Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add AndyZhuang/Opentest --skill tooluniverse-systems-biologygit clone --depth 1 https://github.com/AndyZhuang/OpentestWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/andyzhuang/opentest/tooluniverse-systems-biology)<a href="https://agentmods.dev/skills/andyzhuang/opentest/tooluniverse-systems-biology"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-systems-biology/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/andyzhuang/opentest/tooluniverse-systems-biology"><img src="https://agentmods.dev/badge/skills/andyzhuang/opentest/tooluniverse-systems-biology.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00070 | $0.03095 |
| Opus 5 | $0.00035 | $0.01548 |
| Sonnet 5 | $0.00014 | $0.00619 |
| Haiku 4.5 | $0.00007 | $0.00310 |
Grade A, and why
tooluniverse-systems-biology scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 375 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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
Core Databases Integrated
| Database | Coverage | Strengths |
|---|---|---|
| Reactome | Human-curated reactions & pathways | Detailed mechanistic pathways with reactions |
| KEGG | Reference pathways across organisms | Metabolic maps, disease pathways, drug targets |
| WikiPathways | Community-curated pathways | Emerging processes, collaborative updates |
| Pathway Commons | Integrated meta-database | Aggregates multiple sources (Reactome, KEGG, etc.) |
| BioModels | Computational SBML models | Mathematical/dynamic systems biology models |
| Enrichr | Statistical enrichment | Pathway over-representation analysis |
Workflow Overview
Input → Phase 1: Enrichment → Phase 2: Protein Mapping → Phase 3: Keyword Search → Phase 4: Top Pathways → Report
Phase 1: Pathway Enrichment Analysis
When: Gene list provided (from experiments, screens, differentially expressed genes)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 375 lines · 70 tokens per session scan A 2c46b8a2e979
tooluniverse-systems-biology is a skill published in the GitHub repository AndyZhuang/Opentest (22 stars, last pushed 6mo ago), licensed MIT. It adds 70 tokens to every session and 3,095 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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