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BioHarbor MCP

BioHarbor is an MCP server that enables AI agents to execute real bioinformatics tools like sequence analysis, homology search, and structure prediction on local GPUs. It validates inputs, manages GPU queues, handles long-running jobs via job IDs, and provides compact summaries and provenance for reproducible research.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

BioHarbor MCP logo, by danielLuo2Community listingLocal stdioSource reviewed; not executedPublished by danielLuo2
Vendor documentation

What you can do with it

  • Execute bioinformatics tools like MMseqs2 and ESMFold from AI agents
  • Validate inputs and schedule jobs on available GPUs
  • Retrieve long-running job results via job IDs
  • Generate compact summaries and export provenance

Source and maintenance

Community listingRegistry 0.1.6Apache-2.0
mcp-registry: io.github.danielLuo2/bioharbor@0.1.6Source repository
Last repository push
Latest release
v0.1.6
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

bioharbor 0.1.6

pypi
bioharbor package definition
{
  "version": "0.1.6",
  "transport": "stdio",
  "identifier": "bioharbor",
  "registryType": "pypi",
  "packageArguments": [
    {
      "type": "positional",
      "value": "serve"
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Maintenance history

Public check and source-refresh events. Editorial and ownership records remain private.

  • · repository · passed · metadata changed · updated
  • · backfill · recorded · Pre-expansion baseline; unobserved rich metadata remains unknown

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

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Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "bioharbor-mcp": {
      "command": "uvx",
      "args": [
        "bioharbor==0.1.6",
        "serve"
      ]
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "bioharbor-mcp": {
      "command": "uvx",
      "args": [
        "bioharbor==0.1.6",
        "serve"
      ]
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "bioharbor-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "bioharbor==0.1.6",
        "serve"
      ]
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "bioharbor-mcp": {
      "command": "uvx",
      "args": [
        "bioharbor==0.1.6",
        "serve"
      ]
    }
  }
}

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