IGEM:UNAM-Genomics Mexico/2009/Notebook/H2/2011/04/15

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FBA

The Model Structure

COBRA requires the use of a particular Model structure in MatLab. This structure is described and explained here:

Element Description
rxns Vector containing the abbreviated reaction names, in the same order as they appear on The Matrix.
mets Vector containing the abbreviated metabolite names, in the same order as they appear on The Matrix.
S The grand stochiometry matrix (aka The Matrix), with dimensions nrow=metabolites & ncol=reactions. It is in a "sparse" form.
rev A logical vector of length rxns that hold whether the reaction is reversible.
lb Matrix containing the lower bounds for the fluxes. They are ordered as the reactions.
ub Matrix containing the upper bounds for the fluxes. They are ordered as the reactions.
c Vector specifying the reaction to maximize (as 1) among the others (as 0s).
rules Vector containing the conditional rules for successful expression of a given reaction. They are ordered by reaction.
genes Vector containing all the genes associated with The Matrix. They carry their own order.
rxnGeneMat Matrix in"sparse" format containing the association of genes and metabolites. It's dimensions are nrow=metabolites & ncol=genes.
grRules Vector containing the conditional rules for successful expression fo a given reaction. They are ordered by reaction. Redundant with the vector "rules", however this one implicitly cites the genes involved.
subSystems Vector containing annotation information for the different reactions of the Model. They are ordered by reaction.
rxnNames The full names of all the reactions. They are ordered by reaction.
metNames The full names of all the metabolites. They are ordered by metabolite.
metFormulas The chemical formulae for the different metabolites. Might be of use with balancing?
b N/A
description A description of the Model.