Borrowing it
Nothing to install: this file belongs to biocontext-ai/nucleotide_archive_mcp. 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/biocontext-ai/nucleotide_archive_mcp/main/AGENTS.mdgit clone --depth 1 https://github.com/biocontext-ai/nucleotide_archive_mcpWrote 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/biocontext-ai/nucleotide_archive_mcp/agents-md)<a href="https://agentmods.dev/instructions/biocontext-ai/nucleotide_archive_mcp/agents-md"><img src="https://agentmods.dev/badge/instructions/biocontext-ai/nucleotide_archive_mcp/agents-md/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/instructions/biocontext-ai/nucleotide_archive_mcp/agents-md"><img src="https://agentmods.dev/badge/instructions/biocontext-ai/nucleotide_archive_mcp/agents-md.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 | $0.00487 | $0.00487 |
| Opus 5.5 | $0.00195 | $0.00195 |
| Sonnet 5.5 | $0.00097 | $0.00097 |
| Haiku 4.5 | $0.00049 | $0.00049 |
Grade A, and why
nucleotide_archive_mcp 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 2mo 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 — 39 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Developer Guide
Project Overview
This is an MCP (Model Context Protocol) server that provides access to RNA sequencing datasets from the European Nucleotide Archive (ENA). The goal is to help researchers find publicly available bulk and single-cell RNA-seq datasets for validating hypotheses or reproducing published analyses.
Architecture
Framework: FastMCP - provides the MCP server infrastructure and tool registration APIs Used:
- ENA Portal API (
www.ebi.ac.uk/ena/portal/api) - for searching studies and retrieving metadata - ENA Browser API (
www.ebi.ac.uk/ena/browser/api) - for detailed study summaries and publication links - Europe PMC API (
www.ebi.ac.uk/europepmc/webservices/rest) - for retrieving detailed publication metadata
HTTP Client: httpx (async) Data Validation: Pydantic v2
Code Organization
This is a standard Python package with src/ layout. Tools are decorated with @mcp.tool and automatically registered. When testing wrapped tools, access the underlying function with .fn attribute.
The server exposes ~10 tools for searching studies, retrieving metadata, finding publications, and generating download scripts. Each tool follows ENA's controlled vocabularies for library strategies and sources.
Key Concepts
Study Accessions: Projects have multiple formats (SRP/ERP/DRP or PRJNA/PRJEB/PRJDB). Both work interchangeably.
Library Strategies: 50+ types (RNA-Seq, ChIP-Seq, ATAC-seq, miRNA-Seq, etc.). Pre-defined presets exist for common use cases (bulk, single-cell, etc.).
Publications: Studies link to PubMed IDs via ENA Browser API. Europe PMC enriches this with full metadata including ORCID IDs, citations, and full-text links.
Testing Philosophy
This project uses pytest with async support. Write clean, minimal tests with simple assertions. No verbose output, no boilerplate main functions. Test files live alongside source code and use proper package imports - never manipulate sys.path.
Code Style
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.
- 2mo ago First seen · 39 lines · 487 tokens per session scan A 3212360ae3f4
nucleotide_archive_mcp AGENTS.md is an instructions file published in the GitHub repository biocontext-ai/nucleotide_archive_mcp (1 stars, last pushed 8mo ago), licensed Apache-2.0. It adds 487 tokens to every session, about $0.0019 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.
nucleotide_archive_mcp AGENTS.md compared with instructions from other repositories
| Mod | Type | Stars | Last push | Licence | Scan | Tokens | Works with |
|---|---|---|---|---|---|---|---|
| nucleotide_archive_mcp AGENTS.mdbiocontext-ai/nucleotide_archive_mcp | Instructions file | 1 | 8mo ago | Apache-2.0 | A | 487 | Codex, OpenCode |
| vscode buildNext.instructions.mdmicrosoft/vscode | Instructions file | 195k | yesterday | MIT | A | 9,719 | GitHub Copilot |
| next.js AGENTS.mdvercel/next.js | Instructions file | 143k | yesterday | MIT | A | 7,461 | Codex, OpenCode |
| langchain AGENTS.mdlangchain-ai/langchain | Instructions file | 149k | yesterday | MIT | A | 4,680 | Codex, OpenCode |
| vscode oss-third-party-notices.instructions.mdmicrosoft/vscode | Instructions file | 195k | yesterday | MIT | A | 5,516 | GitHub Copilot |
| vscode copilot-instructions.mdmicrosoft/vscode | Instructions file | 195k | yesterday | MIT | A | 3,093 | GitHub Copilot |
| deepseek-harness AGENTS.mddeepseek-ai/deepseek-harness | Instructions file | 274k | 2d ago | MIT | A | 4,313 | Codex, OpenCode |