INDIVIDUAL MCP TOOL

list_skills

Lists all available bioinformatics skills in the graph, optionally filtered by a domain keyword (e.g., 'rna-seq', 'variant', 'drug').

pipette.bionone authenticationAvailability not checked

LIVE ENDPOINT

https://skillgraph.pipette.bio/mcp

No auth detected

Connect to this endpoint to inspect the live schema for list_skills and invoke it with your own arguments.

{}

Inferred read-only · medium confidence · heuristic, not a guarantee.

No write-capable action terms were found; this is not proof that invocation has no side effects.

CONNECT WITH APPROVAL

Review this server and its permissions before adding it. Secret placeholders must be set locally.

Codex

~/.codex/config.toml

[mcp_servers.skillgraph]
url = "https://skillgraph.pipette.bio/mcp"
enabled = true

Claude Code

.mcp.json

{
  "mcpServers": {
    "skillgraph": {
      "type": "http",
      "url": "https://skillgraph.pipette.bio/mcp"
    }
  }
}

Claude Desktop

Settings → Connectors → Add custom connector

Name: skillgraph
Remote MCP URL: https://skillgraph.pipette.bio/mcp

Add this remote URL as a custom connector in Claude Desktop. Availability depends on the user plan and workspace policy.

Cursor

.cursor/mcp.json

{
  "mcpServers": {
    "skillgraph": {
      "url": "https://skillgraph.pipette.bio/mcp"
    }
  }
}

Visual Studio Code

.vscode/mcp.json

Add to Visual Studio Code

{
  "servers": {
    "skillgraph": {
      "type": "http",
      "url": "https://skillgraph.pipette.bio/mcp"
    }
  }
}

Generic MCP

Client-specific MCP configuration

{
  "name": "skillgraph",
  "transport": "streamable-http",
  "url": "https://skillgraph.pipette.bio/mcp"
}

MCP Inspector

Run the official MCP Inspector locally and enter the indexed Streamable HTTP endpoint.

get_skill — Returns full SKILL.md documentation for a bioinformatics skill, plus its overview, tools, I/O data types, and upstream/downstream connections.
search_skills — Keyword search across skill IDs, trigger keywords, and tool names.
get_transitions — Returns upstream and/or downstream skills connected to a given skill in the pipeline graph, with edge evidence (paper counts, data types, ground truth status).
find_path — Finds the shortest pipeline path between two skills, annotated with data flow (what data types pass between each step), paper counts, and evidence.
get_graph_stats — Returns summary statistics about the SkillGraph knowledge graph: total skills, edges, literature vs inferred edges, and a breakdown of skills by domain (single-cell, variant analysis, drug discovery, etc.).