bio-systems-biology-context-specific-models
Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints. Create models that reflect cell-type specific metabolism. Use when building tissue-specific metabolic models or integrating transcriptomics with FBA.
npx skills add BioTender-max/awesome-bio-agent-skills --skill context-specific-models --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+, numpy 1.26+, pandas 2.2+ 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. # Context-Specific Models **"Build a tissue-specific metabolic model from my expression data"** → Constrain a generic genome-scale model using transcriptomics data to produce a context-specific model reflecting the active metabolism of a particular tissue or condition, using GIMME, iMAT, or INIT algorithms. - Python: custom implementations with `cobra` model manipulation (COBRApy) ## GIMME Algorithm **Goal:** Build a tissue-specific metabolic model by integrating transcriptomics data with a generic genome-scale model, retaining only metabolically active reactions. **Approach:** Map gene expression values to reactions, penalize flux through lowly-expressed reactions while maintaining minimum biomass production, and remove inactive reactions to produce a context-specific mod
- Version Compatibility
- GIMME Algorithm
- iMAT Algorithm
- Expression Data Integration
- Tissue-Specific Human Models
- Validate Context Model
- Related Skills
What does the bio-systems-biology-context-specific-models skill do?
Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints. Create models that reflect cell-type specific metabolism. Use when building tissue-specific metabolic models or integrating transcriptomics with FBA.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill context-specific-models --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.