tooluniverse-systems-biology
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels). Performs pathway enrichment, protein-pathway mapping, keyword searches, and systems-level analysis. Use when analyzing gene sets, exploring biological pathways, or investigating systems-level biology.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-systems-biology --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.
# 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**: 1. **Gene Set Analysis**: Identify enriched pathways from RNA-seq, proteomics, or screen results 2. **Protein Function**: Discover pathways and processes a protein participates in 3. **Pathway Discovery**: Find pathways related to diseases, processes, or phenotypes 4. **Systems Integration**: Connect genes → pathways → processes → diseases 5. **Model Discovery**: Find computational systems biology models (SBML) 6. **Cross-Database Validation**: Compare pathway annotations across multiple sources ## Core Databases Integrated | Database | Coverage | Strengths | |----------|----------|-----------|
- When to Use This Skill
- Core Databases Integrated
- Workflow Overview
- Phase 1: Pathway Enrichment Analysis
- Tools Used
- Workflow
- Decision Logic
- Phase 2: Protein-Pathway Mapping
- Phase 3: Keyword-Based Pathway Search
- Phase 4: Top-Level Pathway Catalog
- Output Structure
- Report Format
- Data Tables
- Tool Parameter Reference
What does the tooluniverse-systems-biology skill do?
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels). Performs pathway enrichment, protein-pathway mapping, keyword searches, and systems-level analysis. Use when analyzing gene sets, exploring biological pathways, or investigating systems-level biology.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-systems-biology --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.