bioinformatics-agent-skills: Instructions file for Codex

AGENTS.md

bioinformatics-agent-skills AGENTS.md is an instructions file for Codex, OpenCode from YuliaNuzhnenko/bioinformatics-agent-skills. It costs 307 tokens per session, scanned A, original, MIT.

Integration instructions for scientific AI-agent skills used with tools such as Cursor, Claude Code, Codex, Gemini CLI, and LangChain. They define where skills go and the YAML header each skill file must contain.

In plain words
What is it for?
Use them when adding, packaging, or integrating computational-biology skills with an AI coding agent, including checking skill metadata and choosing the host-specific skill directory.
Why use it?
They help different agent hosts discover the skills consistently and set clear requirements for metadata, security, and sandboxed code execution.

Instructions file for CodexOpenCode

Written for Codex and OpenCode: the file is AGENTS.md. Also seen: mentions Claude Code; mentions Codex; mentions Gemini CLI.

This is YuliaNuzhnenko/bioinformatics-agent-skills's own configuration. It tells Codex and OpenCode how to work on bioinformatics-agent-skills itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything bioinformatics-agent-skills configures โ†’

Reuse

Borrowing it

Nothing to install: this file belongs to YuliaNuzhnenko/bioinformatics-agent-skills. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/YuliaNuzhnenko/bioinformatics-agent-skills/main/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/YuliaNuzhnenko/bioinformatics-agent-skills

Made for: Codex, OpenCode.

Wrote 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.

agentmods badge for bioinformatics-agent-skills AGENTS.md

README.md
[![agentmods](https://agentmods.dev/badge/instructions/yulianuzhnenko/bioinformatics-agent-skills/agents-md/github.svg)](https://agentmods.dev/instructions/yulianuzhnenko/bioinformatics-agent-skills/agents-md)
Your own site
<a href="https://agentmods.dev/instructions/yulianuzhnenko/bioinformatics-agent-skills/agents-md"><img src="https://agentmods.dev/badge/instructions/yulianuzhnenko/bioinformatics-agent-skills/agents-md/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80ร—15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80ร—15 button for bioinformatics-agent-skills AGENTS.md

Your own site ยท 80ร—15
<a href="https://agentmods.dev/instructions/yulianuzhnenko/bioinformatics-agent-skills/agents-md"><img src="https://agentmods.dev/badge/instructions/yulianuzhnenko/bioinformatics-agent-skills/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 307 This file is loaded in full into every session.
When invoked 307 The same file โ€” it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file โ€” not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00307 $0.00307
Opus 5.5 $0.00123 $0.00123
Sonnet 5.5 $0.00061 $0.00061
Haiku 4.5 $0.00031 $0.00031

Measured 1mo ago against content hash c729ad0fb98c, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

bioinformatics-agent-skills AGENTS.md scanned grade A with 0 findings against 26 rules in 11 categories โ€” prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency โ€” measured 1mo 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.

AGENTS.md ยท 39 lines

What it actually says

Agent Integration & Specification Guide ๐Ÿค–

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).


๐Ÿ“Œ 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)

๐Ÿงช 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]
---

๐Ÿ”’ 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.

Changes

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.

  1. 1mo ago First seen ยท 39 lines ยท 307 tokens per session scan A c729ad0fb98c

Subscribe to this mod's changes

bioinformatics-agent-skills AGENTS.md is an instructions file published in the GitHub repository YuliaNuzhnenko/bioinformatics-agent-skills (10 stars, last pushed 2mo ago), licensed MIT. It adds 307 tokens to every session, about $0.0012 per session on Opus 5.5. 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.

Related

Other instructions, from other repositories

vscode buildNext.instructions.md

Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).

microsoft/vscode ยท 9,715 tokens

next.js AGENTS.md

AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.

vercel/next.js ยท 7,786 tokens

vscode oss-third-party-notices.instructions.md

Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, cache eligibility and rollout and applying the notice (cutover).

microsoft/vscode ยท 5,262 tokens

langchain AGENTS.md

AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.

langchain-ai/langchain ยท 4,680 tokens

vscode copilot-instructions.md

Copilot instructions for microsoft/vscode, covering vs code copilot instructions, project overview, root folders, core architecture (src/ folder) and built-in extensions (extensions/ folder).

microsoft/vscode ยท 2,731 tokens

deno copilot-instructions.md

Copilot instructions for denoland/deno, covering deno development guide for github copilot, network access, high level overview, key directories and key files to understand first.

denoland/deno ยท 3,077 tokens