bio-systems-biology-flux-balance-analysis
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy. Predict growth rates, metabolic fluxes, and optimal resource utilization. Use when predicting metabolic phenotypes or optimizing flux distributions.
npx skills add BioTender-max/awesome-bio-agent-skills --skill flux-balance-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: COBRApy 0.29+ 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. # Flux Balance Analysis **"Predict growth rate and metabolic fluxes for my organism"** → Solve a linear program over a genome-scale metabolic model to find the optimal flux distribution that maximizes biomass (or a custom objective), and assess flux ranges with FVA. - Python: `model.optimize()`, `cobra.flux_analysis.flux_variability_analysis()` (COBRApy) ## Load Models ```python import cobra # Load built-in test models model = cobra.io.load_model('textbook') # E. coli core (95 reactions) model = cobra.io.load_model('iJO1366') # Full E. coli (2583 reactions) # Load from file model = cobra.io.read_sbml_model('model.xml') model = cobra.io.load_json_model('model.json') # BiGG models available at: http://bigg.ucsd.edu/models ``` ## Basic FBA **Goal:** Predict optimal metabolic flux distributions and gro
- Version Compatibility
- Load Models
- Basic FBA
- Set Media Conditions
- Flux Variability Analysis (FVA)
- Production Envelope
- Phenotype Phase Plane
- Parsimonious FBA (pFBA)
- Loopless FBA
- Related Skills
What does the bio-systems-biology-flux-balance-analysis skill do?
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy. Predict growth rates, metabolic fluxes, and optimal resource utilization. Use when predicting metabolic phenotypes or optimizing flux distributions.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill flux-balance-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.