alterlab-cobrapy - Analyze genome-scale metabolic models with COBRApy
Build and analyze constraint-based metabolic models with FBA, FVA, knockout studies, flux sampling, gapfilling, and SBML or JSON/YAML model I/O.
Tags
Updated: 2026-10-01Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Load metabolic models
- Inspect model components
- Run flux balance analysis
- Run flux variability analysis
- Analyze gene knockouts
- Analyze reaction knockouts
- Manage growth media
- Sample feasible fluxes
- Calculate production envelopes
- Gapfill metabolic models
- Build metabolic models
- Read and write model files
Inputs
- SBML, JSON, or YAML model files
- Model identifiers
- Objective reaction
- Medium constraints
- Knockout targets
- Sampling parameters
- Gapfill reaction model
- Analysis options
Outputs
- Optimization solutions
- Flux variability results
- Knockout phenotype results
- Flux samples
- Production envelope data
- Gapfill reaction sets
- Updated model files
- Model status and flux values
Requirements
- Python environment with uv
- COBRApy installed
- optlang-compatible solver
- pandas below version 3
- Network access for remote model loading
- Network access for repository gapfilling