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EPFL-LCSB / pytfa

A Python 3 implementation of Thermodynamics-based Flux Analysis
https://lcsb.epfl.ch/
Apache License 2.0
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Get new delta G values after adding metabolomics data #43

Closed sulheim closed 4 years ago

sulheim commented 4 years ago

How can I get the effective delta G of each reaction after the log concentration of all metabolites have been included?

realLCSB commented 4 years ago

Good day Sulheim,

You can access the Gibbs free energy of each reaction through the following commands:

solution = model.optimize()
solution.raw.loc[model.delta_g.get_by_id(my_reaction_name).name]
# -- OR, after the model has been optimized and no changes have been made to it --
model.delta_g.get_by_id(my_reaction_name).primal

Note that the may model.delta_g works is the same as model.reactions. So if you're interested in PGI for instance, you can type model.delta_g.PGI.

Finally, I would like to stress that the Gibbs free energy value you will get is only one solution, you should perform a variability analysis (with your physiology constrained) to have an idea of the feasible range for the value.

Hope it helps, Cheers, Pierre