# NeKo Biological Network Builder

Builds and analyses signalling networks from interaction databases. Useful when a model should come from known interactions instead of a blank sheet.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 20
- Author: marcorusc
- License: GPL-3.0 · policy=link-only · description only; the file stays with the author
- Source: https://github.com/marcorusc/mcp-biomodelling-servers/tree/HEAD/neko
- Updated: 2026-10-22
- HTML: https://affpapa.org/en/nevibecode/mcp/neko-biological-network-builder

## What it does

NeKo is one of four servers shipped in the `mcp-biomodelling-servers` package. It pulls interactions out of databases, assembles them into a signalling network, and then helps you inspect the result. The other three are MaBoSS, BioMASS and PhysiCell, each with its own job.

The package installs as a whole: `python -m pip install mcp-biomodelling-servers`. Modelling dependencies arrive with it, among them `nekomata` from 1.10.2 up to but not including 2.0, plus PyGraphviz. NeKo history diagrams render through PyGraphviz, whose wheels carry Graphviz, so a separate `dot` binary is not needed. Python 3.10–3.15 is required. There is also an isolated route: `uvx --from mcp-biomodelling-servers mcp-neko-server`.

The server speaks MCP over stdio, so in a terminal it sits waiting for a client on standard input. A package resolver set to reject every pre-release will fail the install, because the `cmaboss` engine exists only as `1.0.0b*` builds.

## Requirements
- Needs: Python and uv (commands run via uvx)

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add neko -- uvx mcp-biomodelling-servers
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### Codex

**Platform CLI**
```bash
codex mcp add neko -- uvx mcp-biomodelling-servers
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "neko": {
            "command": "uvx",
            "args": [
                "mcp-biomodelling-servers"
            ]
        }
    }
}
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "neko": {
            "type": "stdio",
            "command": "uvx",
            "args": [
                "mcp-biomodelling-servers"
            ]
        }
    }
}
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add neko uvx mcp-biomodelling-servers
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

## When to use it
- assemble a signalling network from interaction database records
- break a finished network down into nodes and edges
- wire biological modelling into an agent inside an editor
- run NeKo from an isolated environment without hand-editing configs
- draw a history diagram of a network

## Example prompts
- Build a signalling network from the interactions in the database and list which nodes made it in
- Break this network down: which edges lead into the hub node
- Start NeKo with `uvx --from mcp-biomodelling-servers mcp-neko-server` and draw the network history diagram

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