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Kappybara MCP Server

by metareflection
GitHub
Python
MIT License
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Kappybara MCP Server

An MCP (Model Context Protocol) server for running Kappa simulations using the Kappybara package. This allows LLMs to run rule-based simulations of molecular interaction systems directly.

Python packages used:

Features

  • Run Kappa Simulations: Execute Kappa models with customizable parameters using kappybara

  • CSV Output: Get simulation results as CSV data for easy analysis

  • Example Models: Built-in example models (reversible binding, linear polymerization)

  • Pure Python: Uses the kappybara Python library for all simulations

Installation

  1. Clone or download this repository

  2. Install dependencies:

pip install -r requirements.txt

Usage

Running the MCP Server

fastmcp run main.py

Using with Claude Desktop

fastmcp install claude-desktop main.py

Available Tools

run_kappa_simulation

Run a Kappa simulation and return results with stdout, stderr, and CSV output.

Parameters:

  • kappa_code (string, required): The Kappa model code to simulate

  • time_limit (float, default: 100.0): Maximum simulation time

  • points (int, default: 200): Number of data points to collect

  • seed (int, optional): Random seed for reproducibility

Returns: JSON string with three fields:

  • stdout: Standard output from the simulation

  • stderr: Standard error output (warnings, errors)

  • output: CSV data with simulation results

Example:

kappa_code = """ %init: 100 A(x[.]) %init: 100 B(x[.]) %obs: 'AB' |A(x[1]), B(x[1])| A(x[.]), B(x[.]) <-> A(x[1]), B(x[1]) @ 1, 1 """ result = run_kappa_simulation(kappa_code, time_limit=50, points=100) # Result is a JSON string like: # { # "stdout": "", # "stderr": "", # "output": "time,AB\n0.0,0\n0.01,1\n..." # }

Available Resources

kappa://examples/simple

A simple reversible binding model (kappybara syntax).

kappa://examples/polymerization

A linear polymerization model (kappybara syntax).

Kappa Language Basics (Kappybara Syntax)

Kappybara uses a specific syntax for Kappa models. Here's a quick reference:

Basic Syntax

%init: 100 AgentName(site1[.], site2[state]) # Initialize agents %obs: 'Observable' |pattern| # Define observable pattern -> pattern @ rate # Define rule (irreversible) pattern <-> pattern @ rate1, rate2 # Define rule (reversible)

Binding Sites

  • [.] - unbound site

  • [1], [2], etc. - bound sites (bond labels)

  • [_] - wildcard for any binding state

Example: Reversible Binding

%init: 100 A(x[.]) %init: 100 B(x[.]) %obs: 'A_free' |A(x[.])| %obs: 'B_free' |B(x[.])| %obs: 'AB_complex' |A(x[1]), B(x[1])| // Reversible binding with forward rate 0.001 and reverse rate 0.1 A(x[.]), B(x[.]) <-> A(x[1]), B(x[1]) @ 0.001, 0.1

Development

Project Structure

kappybara-mcp/ ├── main.py # MCP server implementation ├── requirements.txt # Python dependencies ├── README.md # This file └── test_example.py # Example test/demo script

Testing

Run the test example:

python test_example.py

How It Works

  1. The MCP server exposes Kappa simulation capabilities through the Model Context Protocol

  2. LLMs can call the run_kappa_simulation tool with Kappa code (using kappybara syntax) and parameters

  3. The server uses the Kappybara Python library to parse the model and run the simulation

  4. Results are returned as JSON with stdout, stderr, and CSV output that can be analyzed or visualized

References

License

MIT

This server cannot be installed

-
security - not tested
A
license - permissive license
-
quality - not tested

How are these scores calculated?

remote-capable server

The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.

Enables LLMs to run rule-based molecular interaction simulations using the Kappa language through the Kappybara package. Returns simulation results as CSV data for analysis of biochemical systems and molecular binding dynamics.

  1. Features
    1. Installation
      1. Usage
        1. Running the MCP Server
        2. Using with Claude Desktop
        3. Available Tools
        4. Available Resources
      2. Kappa Language Basics (Kappybara Syntax)
        1. Basic Syntax
        2. Binding Sites
        3. Example: Reversible Binding
      3. Development
        1. Project Structure
        2. Testing
      4. How It Works
        1. References
          1. License

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