NeKo Biological Network Builder MCP Server

The NeKo server builds, curates, analyzes, and exports signalling networks through the Model Context Protocol (MCP). It uses NeKo to construct networks from curated interaction databases or existing SIF files, and it preserves topology changes in NeKo's native branching history.

People connecting database tools to Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

VERIFIED ACTIVE

LAST COMMIT 2026-08-19 · ★ 18 · #33 OF 151 MAINTAINED DATABASE · VERIFIED 2026-08-25

Python servers · how we verify → /methodology

01 · Install NeKo Biological Network Builder

Claude Code

claude mcp add marcorusc-mcp-biomodelling-servers-neko -- uvx mcp-biomodelling-servers

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "marcorusc-mcp-biomodelling-servers-neko": {
      "command": "uvx",
      "args": [
        "mcp-biomodelling-servers"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

license no standard license detected - usage rights unclear; check the repo before commercial use

pypi package mcp-biomodelling-servers - check the name against the project README before installing (PyPI has no namespace ownership)

registry namespace io.github.marcorusc is GitHub-verified and matches the repo owner

03 · What NeKo Biological Network Builder can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

Latest releases

v2.2.0 · 2026-08-13

NeKo policy-semantics release. Updates the NeKo MCP interface to explicit path_policy and reuse_policy options, propagates those policies through session defaults and previews, adds concise strategy guidance, and…

v2.0.0 · 2026-08-03

Highlights · Upgrades the NeKo, MaBoSS, and PhysiCell servers to the stable MCP Python SDK 2.x and MCP 2026-07-28 protocol generation. · Adds explicit application session handles, per-session concurrency protection…

v1.0.0 · 2026-04-16

Three MCP servers for systems biology modelling, now available on PyPI and the MCP Registry. · Servers · NeKo (io.github.marcorusc/NeKo) - biological network construction from gene lists using pathway databases…

04 · Who maintains NeKo Biological Network Builder

NeKo Biological Network Builder is maintained by marcorusc. We track 3 MCP servers from marcorusc - 3 actively maintained, 18 combined GitHub stars, oldest repo from Aug 2025.

05 · Facts

repository: github.com/marcorusc/mcp-biomodelling-servers
category: database - ranked #33 of 151 actively-maintained database servers as of 2026-08-25.
release cadence: 2 releases in the last 90 days (latest 2026-08-13)
registry: io.github.marcorusc/NeKo (active, first published 2026-04-16 · 4 versions)
packages: pypi:mcp-biomodelling-servers

06 · NeKo Biological Network Builder FAQ

What is NeKo Biological Network Builder?

Is NeKo Biological Network Builder still maintained?

Yes - as of 2026-08-25, its last commit was 2026-08-19 and it shipped 2 releases in the last 90 days. We re-verify nightly.

How do I install NeKo Biological Network Builder?

Run `uvx mcp-biomodelling-servers`. You can also paste the ready-made client config above.

Does NeKo Biological Network Builder run locally?

Yes - it's a stdio server: it runs on your machine (via uvx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to NeKo Biological Network Builder

Alternatives to NeKo Biological Network Builder

Maintained database servers if NeKo Biological Network Builder isn't the fit.

Pairs well with

Servers that cover what NeKo Biological Network Builder doesn't - only shown when the pairing reason fits the companion.

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