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Questions tagged [cbmpy]

CBMPy is an open-source Python based framework to simulate and edit genome-scale stoichiometric metabolic models.

About CBMPy

CBMPy is a based platform for constraint-based modelling and analysis in biology. It implements popular analyses such as Flux Balance Analysis (FBA), Flux Variability Analysis (FVA), element/charge balancing, network analysis and model editing as well as advanced methods developed specifically for the ecosystem modelling: minimal distance methods, flux minimization and input selection.

CBMPy fully supports a number of open community standards, including SBML Level 3 Core, the SBML Level 3 Flux Balance Constraints (FBC) package, and the SBML Level 3 Groups package, as well as the OMEX format and the creation of COMBINE archives. Models can be read/written in SBML FBC versions 1 and 2 as well as older SBML Level 2 dialects.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Official Resources

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Flux variability analysis only for transport reactions between compartments?

I would like to do a FVA only for selected reactions, in my case on transport reactions between compartments (e.g. between the cytosol and mitochondrion). I know that I can use selected_reactions in doFVA like this: import cbmpy as cbm mod =…
Vinz
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Add new reactions with GPR

I have a model and want to add an entire new pathway to it. Some of the metabolites already exist in the model, others have to be created. I also have to add GPRs to the reactions using genes not yet present in the model. I found the function…
Hetitus
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How to add annotation to a gene in SBML?

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.
Vinz
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How to set a flux ratio as a constraint?

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…
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How to create a genome scale metabolic model in cbmpy from scratch?

So the previous question was apparently not wisely asked. So here is the rephrased original question: I am planing on building up a new GSMM from nothong (i.e. I need a empty model, 0 reaction/metabolite/compartment/GPR/annotation, but with a proper…
Neil Tang
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