原始内容
🦞 Lobster
Bioinformatics co-pilot to automate redundant omics-related tasks so you can focus on science
📋 Table of Contents
- What is Lobster AI? - Overview and use cases
- Quick Start - Install in 3 commands
- LLM Providers - Ollama, Anthropic, AWS Bedrock, Google Gemini
- Features - Single-cell, bulk RNA-seq, proteomics, visualization
- Case Studies - Real-world examples
- Roadmap - 2026 development plans
- Use with Claude Code - IDE integration
- Documentation - Wiki and guides
- Community & Support - Get help
- License - AGPL-3.0-or-later
✨ What is Lobster AI?
Lobster AI combines specialized AI agents with open-source bioinformatics tools to analyze multi-omics data through natural language. Describe your analysis needs - no coding required.
Perfect for:
- 🧬 Bioinformatics researchers analyzing RNA-seq data
- 💻 Computational biologists seeking intelligent workflows
- 🔬 Life science teams needing reproducible results
- 📚 Students learning modern bioinformatics
⚡ Quick Start
# Install Lobster globally
uv pip install lobster-ai
# Configure (interactive wizard)
lobster init
# Start analyzing
lobster chat
Don't have uv? Install it: macOS/Linux | Windows
Alternative installation methods: See Complete Installation Guide or Wiki
📺 Getting Started
1️⃣ Install in 30 seconds |
2️⃣ Configure in 1 minute |
3️⃣ Start analyzing with natural language
🏗️ Architecture Overview
Lobster is a modular bioinformatics platform with pluggable execution environments, LLM providers, and integrated data management:
Component Matrix
| Layer | Component | Configuration | Use Case |
|---|---|---|---|
| Execution | Local | Default (no setup) | Privacy-first, offline, cost-sensitive |
| Cloud | LOBSTER_CLOUD_KEY |
Team collaboration, scaling, managed infrastructure | |
| LLM Provider | Ollama | ollama pull gpt-oss:20b |
Local-only, unlimited usage, offline |
| Anthropic | ANTHROPIC_API_KEY |
Best quality, quick start, cloud/local | |
| AWS Bedrock | AWS credentials | Enterprise, compliance, high throughput | |
| Google Gemini | GOOGLE_API_KEY |
Long context, multimodal, free tier available | |
| Data Sources | GEO/SRA/ENA | Auto-configured | Transcriptomics datasets |
| PRIDE/MassIVE | Auto-configured | Proteomics datasets | |
| PubMed/PMC | NCBI_API_KEY (optional) |
Literature mining, metadata extraction | |
| Data Management | DataManagerV2 | Auto-configured | Multi-modal data orchestration, provenance tracking |
Configuration & Deployment
Lobster supports four deployment patterns optimized for different use cases:
| Pattern | Best For | Key Features |
|---|---|---|
| Local + Ollama | Privacy, learning, zero cost | Offline, unlimited usage, 100% local |
| Local + Anthropic | Quality, development | Best accuracy, quick setup, flexible |
| Local + Gemini | Cost optimization, free tier | Long context, multimodal, free tier available |
| Cloud + Bedrock | Production, teams | Enterprise SLA, high limits, scalable |
Learn more:
- 📖 Deployment Patterns Guide - Detailed setup for each pattern
- 🔄 Provider Auto-Detection - How Lobster selects providers
- ⚙️ Complete Configuration Guide - All configuration options
🧬 Features
| Category | Capabilities | Docs | Status |
|---|---|---|---|
| 🧬 Single-Cell RNA-seq | QC, Clustering, Annotation, Markers, Trajectories | Tutorial | ✅ Available |
| 📊 Bulk RNA-seq | Differential expression, Complex designs, Formula-based stats | Tutorial | ✅ Available |
| 📚 Literature Mining | PubMed search, Full-text retrieval, Methods extraction | Guide | ✅ Available |
| 🗄️ Dataset Discovery | GEO, SRA, PRIDE, ENA search and validation | Guide | ✅ Available |
| 📈 Visualization | UMAP, Volcano plots, Heatmaps, Interactive figures | Examples | ✅ Available |
| 🧪 Metadata Assistant | Cross-dataset harmonization, ID mapping | Guide | ⭐ Premium |
| 🔬 Proteomics | DDA/DIA workflows, Missing values, Normalization | Tutorial | ⭐ Premium |
📊 Interactive Dashboard (Alpha)
Real-time analysis monitoring with live updates and visualization
Dashboard for deep-diving into omics anlaysis.
#start with
lobster dashboard
#or during CLI session with
❯ /dashboard
📘 Case Studies
🧬 Single-Cell Analysis
Download → QC → Cluster → Annotate in one conversation
❯ Download GSE109564, perform QC, cluster cells, and find markers
✓ Downloaded 5,000 cells × 20,000 genes
✓ Quality control: filtered to 4,477 high-quality cells
✓ Identified 12 distinct clusters
✓ Generated UMAP visualization with marker genes
📚 Literature Mining
Find papers, extract methods, discover datasets
❯ Find papers about CRISPR screens in cancer and extract their GEO datasets
Found 47 papers with 23 associated GEO datasets
Extracted methods from 12 papers with full-text access
Cached metadata for all datasets in workspace
📈 Visualization
Publication-ready figures with natural language
❯ Create a UMAP colored by cell type with cluster labels
Generated interactive UMAP visualization
Saved as: geo_gse109564_umap_celltype.html
Also exported as PNG for publications
More examples in our cookbook →
🗓️ Roadmap
2026 Development:
- Custom feature agent (bring your tools/best practices)
- Knowledge graph integration for multi-dataset analysis
- Lobster Cloud compute infrastructure
- Enhanced multi-omics workflows (MuData integration)
- Community-contributed agent marketplace
Submit feature ideas: GitHub Discussions
🔧 Use with Claude Code
Lobster integrates with Claude Code as an Agent Skill, allowing you to run bioinformatics analyses directly from your development environment.
Quick Setup
# 1. Install Lobster
uv pip install lobster-ai
lobster init
# 2. Install Lobster Skill for Claude Code
curl -fsSL https://raw.githubusercontent.com/the-omics-os/lobster-local/main/claude-skill/SKILL.md \
-o ~/.claude/skills/lobster/SKILL.md --create-dirs
# 3. Start Claude Code
claude
Usage Examples
Claude Code will automatically invoke Lobster when you mention bioinformatics tasks:
# In Claude Code, just ask naturally:
You: "Analyze the single-cell dataset in data/counts.h5ad"
Claude: I'll use Lobster to analyze this single-cell dataset...
[Invokes: lobster query "analyze data/counts.h5ad..."]
You: "Download GSE109564 and run quality control"
Claude: I'll use Lobster to download and analyze this dataset...
[Invokes: lobster query "download GSE109564 and run QC"]
You: "Find papers about CRISPR screens in cancer"
Claude: I'll use Lobster to search the literature...
[Invokes: lobster query "search pubmed for CRISPR screens cancer"]
What this enables:
- 🧬 Run bioinformatics analyses without leaving your IDE
- 📊 Extract data and generate reports programmatically
- 🔄 Combine Lobster with your development workflow
- 🤖 Let Claude handle the complexity of bioinformatics commands
Learn more about Agent Skills →
📚 Documentation
| Resource | Description |
|---|---|
| Getting Started | First-time user guide |
| Installation | Detailed installation options |
| Configuration | LLM providers, API keys, settings |
| CLI Commands | Interactive command reference |
| Examples Cookbook | Real-world analysis recipes |
| Troubleshooting | Common issues and solutions |
| FAQ | Frequently asked questions |
Full reference: README_FULL.md | Wiki Home
🤝 Community & Support
- 💬 Discussions: GitHub Discussions
- 🐛 Bug Reports: GitHub Issues
- 📧 Email: info@omics-os.com
- 🌐 Website: omics-os.com
- ⭐ Premium: info@omics-os.com for pricing
Contributing: We welcome contributions! See CONTRIBUTING.md for guidelines.
📄 License
Lobster AI is open source under AGPL-3.0-or-later.
This license ensures all users receive the freedoms to use, study, share, and modify the software. Documentation is licensed CC-BY-4.0.
Commercial licensing: Contact info@omics-os.com
Transform Your Bioinformatics Research Today
uv pip install lobster-ai && lobster chat
Made with sleep deprivation ☕️ by Omics-OS