Getting Started

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

Features

• Operate local softwares such as PyMol and napari using natural language.
• Retrieval of sequences, protein structures etc. from databases including Uniprot.
• Remote operation of usegalaxy.org.
• Plus everything that comes with a standard coding agent.

Installation

Install as a Claude Code plugin

Clone the repository, then point Claude Code at it using the --plugin-dir flag:

git clone https://github.com/AmadeusBio-ai/mvp.git
claude --plugin-dir ./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 setup instructions on Windows/macOS/Linux.

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

To prevent dependency conflicts, Napari and its MCP plugin must be installed in an isolated virtual environment.

See Napari Integration & Setup for detailed isolation and configuration steps.

Galaxy-plugin

Install galaxy-plugin to allow Claude Code to remotely operate usegalaxy.org.

git clone https://github.com/AmadeusBio-ai/galaxy-plugin.git
claude --plugin-dir ./galaxy-plugin

Prerequisites

1. uv / uvx installed and on PATH.
2. A Galaxy API key — get one at User -> Preferences -> Manage API Key on usegalaxy.org (or whatever Galaxy instance you use).

See galaxy-plugin for a step-by-step setup process.

Additional Information

Credits & Acknowledgments