AmadeusBio.ai
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AmadeusBio.aiYOUR BIOINFORMATIC AGENT, IN SILICO.
On this pageDemoCurrent featuresGet StartedGalaxy-pluginCredits & Acknowledgments

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 and napari using natural language.
  2. Retrival of sequences, protein structures etc. from databases including Uniprot.
  3. Remote operation of usegalaxy.org.
  4. 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/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 instruction 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 step by step set up process.

Credits & Acknowledgments

ProjectAuthor / RepositoryHow it was used
SciAgent-Skillsjaechang-hits/SciAgent-SkillsUtilized skills
pymol-mcpvrtejus/pymol-mcpAdapted for PyMol integration
napari-mcproyerlab/napari-mcpIntegrated capabilities
galaxy-mcpgalaxyproject/galaxy-mcpremote control galaxy
Agent Monitorhoangsonww/Claude-Code-Agent-MonitorAdapted for the Agents dashboard
Fumadocsfuma-nama/fumadocsWebsite built using this template
info@amadeusbio.ai