🧬 MedgeClaw

An AI-Powered Biomedical Research Assistant

English | 中文

An open-source biomedical AI research assistant built on OpenClaw and Claude Code, integrating 140 K-Dense Scientific Skills for bioinformatics, drug discovery, clinical research, and more.

Talk to your research assistant via WhatsApp, Slack, or Discord → it runs the analysis → you view results in RStudio or JupyterLab.

Architecture

User (voice / text via WhatsApp · Slack · Feishu · Discord)
        ↓
OpenClaw Gateway  (conversation layer)
        ↓  biomed-dispatch skill
Claude Code  (execution layer)
        ↓  K-Dense Scientific Skills (140 skills)
R + Python Analysis Environment (Docker)
        ↓                    ↓                    ↓
Research Dashboard :77xx    RStudio :8787       Feishu Rich Cards
  (real-time progress,      / JupyterLab :8888    (SVG panels → PNG
   code & output preview)   (interactive)          → interactive cards)

What's Included

| Component | Description | | ----------------------------- | ---------------------------------------------------------------------------------- | | OpenClaw | Conversational AI gateway — connects to your messaging apps | | Claude Code | Executes complex analysis workflows autonomously | | K-Dense Scientific Skills | 140 ready-to-use skills: genomics, drug discovery, clinical research, ML, and more | | Research Dashboard | Real-time web dashboard showing progress, code, outputs, and file previews | | R Environment | DESeq2, Seurat, edgeR, clusterProfiler, survival, ggplot2, and more | | Python Environment | Scanpy, BioPython, PyDESeq2, lifelines, scikit-learn, and more | | RStudio Server | Browser-based R IDE at localhost:8787 | | JupyterLab | Browser-based Python/R notebooks at localhost:8888 | | biomed-dispatch | The bridge skill that routes your requests to Claude Code | | CJK Visualization | Auto-detects CJK fonts for matplotlib, no more tofu blocks in Chinese plots | | SVG UI Templates | Professional SVG panels for lists, checklists, pipeline status, and rich reports | | Feishu Rich Card | Send image-rich interactive cards in Feishu group chats for progress reports |

Prerequisites

Node.js 22+ — nodejs.org
Docker + docker-compose — docs.docker.com
Git
An API key from one of the supported model providers (see below)

Quick Start

# 1. Clone with submodules (includes K-Dense Scientific Skills)
git clone --recurse-submodules https://github.com/xjtulyc/MedgeClaw
cd MedgeClaw

# 2. Configure environment
cp .env.example .env
nano .env  # Fill in your API key and provider settings

# 3. Run setup
bash setup.sh

# 4. Sync MedgeClaw configuration to OpenClaw
python3 sync.py
openclaw gateway restart

# 5. Start the analysis environment
docker compose up -d

# 6. Start OpenClaw
openclaw onboard

Then open your messaging app and start talking to your assistant.

Environment Configuration

The .env file controls:

API settings: Provider, base URL, model, API key
Third-party proxy fix: ANTHROPIC_SMALL_FAST_MODEL (required for non-Anthropic endpoints)
Path overrides (optional): MEDGECLAW_ROOT, OPENCLAW_DIR
Docker settings: Container name, RStudio/Jupyter passwords

See .env.example for all available options.

Model Providers

Edit .env to choose your provider. All providers are drop-in replacements — no other changes needed.

| Provider | Base URL | Notes | | ------------------------------ | ------------------------------------ | ---------------- | | Anthropic Claude (default) | https://api.anthropic.com | Best quality | | MiniMax 2.1 | https://api.minimax.chat/anthropic | Available in CN | | GLM-4.7 (Z.ai) | https://api.z.ai/api/anthropic | Available in CN | | DeepSeek | https://api.deepseek.com/anthropic | Low cost | | Ollama (local) | http://localhost:11434/v1 | Fully offline |

⚠️ Using Third-Party API Proxies

If you use a third-party API proxy (MiniMax, GLM, DeepSeek, or any non-Anthropic endpoint), you must configure ANTHROPIC_SMALL_FAST_MODEL in your .env file. Without this, Claude Code will fail silently.

Why

Claude Code runs a pre-flight safety check before every bash command, using a lightweight "small fast model" (defaults to claude-3-5-haiku). Most third-party proxies don't support Haiku, causing the pre-flight to return 503 errors and hang indefinitely with:

⚠️ [BashTool] Pre-flight check is taking longer than expected.

Fix

Add this line to your .env:

# Required for third-party API proxies:
ANTHROPIC_SMALL_FAST_MODEL=claude-sonnet-4-20250514  # or any model your proxy supports

Then re-run bash setup.sh to apply.

How to verify

# Should complete in < 30 seconds. If it hangs, your SMALL_FAST_MODEL is wrong.
claude --dangerously-skip-permissions -p 'run: echo hello'

Usage Examples

Once OpenClaw is running, send messages like:

Analyze RNA-seq data at data/counts.csv vs data/meta.csv, treatment vs control

Search PubMed for recent papers on CRISPR base editing, summarize top 10

Run survival analysis on data/clinical.csv, time=OS_months, event=OS_status

Perform single-cell RNA-seq analysis on the 10X data in data/10x/

Virtual screen EGFR inhibitors from ChEMBL (IC50 < 50nM), generate SAR report

Results are saved to ./outputs/ and viewable in RStudio (localhost:8787) or JupyterLab (localhost:8888).

📊 Research Dashboard

Every analysis task automatically spawns a live web dashboard — no need to wait for completion or check logs.

Features:

Real-time progress bar — sticky header, always visible
Analysis plan overview — all steps listed with completion status (✅/⏳)
Step-by-step breakdown — each step shows: description → code (collapsible) → outputs
Inline previews — images render directly, tables load from CSV files, text results highlighted
Full script access — click to load the complete .py file, not just snippets
Copy & download everywhere — 📋 copy code/tables/text, ⬇ download images/CSVs
Color-blind friendly — IBM accessible palette + GitHub Dark theme
File browser — browse all output artifacts with one-click preview

How it works:

AI completes a step → updates state.json → dashboard auto-refreshes (2s polling)

Three files, zero dependencies: dashboard.html + state.json + dashboard_serve.py.

See docs/dashboard.md for the full specification.

Directory Structure

MedgeClaw/
├── docker/
│   ├── Dockerfile          # R + Python + RStudio + Jupyter
│   └── entrypoint.sh
├── skills/
│   ├── biomed-dispatch/    # Core bridge skill: routes tasks to Claude Code
│   │   └── SKILL.md
│   ├── dashboard/          # Research Dashboard: real-time task visualization
│   │   ├── SKILL.md        # Dashboard specification & state.json schema
│   │   ├── dashboard.html  # Single-file frontend (dark theme, IBM palette)
│   │   └── dashboard_serve.py  # Threaded HTTP server
│   ├── cjk-viz/            # CJK font detection for matplotlib
│   │   └── SKILL.md
│   ├── svg-ui-templates/   # Professional SVG panels (list, checklist, pipeline, report)
│   │   ├── SKILL.md
│   │   ├── assets/         # 4 template SVGs
│   │   └── references/     # Template guide
│   └── feishu-rich-card/   # Send image-rich interactive cards in Feishu
│       ├── SKILL.md
│       └── references/     # send_card.py helper
├── scientific-skills/      # git submodule → K-Dense (140 skills)
├── data/                   # Per-task data & analysis directories
│   └── <task_name>/
│       ├── dashboard/      # state.json + dashboard.html (auto-created)
│       └── output/         # Analysis outputs (CSV, PNG, etc.)
├── docs/                   # Project documentation
├── docker-compose.yml
├── setup.sh
├── CLAUDE.md               # Project instructions for Claude Code
├── .env.example
└── .gitmodules

🔄 Project Synchronization

MedgeClaw integrates with OpenClaw via a configuration-driven sync mechanism.

How it works

Configuration: .medgeclaw-sync.yml defines what to sync
Sync script: sync.py reads the config and performs the sync
Environment: .env defines paths (optional, auto-detected by default)

When to sync

Run python3 sync.py after:

Initial setup
Modifying project documentation (MEDGECLAW.md, IDENTITY.md)
Adding/updating custom skills in skills/
Changing sync configuration in .medgeclaw-sync.yml

What gets synced

Project docs → OpenClaw workspace
Custom skills → OpenClaw workspace/skills/
Identity/context → SOUL.md, AGENTS.md (appended)
Skill paths → openclaw.json

See SYNC_README.md for details.

Updating K-Dense Scientific Skills

git submodule update --remote scientific-skills

Contributing

Contributions welcome. The most valuable contributions are:

Impr

MedgeClaw

Install / Use

README