Transform your bioinformatics research with AI agents that understand your data and provide expert analysis insights.

• ✨ What is Lobster AI?
• 🚀 Quick Start
• 💡 Example Usage
• 🧬 Features
• 🔧 Configuration
• 📚 Documentation
• 🤝 Community & Support
• 📄 License

Lobster AI is a bioinformatics platform that combines specialized AI agents with open-source tools to analyze complex multi-omics data (starting with transcriptomics). Simply describe your analysis needs in natural language - no coding required.

Perfect for:

• Bioinformatics researchers analyzing RNA-seq data
• Computational biologists seeking intelligent analysis workflows
• Life science teams requiring reproducible, publication-ready results
• Students learning modern bioinformatics approaches

• Python 3.12 or higher
• An LLM API key (Claude or AWS Bedrock)

# 1. Clone the repository
git clone https://github.com/the-omics-os/lobster-local.git
cd lobster-local

# 2. Install with make (automatically creates .env file)
make install

# 3. Configure your API key
# The .env file is automatically created during installation
# Edit it with your preferred editor:

# macOS:
open .env

# Linux:
nano .env

# Windows (untested):
notepad .env

# Add your API key to the .env file:
# ANTHROPIC_API_KEY=sk-ant-api03-your-key-here

# 4. Activate the virtual environment
source .venv/bin/activate

# 5. Start analyzing!
lobster chat
# or if you want to see the reasoning
lobster chat --reasoning

# Optional: Install globally to use 'lobster' from any directory
make install-global

Rate Limits

Anthropic's API has conservative rate limits for new accounts. If you encounter rate limit errors:

1. Wait and retry - Limits reset after a short period (typically 60 seconds)
2. Request increase - Visit Anthropic Rate Limits Documentation
3. Use AWS Bedrock - Recommended for production use with higher limits
4. Contact us - Email info@omics-os.com for assistance

Recommended Setup by Use Case:

For AWS Bedrock setup, see the Configuration Guide.

🦞 lobster chat

Welcome to Lobster AI - Your bioinformatics analysis assistant

🦞 You: Download GSE109564 and perform single-cell clustering analysis

🦞 Lobster: I'll download and analyze this single-cell dataset for you...

✓ Downloaded 5,000 cells × 20,000 genes
✓ Quality control: filtered to 4,477 high-quality cells
✓ Identified 12 distinct cell clusters
✓ Generated UMAP visualization and marker gene analysis

Analysis complete! Results saved to workspace.

# Download and analyze GEO datasets
🦞 You: "Download GSE12345 and perform quality control"

# Analyze your own data
🦞 You: "Load my_data.csv and identify differentially expressed genes"

# Generate visualizations
🦞 You: "Create a UMAP plot colored by cell type"

# Perform complex analyses
🦞 You: "Run pseudobulk aggregation and differential expression between conditions"

• Quality control and filtering
• Normalization and scaling
• Clustering and UMAP visualization
• Cell type annotation
• Marker gene identification
• Pseudobulk aggregation

• Differential expression with pyDESeq2
• R-style formula-based statistics
• Complex experimental designs
• Batch effect correction

• Support for CSV, Excel, H5AD, 10X formats
• GEO dataset downloading
• Literature mining via PubMed
• Automatic visualization generation

• Mass spectrometry proteomics (DDA/DIA workflows)
• Affinity proteomics (Olink panels, antibody arrays)
• Missing value handling and normalization
• Pathway enrichment analysis

• Cross-platform data integration
• Multi-modal analysis workflows

• Scalable cloud computing
• No local hardware requirements

The .env file is automatically created during installation (make install calls setup-env). You just need to edit it with your API credentials.

Edit the .env file:

# macOS - Opens in default text editor (TextEdit, etc.)
open .env

# Linux - Use nano or your preferred editor
nano .env

# Windows (⚠️ untested platform)
notepad .env

Choose ONE LLM provider:

Option 1: Claude API (Recommended for quick start)

# Get your key from https://console.anthropic.com/
ANTHROPIC_API_KEY=sk-ant-api03-your-key-here

⚠️ Note: Claude API has rate limits for new accounts. For production use, consider AWS Bedrock.

Option 2: AWS Bedrock (Recommended for production)

# Requires AWS account with Bedrock access
AWS_BEDROCK_ACCESS_KEY=AKIA...
AWS_BEDROCK_SECRET_ACCESS_KEY=your-secret-key

# Enhanced literature search (optional)
NCBI_API_KEY=your-ncbi-api-key  # Get from NCBI

# Force specific provider (auto-detected by default)
LOBSTER_LLM_PROVIDER=anthropic  # or "bedrock"

# Cloud mode (optional - contact info@omics-os.com for access)
LOBSTER_CLOUD_KEY=your-cloud-api-key

• ✅ macOS: Fully tested and supported
• ✅ Linux: Tested and supported
• ⚠️ Windows: Not currently tested (may work but no guarantees)

• Full Documentation - Guides and tutorials
• Example Analyses - Real-world use cases
• Architecture Overview - Technical details

• 🐛 Report Issues - Bug reports and feature requests
• 📧 Email Support - Direct help from our team

Need custom integrations or dedicated support? Contact us

Lobster AI is open source under the Apache License 2.0 (see LICENSE). Documentation is licensed CC-BY-4.0. Contributions are accepted under a Contributor License Agreement to preserve future licensing flexibility.