bio-systems-biology-model-curation
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation. Ensure models meet SBML standards and produce biologically meaningful predictions. Use when improving draft models or preparing models for publication.
npx skills add BioTender-max/awesome-bio-agent-skills --skill model-curation --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 - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Model Curation **"Validate and improve the quality of my metabolic model"** → Score a genome-scale model against SBML community standards using memote, then gap-fill blocked reactions and fix stoichiometric inconsistencies using COBRApy to ensure biologically meaningful predictions. - CLI: `memote report snapshot` for quality scoring - Python: `cobra.flux_analysis.gapfilling.gapfill()` for gap-filling ## Memote Quality Assessment **Goal:** Evaluate the quality and standards compliance of a genome-scale metabolic model to identify areas needing curation. **Approach:** Run memote snapshot to score the model against SBML community standards, then use the Python API to inspect individual test failures and guide manual fixes. ```bash # In
- Version Compatibility
- Memote Quality Assessment
- Memote Python API
- Gap-Filling
- Identify Dead-End Metabolites
- Check Mass and Charge Balance
- Fix Gene-Protein-Reaction Rules
- Annotation Standards
- Related Skills
Install memote pip install memote Run full quality report memote report snapshot model.xml --filename report.html Quick score memote run model.xml Continuous integration testing memote run --pytest-args "--tb=short" model.xml
What does the bio-systems-biology-model-curation skill do?
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation. Ensure models meet SBML standards and produce biologically meaningful predictions. Use when improving draft models or preparing models for publication.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill model-curation --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.