Computing the maximum growth rate of a microbial community at community steady-state
Matlab
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auxiliary_functions
doc
README.md
SteadyComCplex.m
SteadyComFVACplex.m
SteadyComPOACplex.m
createCommModel.m

README.md

SteadyCom

Update on Jul 26, 2017

SteadyCom is now integrated into the COnstraint-Based Reconstruction and Analysis (COBRA) Toolbox which supports a wide range of solvers. Please see https://opencobra.github.io/cobratoolbox The code here supports only the IBM ILOG Cplex solver.


Computing the maximum growth rate of a microbial community at community steady-state.

Chan SHJ, Simons MN, Maranas CD (2017) SteadyCom: Predicting microbial abundances while ensuring community stability. PLoS Comput Biol 13(5): e1005539. https://doi.org/10.1371/journal.pcbi.1005539

Main functions:

createCommModel: create a community model from individual models

SteadyComCplex: given a community model constructed by createCommModel, find the maximum community growth rate by the SteadyCom procedure

SteadyComFVACplex: perform FVA under the SteadyCom framework

SteadyComPOACplex: perform pairwise FVA under the SteadyCom framework

See SteadyCom/doc/index.html for detailed documentations