Tooluniverse Systems Biology
Integrates five major pathway databases (Reactome, KEGG, WikiPathways, BioCarta, NCI-PID) for systems biology analysis. Run pathway enrichment on gene lists from RNA-seq or proteomics, map proteins to their biological pathways across multiple sources, or search by keyword to find relevant pathways and computational models. The skill emphasizes compute over description, pushing you to run actual Python enrichment statistics rather than theorizing. One smart touch is the built-in skepticism about enrichment versus causation, reminding you that three genes hitting a 200-member pathway means less than fifteen genes in a 40-member one. Cross-database validation is baked in since pathway annotations frequently disagree between sources.
- skills.sh installs
- 436
- GitHub stars
- 1.8K
- last updated
- Aug 21, 2026
Install
$ npx -y skills add mims-harvard/tooluniverse --skill tooluniverse-systems-biology --agent claude-codeInstalls into .claude/skills of the current project.
Files
Systems Biology & Pathway Analysis
Comprehensive pathway and systems biology analysis integrating multiple curated databases to provide multi-dimensional view of biological systems, pathway enrichment, and protein-pathway relationships.
When to Use This Skill
Triggers:
- "Analyze pathways for this gene list"
- "What pathways is [protein] involved in?"
- "Find pathways related to [keyword/process]"
- "Perform pathway enrichment analysis"
- "Map proteins to biological pathways"
- "Find computational models for [process]"
- "Systems biology analysis of [genes/proteins]"
Use Cases:
- Gene Set Analysis: Identify enriched pathways from RNA-seq, proteomics, or screen results
- Protein Function: Discover pathways and processes a protein participates in
- Pathway Discovery: Find pathways related to diseases, processes, or phenotypes
- Systems Integration: Connect genes → pathways → processes → diseases
- Model Discovery: Find computational systems biology models (SBML)
- Cross-Database Validation: Compare pathway annotations across multiple sources
Sponsors
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- Repository
- github.com/mims-harvard/tooluniverse
- Categories
- Backend & APIs, Design & UI/UX, Databases
- First seen
- Jun 3, 2026
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