User:Daniela A. Garcia S./Notebook/Modeling 2011 UNAM Genomics-Mexico/2011/04/03

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Procedure
1. Reading SBML format models into Matlab

model = readCbModel(fileName);

It can also be downloaded directly, as the ecoli_core_model

2. Changing lower and/or upper bounds of ﬂux

model = changeRxnBounds(model, rxnNameList, boundValue, boundType);

For exchange reactions, negative lower bounds allow entry into the system, whereas positive upper bounds allow exit from the system.

3. Changing the objective function

model = changeObjective(model,rxnNameList,objectiveCoeff)

ObjectiveCoeff is not used in the FBA Tutorial

4. Adding or removing reactions

model = addReaction(model,rxnName,metaboliteList,stoichCoeffList);

metaboliteList and stoichCoeffList contain the names of the metabolites participating in the reaction (name designated in rxnName) and the corresponding stoichiometric coefﬁcients in a vector. By default, reversible reaction.

model = removeRxns(model,rxnRemoveList);

5.Printing out reaction formulas

printRxnFormula(model,rxnNameList);


 * This are the basical points to work with a SBML file


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