PrintBiomass whereabouts or replacement function

[Leandro Antunes Berti]

Hi,

We are looking to extract the biomass precursors and its fractions from my model, but when following Thiele and Palson protocol I was unable to find the PrintBiomass function.

There is a kind of solution in the group where someone says to use printRxnFormula, but this functions just print all the formulas.

We need the function or any other way to extract these values do be able to use the command addDemandReaction.

Best regards,

Leandro

[Nathan Lewis]

try printRxnFormula(model,<put the biomass function reaction name here>)

or if you know the model is set up to optimize the biomass. try 

printRxnFormula(model,model.rxns(model.c~=0))

Nathan E. Lewis

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[Farhad]

Hi Leonardo,

There is an excel file in the supplementary info coming with the original paper. If you have it, you can find details of all reactions including the complete Biomass reaction in that excel file (table2 of msb201165-s2.xls). If you don't, you can download it from:

http://www.nature.com/msb/journal/v7/n1/suppinfo/msb201165_S1.html#msb201165-s2 (for iJO1366)

or
The BIGG Database (for iAF1260)

depending on the model you are working with.

Farhad

[Leandro Antunes Berti]

Many thanks Farhad!

I will donwload it and check if it works. 

Best regards,

Leandro