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 agentmods add instructions/yulianuzhnenko/bioinformatics-agent-skills/agents-mdgit clone --depth 1 https://github.com/YuliaNuzhnenko/bioinformatics-agent-skillsWhat 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 | $0.00307 | $0.00307 |
| Opus 5 | $0.00153 | $0.00153 |
| Sonnet 5 | $0.00061 | $0.00061 |
| Haiku 4.5 | $0.00031 | $0.00031 |
Grade A, and why
bioinformatics-agent-skills AGENTS.md 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 yesterday.
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.
What it actually says
Agent Integration & Specification Guide 🤖
This document provides technical guidance for integrating Bioinformatics & Scientific AI Agent Skills with autonomous coding agents (Cursor, Claude Code, Google Antigravity, OpenAI Codex, Gemini CLI, LangChain).
📌 Supported Agent Host Architectures
| Agent Host | Recommended Skill Directory | Configuration Hook |
|---|---|---|
| Cursor | .cursor/skills/ or .cursorrules |
Automatic discovery via .cursorrules |
| Claude Code CLI | ~/.agents/skills/ |
claude --prompt or global config |
| Google Antigravity | .agents/skills/ |
Agent Tools registry |
| LangChain / AutoGPT | skills/ |
Custom Tool Loader (scan_skills.py) |
🧪 Skill Frontmatter Specification
Every SKILL.md file MUST conform to the YAML frontmatter schema:
---
name: skill-name-slug
description: Clear, 1-line description of the skill capability.
version: "1.0.0"
metadata:
author: Yulia Nuzhnenko
domain: Scientific Domain Name
frameworks: [Framework1, Framework2]
---
🔒 Security & Sandboxing
Skills execute code within the host agent's environment. Ensure network permissions and local file access are appropriately scoped before running tasks against production datasets.
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.
- yesterday First seen · 39 lines · 307 tokens per session scan A c729ad0fb98c
bioinformatics-agent-skills AGENTS.md is an instructions file published in the GitHub repository YuliaNuzhnenko/bioinformatics-agent-skills (8 stars, last pushed 23d ago), licensed MIT. It adds 307 tokens to every session, about $0.0015 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 2026-08-31.
Other instructions, from other repositories
scientific-agent-skills AGENTS.md
AGENTS.md instructions for K-Dense-AI/scientific-agent-skills, covering repository guidance, what belongs here, layout, creating a skill and skill title.
scientific-agent-skills CLAUDE.md
Claude Code instructions for K-Dense-AI/scientific-agent-skills: Repository guidance for this project lives in AGENTS.md. Read it and follow it.
asb-skill-collections CLAUDE.md
Instructions for HolobiomicsLab/asb-skill-collections, covering claude.md — asb metabolomics skills, install (claude code plugin) and use.
cryocore AGENTS.md
Instructions for BioSymphony/cryocore, covering biosymphony cryocore agent guide, operating rules, ownership boundary, dev commands and key patterns and conventions.
asb-skill-collections copilot-instructions.md
Instructions for HolobiomicsLab/asb-skill-collections: This repository publishes the ASB Metabolomics Skill Collection (collections/metabolomics/v2/): 5,859 evidence-grounded skills over 909 software tools for computational LC-MS/MS metabolomics, each derived from a peer-reviewed method paper.
structure-factory AGENTS.md
Instructions for BioSymphony/structure-factory, covering biosymphony structure factory agent guide, mission, how to drive a mission, compute available and orchestrators supported.