domains / families / science / community-metabolic-modeling

community-metabolic-modeling

separate

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.

When to use

• 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
• judging how member-model quality and namespace propagate into community predictions
• metagenome-scale gut community modeling
• coexistence at a common community growth rate

When not to use

• modeling a community as one pooled bag model
• hand-merging models by prefix

Skill page

Source