cbmpy

问题 In some datasets, I sometimes observe fixed flux ratios which I would like to incorporate into my simulations. How could I do this in CBMPy? For example, I have the model from here and would now like to constrain the ratio of succinate efflux and pyruvate efflux to 2.0. I know how to set constraints on individual reactions: import cbmpy # downloaded from http://bigg.ucsd.edu/models/e_coli_core ecoli = cbmpy.CBRead.readSBML3FBC('e_coli_core.xml') ecoli.setReactionBounds('R_EX_pyr_e', 1.0, 1000

问题 I have a genome-scale stoichiometric metabolic model iMM904.xml and when I open it in a text editor I can see that certain genes have annotation added to them, e.g. <fbc:geneProduct fbc:id="G_YLR189C" fbc:label="YLR189C" metaid="G_YLR189C"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Description rdf:about="#G_YLR189C"> <bqbiol:isEncodedBy> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org