🦞 Lobster

Bioinformatics co-pilot to automate redundant omics-related tasks so you can focus on science

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📋 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

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✨ 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

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⚡ 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

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📺 Getting Started

1️⃣ Install in 30 seconds uv pip install lobster-ai

2️⃣ Configure in 1 minute lobster init

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🏗️ 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

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🧬 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

Full documentation →

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📊 Interactive Dashboard (Alpha)

Dashboard for deep-diving into omics anlaysis.

#start with 
lobster dashboard
#or during CLI session with
❯ /dashboard

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📘 Case Studies

🧬 Single-Cell Analysis

Download → QC → Cluster → Annotate in one conversation

``$\text{bash} ❯ \text{Download} \text{GSE109564}, \text{perform} \text{QC}, \text{cluster} \text{cells}, \text{and} \text{find} \text{markers}

✓ \text{Downloaded} 5{,}000 \text{cells} \times 20{,}000 \text{genes} ✓ \text{Quality} \text{control}: \text{filtered} \text{to} 4{,}477 \text{high}-\text{quality} \text{cells} ✓ \text{Identified} 12 \text{distinct} \text{clusters} ✓ \text{Generated} \text{UMAP} \text{visualization} \text{with} \text{marker} \text{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 →

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🗓️ 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

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🔧 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 →

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📚 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

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🤝 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.

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📄 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

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