cobrapy

combined

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis. Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model validation for systems biology and metabolic engineering.

When to use

Use for loading/building metabolic networks, optimizing their steady-state fluxes, knockout screens, medium design, feasible-space sampling, and gap-filling hypotheses. FBA is a constraint-based prediction; it does not infer kinetic rates…
Use this skill when the request matches its documented task boundary.
Use it when the user can provide the required inputs and expects a structured deliverable.
Prefer this skill for repeatable, checklist-driven execution rather than open-ended brainstorming.

When not to use

Do not use this skill when the required source data, identifiers, files, or credentials are missing.
Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.

Skill page

Conflict

The K-Dense-AI copy is a highly specific, version-pinned (cobra 0.32.1) procedural guide with critical warnings about deprecated arguments (e.g., `loopless=True`), solver selection, and reproducibility. The FreedomIntelligence copy provides a broader API reference including features omitted by K-Dense (production envelopes, gapfilling, model construction) but uses deprecated syntax (`loopless=True`) and lacks version pinning. The aipoch copy is a generic wrapper with no unique technical value. Because K-Dense is the most 'authentic' procedure but lacks the full feature set of FreedomIntelligence, and FreedomIntelligence contains outdated/incorrect syntax for the current version, combining them is necessary to provide a complete and correct skill.