bio-systems-biology-metabolic-reconstruction
Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis. Use when creating metabolic models for organisms without existing models.
npx skills add BioTender-max/awesome-bio-agent-skills --skill metabolic-reconstruction --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+, NCBI BLAST+ 2.15+ 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. # Metabolic Reconstruction **"Build a metabolic model for my organism from its genome"** → Generate a genome-scale metabolic model by mapping protein sequences to a universal reaction database, then gap-filling to ensure growth capability on specified media. - CLI: `carve` (CarveMe) for automated reconstruction from protein FASTA - CLI: `gapseq find` + `gapseq draft` + `gapseq fill` for pathway-based reconstruction ## CarveMe (Recommended) ```bash # Install CarveMe pip install carveme # Basic reconstruction from protein FASTA carve genome.faa -o model.xml # Specify output format carve genome.faa -o model.xml --format sbml carve genome.faa -o model.json --format json # Gap-fill for specific media carve genome.faa -o m
- Version Compatibility
- CarveMe (Recommended)
- CarveMe Options
- gapseq (Alternative)
- Python API for CarveMe
- Load and Inspect Draft Model
- Quality Metrics
- Multiple Genome Reconstruction
- Community Model Construction
- Related Skills
Install CarveMe pip install carveme Basic reconstruction from protein FASTA carve genome.faa -o model.xml Specify output format carve genome.faa -o model.xml --format sbml carve genome.faa -o model.json --format json Gap-fill for specific media carve genome.faa -o model.xml --gapfill M9 Available media: M9, LB, M9[glc], M9[glyc], etc.
What does the bio-systems-biology-metabolic-reconstruction skill do?
Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis. Use when creating metabolic models for organisms without existing models.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill metabolic-reconstruction --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.