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Releases: Sepanta-Yalameha/SIMBIOLOGY-MCP

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v0.1.0

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@yojith yojith released this 20 Jul 00:29
v0.1.0
33f13e9

Summary

This is the initial public release of the SimBiology MCP Server.

It provides an MCP server for MATLAB SimBiology and a packaged synthetic biology modelling skill, with tools for:

  • Creating and modifying models, compartments, species, reactions, and parameters
  • Configuring and running simulations
  • Managing doses and variants
  • Exporting simulation results to CSV and PNG
  • Analysing exported series
  • Retrieving literature context from PubMed and biological-part metadata from the iGEM Registry

Installation

SimBiology MCP Server is available on PyPI and can be installed with uv, pip, or a local Git checkout. See the README for requirements and MCP client setup.

Example quick start with uv:

uv tool install simbiology-mcp

# Install MATLAB Engine, configure the server for Claude Code at the user level
simbiology-mcp setup --client claude-code --user

# Start a Claude Code session and verify all MCP tools are readily accessible

What's Changed

  • Merging some initial setup work by @yojith in #1
  • 2 flesh out engine package by @yojith in #3
  • 4 create base tools package and mcp server by @yojith in #5
  • 6 add some tools and external apis by @yojith in #7
  • Add simulation tools: run, configure, and read settings by @Sepanta-Yalameha in #8
  • Improved adding and modifying reactions, and improved error messaging by @yojith in #11
  • 12 add deployment pipeline by @yojith in #14
  • Add doses and variants with simulate integration by @Sepanta-Yalameha in #15
  • Check's if matlab engine is installed, says to run simbiology-mcp-setup if not by @yojith in #17
  • Make exports reflect the actual simulation; add determinism eval prompt by @Sepanta-Yalameha in #18
  • Add iGEM search tools and exact part lookup by @yojith in #20
  • Require units on create tools by @yojith in #22
  • Improve export outputs and decouple simulation payload limits by @yojith in #25
  • Add CSV analysis tools for exported simulation results by @yojith in #27
  • Format Python files with Black by @yojith in #28
  • Add packaged get-skill helper and refresh docs by @yojith in #31
  • Add autosave recovery and helper coverage by @yojith in #36
  • Remove legacy venv bootstrap files by @yojith in #37
  • Tests updated to match new text location update by @yojith in #39
  • Client-aware get-skill installer; fix stale setup command by @Sepanta-Yalameha in #38
  • Refactor repo packages under simbiology_mcp (split branch) by @yojith in #45
  • Migrate repo packages and add MCP client configuration by @yojith in #43
  • Prepare README and CHANGELOG for release by @yojith in #41
  • Add MCP client configuration, hardened for Windows by @Sepanta-Yalameha in #48
  • Support Copilot CLI project setup and skill installation by @yojith in #50
  • Rename the synthetic biology modelling skill by @yojith in #52

Contributors

This initial release was developed by:

Full Changelog: https://github.com/Sepanta-Yalameha/SIMBIOLOGY-MCP/commits/v0.1.0

Contributors

yojith and Sepanta-Yalameha
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