bio-systems-biology-community-metabolic-modeling

name	bio-systems-biology-community-metabolic-modeling
description	Builds and simulates multi-species metabolic community models from member genome-scale models, using MICOM for abundance-weighted steady-state community FBA and cooperative tradeoff, SMETANA for cross-feeding and competition scoring, and SteadyCom/COMETS for common-growth-rate and dynamic simulation. Use when modeling a microbiome or co-culture, predicting cross-feeding and competition, abundance-weighting members from metagenomics, choosing steady-state vs dynamic community modeling, avoiding the compartment-pooling artifact, or judging how member-model quality and namespace propagate into community predictions.
tool_type	python
primary_tool	micom

Version Compatibility

Reference examples tested with: MICOM 0.33+, COBRApy 0.29+, Python 3.10+ (SMETANA and COMETS are separate installs)

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Note: community FBA needs a QP solver for MICOM's cooperative tradeoff (HiGHS/CPLEX/Gurobi). Member models must share a namespace (BiGG vs ModelSEED), reconciled via MetaNetX before combining. SMETANA is a separate CLI (github.com/cdanielmachado/smetana); COMETS uses the cometspy toolbox.

Community Metabolic Modeling