Borrowing it
Nothing to install: this file belongs to nickzren/biomed-agent. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/nickzren/biomed-agent/main/AGENTS.mdgit clone --depth 1 https://github.com/nickzren/biomed-agentWrote 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/instructions/nickzren/biomed-agent/agents-md)<a href="https://agentmods.dev/instructions/nickzren/biomed-agent/agents-md"><img src="https://agentmods.dev/badge/instructions/nickzren/biomed-agent/agents-md.svg" alt="Measured on agentmods" 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 | $0.01130 | $0.01130 |
| Opus 5 | $0.00565 | $0.00565 |
| Sonnet 5 | $0.00226 | $0.00226 |
| Haiku 4.5 | $0.00113 | $0.00113 |
Grade A, and why
biomed-agent 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 8d 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 — 107 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Agent Guide - biomed-agent
This repo is the agent-facing workspace for biomedical research over five local MCP servers. Codex and Claude Code do the routing, evidence gathering, synthesis, and safety framing. The MCP repos provide tools and data.
Current Direction
The historical Python app owned an OpenAI/LangChain reasoning loop in core/agent.py and a Streamlit UI in ui/app.py. That path is legacy and has been removed from the active design. Do not rebuild in-repo LLM orchestration, chat, query synthesis, or Streamlit UI here.
Use skills/biomed-research/SKILL.md for the biomedical research workflow. Use mcp.json as the example MCP registration map for the five sibling servers.
Role
The agent is the router and synthesizer across:
| Server | Strength |
|---|---|
opentargets |
Target-disease evidence, drugs, genetics, variants, studies, clinical trials |
monarch |
HPO phenotypes, rare-disease ontology, model organism context, semantic similarity |
mygene |
Gene, transcript, protein, variant, expression, ontology, and ID aggregation |
mychem |
Chemical, compound, drug, structure, mechanism, target, and identifier aggregation |
mydisease |
Disease, symptom, phenotype, OMIM, Orphanet, MONDO, HPO, and DisGeNET aggregation |
Keep source-specific tool logic in the MCP repos. This repo owns cross-server routing, diagnostics, and the research contract.
Research Contract
For biomedical factual answers:
- Resolve names to canonical IDs before deeper calls.
- Prefer the narrowest relevant server and curated tools.
- Fan out only when the question truly spans target, disease, drug, variant, phenotype, or trial evidence.
- Prefer source-backed observations over model prior knowledge.
- Attribute every material claim to an observation.
- State missing or conflicting evidence directly.
Final answers should include:
answer: concise biomedical synthesis.confidence:high | medium | low.citations: up to 8{observation_id, tool, note}entries.limitations: uncertainty, missing evidence, source caveats, and safety notes.safety_note: present for personalized medical advice requests.
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.
- 8d ago First seen · 107 lines · 1,130 tokens per session scan A 4397f2d8a203
biomed-agent AGENTS.md is an instructions file published in the GitHub repository nickzren/biomed-agent (15 stars, last pushed 3mo ago), licensed Apache-2.0. It adds 1,130 tokens to every session, about $0.0056 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 2026-08-30.
Other instructions, from other repositories
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.
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
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).
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
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.
spec-kit AGENTS.md
AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.