Documentation

Everything you need to know about publishing and using MCP tools.

What is AIBioAgentTools?

AIBioAgentTools is the open registry for bioinformatics Model Context Protocol (MCP) tools. MCP tools are standardized interfaces that allow AI assistants to call bioinformatics software — from sequence alignment (BWA, Bowtie2) to variant calling (GATK, DeepVariant) to data processing (SAMtools, BCFtools).

Anyone can publish a tool; anyone can discover and install tools from the registry.

How to publish a tool

  1. 1

    Create an account

    Sign up with your email at the Sign In page. Your display name will appear on your published tools.

  2. 2

    Prepare your GitHub repo

    Host your MCP server on a public GitHub repository. It must have a README.md — fetched automatically and displayed on your tool page.

  3. 3

    Fill in the publish form

    Choose a unique package name (lowercase, hyphens only, e.g. samtools-mcp). Paste your GitHub URL, write a short description, and add keywords.

  4. 4

    Submit

    Click "Publish Tool". The README is fetched from GitHub and stored. Your tool is immediately live and searchable.

Package naming rules

  • ✓ Lowercase letters (a–z), numbers (0–9), and hyphens (-) only
  • ✓ Must start and end with a letter or number
  • ✓ Must be globally unique
  • ✗ No spaces, underscores, uppercase letters, or special characters

Valid examples:

samtools-mcpbwa-mcpblast-servergatk-toolsdeepvariant-mcp

Search & Discovery

Tools are searchable by name (prefix match) and by keywords. Add relevant keywords like tool category (alignment), underlying software (bwa), and data type (rna-seq) for maximum visibility.