AmadeusBio

You can open /docs and see the documentation.

Overview

AmadeusBio.ai is a coding agent (i.e Claude Code) based plugin that provides the instructions and protocols for agents to perform bioinformatic analysis.

Demo

Current features include:

  1. Operate local softwares such as PyMol using natural language.
  2. Retrival of sequences, protein structures etc. from databases including Uniprot.
  3. Plus everything that come with coding agent.

Get Started

Install as a Claude Code plugin

Clone the repo, then point Claude Code at it with --plugin-dir:

git clone https://github.com/starryark/AmadeusBio.ai_mvp.git
claude --plugin-dir ./AmadeusBio.ai_mvp

Inside Claude Code, the bundled skills are available under the amadeusbio-mvp: namespace, e.g. /amadeusbio-mvp:pymol-molecular-visualization. The two agents (PyMol-Software-Operator, protein-structure-downloader) are auto-discovered and triggered by description-match.

PyMOL side (one-time, only if you use the PyMOL agent)

The pymol-molecular-visualization skill talks to a live PyMOL session over localhost:9876. Install the PyMOL-side plugin once:

  1. Open PyMOL → Plugin → Plugin Manager → Install New Plugin.
  2. Select the pymol-mcp-socket-plugin/ directory in this repo.
  3. Restart PyMOL. Verify with pymol -d "mcp_start" from a terminal.

See PyMol-Integration for full PATH/wrapper setup on Windows/macOS/Linux.