SteadyCom

(The functions in this repository are already incorporated into the COBRA toolbox since 2018. It is recommended to install COBRA toolbox to use them. Check out this tutorial.)

Matlab implementation for 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:

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

SteadyComFVA: perform FVA under the SteadyCom framework

SteadyComPOA: perform pairwise FVA under the SteadyCom framework

Remark:

• Using the ibm_cplex solver for the COBRA toolbox is usally the fastest when running this code because the code directly calls the cplex object in Matlab
• Use createMultipleSpeciesModel to create a community model from individual models
• Use getMultiSpeciesModelId to retreive the IDs needed for SteadyCom from the created model
• See the [tutorial] for a detailed example