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ClawBio

Official
A local-first AI skill library for bioinformatics
How to install ↓ Compare GitHub source repository ↗
Category
Other #51 of 230
Stars
★ 1.2k Very popular
Transport
stdio (local process)
Runtime
Python 3.11+
Credentials
No credential needed
License
Other / unspecified
Last commit
63FMRS · C

The supplied sources identify a PyPI MCP package at version 0.6.1 with a stdio configuration example. The server defaults to demo data and offers an optional local-file access switch; no specific MCP tool names are listed in the supplied manifest.

Strongest · Documentation 14/20 Weakest · Reliability 10/20

Reliability
10/20
Security and permissions
14/20
Maintenance
12/20
Documentation
14/20
Setup experience
13/20
Why each score
Reliability 10/20
The manifest clearly declares a PyPI package, stdio transport, and MCP entry arguments, while the README supplies client configuration and many demo commands. However, static materials do not verify MCP initialization, tool listing, or actual tool behavior. The claimed test counts and green status are not supported by reviewable, server-specific CI evidence, and manifest version 0.6.1 conflicts with the README's 0.5.0 references, so points are deducted.
Security and permissions 14/20
Demo-only execution is the default, and local file access requires an explicit environment variable; the manifest describes this boundary. Hosted inference and remote Galaxy execution are disclosed, and Galaxy requires an API key; no real secrets appear in the setup examples. Points are deducted because per-tool permissions, sensitive genomic-data flows, confirmation for remote operations, and failure isolation are not reviewably specified, while some capabilities process clinical or personal genomic data.
Maintenance 12/20
The repository is not archived, and the supplied materials show versioning, a CI badge, contribution guidance, an MIT license claim, and identifiable repository ownership, indicating a maintenance foundation. Points are deducted because there is no verifiable evidence of commit cadence, release history, dependency-update practice, security-response channel, or issue-handling quality. The manifest says NOASSERTION while the README says MIT, creating governance inconsistency.
Documentation 14/20
The README covers installation, client configuration, operating modes, skill scope, data boundaries, external services, reproducibility, and many command examples. Points are deducted because it lacks a reviewable MCP tool inventory, parameter and return schemas, error behavior, compatibility matrix, cost or rate-limit disclosure, and systematic troubleshooting. Version and capability descriptions are also inconsistent.
Setup experience 13/20
Python, pip, conda, uvx, and stdio configurations for several mainstream clients are provided, with concise steps and documented Python and optional environment-variable requirements. Points are deducted because no committed evidence verifies an actual MCP handshake or client connection, some skills require additional tools, and full functionality may require source checkout or external-service configuration; static evidence therefore does not support a higher score.

Static review · not runListed 2026-08-14

Read the FMRS scoring method →

Fit and risk

What it can accessRuns commands or codeUses the network

Best for

  • Researchers needing local-first and reproducible bioinformatics workflows
  • Users who want an AI agent to orchestrate existing bioinformatics skills
  • Developers learning genome-analysis workflows with demo data

Not for

  • Users seeking a general database, cloud-storage, or browser-automation server
  • Clinical diagnosis or prescribing decisions
  • Use cases that require direct patient-genome access by default

Required permissions

  • The default mode runs demo data only
  • With CLAWBIO_MCP_ALLOW_LOCAL_FILES=1, skills may read and write local files
  • Depending on the skill invoked, some workflows access external annotation, genomic, or Galaxy services

Risks and side effects

  • Pharmacogenomic and clinical-variant results should not replace professional medical judgment
  • After local-file access is enabled, skills may process or write input and output files
  • Skills using external APIs or Galaxy may send relevant queries or data to external services
  • Some reproductions require the original external inputs or external tools to remain available

Setup

Before you start

Runtime：Python 3.11+

GALAXY_API_KEY optionalsecret Optional Galaxy API key, only needed to remotely execute Galaxy tools via the Galaxy Bridge skill; obtain it from your usegalaxy.org account settings.
Other optional settings (1)
CLAWBIO_MCP_ALLOW_LOCAL_FILES optional Set to 1 to allow skills to read/write local files; when unset the server runs demo data only, so genomic data never leaves the machine.

With Python 3.11+ available, add the configuration to an MCP-compatible client using the provided uvx command. The server uses demo data by default. Set CLAWBIO_MCP_ALLOW_LOCAL_FILES=1 if skills need to read or write local files.

.cursor/mcp.json 
{"mcpServers":{"clawbio":{"command":"uvx","args":["--from","clawbio[mcp]","clawbio","mcp"]}}}

Shown for Cursor. Other clients may use a different file or key (VS Code uses "servers") — the configurator below converts it.

.vscode/mcp.json
{
  "servers": {
    "clawbio": {
      "command": "uvx",
      "args": [
        "--from",
        "clawbio[mcp]",
        "clawbio",
        "mcp"
      ]
    }
  }
}

Goes in your project's .vscode/mcp.json (VS Code uses a "servers" key).

Terminal
claude mcp add clawbio -- uvx --from 'clawbio[mcp]' clawbio mcp

Run it in a terminal; replace any <…> placeholders with your own values first.

Generate and validate client config

Check that it works

Confirm the clawbio server appears in your MCP client after launching via uvx --from clawbio[mcp] clawbio mcp, then ask for the PharmGx demo report; receiving a genotype report (e.g. CYP2D6 status) proves the connection works.

Troubleshooting

  1. Confirm Python 3.11+ and uvx are installed
  2. Check the client configuration command, arguments, and JSON syntax
  3. Validate the connection first with the default demo mode
  4. If local files are required, confirm CLAWBIO_MCP_ALLOW_LOCAL_FILES=1 is set
  5. For skills requiring external services, check that the required services, tools, and credentials are configured

Things to try

Once connected, you can ask your AI assistant things like:

  • Run the PharmGx reporter on demo data and show me the drug dosage recommendations
  • Look up rs3798220 across GWAS Catalog, gnomAD and ClinVar
  • Run an ancestry PCA demo against the SGDP reference panel
  • Search the UK Biobank schema for fields measuring grip strength

Use cases

Run pharmacogenomics and variant-annotation analyses
Query genomic resources including GWAS Catalog, ClinVar, and gnomAD
Run ancestry PCA, polygenic risk, single-cell, and RNA-seq workflows
Produce reproducibility outputs containing commands, environment metadata, and checksums

Supported clients

CursorPartial support
ZedPartial support
VS CodePartial support
Claude DesktopPartial support

Listed from the project's documentation, not tested by this site.

Overview

ClawBio is a bioinformatics-native AI agent skill library covering pharmacogenomics, GWAS, variant interpretation, ancestry, single-cell, and RNA-seq. Its MCP server runs locally over stdio, defaults to demo data, and states that genomic data is not sent off the machine by default.

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Source revision dece7548d869 Data synced 2026-10-11 Read the FMRS scoring method