary16',0.9,'u'); %uptake of glutamine solution=optimizeCbModel(model,'max',0,true); z=solution.x; %Simulation with addtional amino acids %List of amino acid exhange reactions aaRxns= {'Boundary3','Boundary4','Boundary5','Boundary8','Boundary10','Boundary16','Boundary18','Boundar51','Boundary53','Boundary61'}; for r = aaRxns model=changeRxnBounds(model,r,1,'u'); %Change the max uptake of each AA %FA ACADL reactions 'R01279MM','R03990MM','R03858MM' end solution=optimizeCbModel(model,'max',0,true); w=solution.x; fprintf(fid,'%d\t%d\t%d\t%d\n',x,y,z,w) fclose(fid);