lobster-ai 1.0.2

Multi-Agent Bioinformatics Analysis System powered by LangGraph

🦞 Lobster AI

Multi-agent bioinformatics engine. Analyze multi-omics data in natural language.

Documentation · PyPI · Omics-OS Cloud · Agent Template

---

What is Lobster AI?

Lobster AI is an open-source multi-agent platform for bioinformatics. Describe your analysis in natural language — Lobster routes it to specialized AI agents that handle single-cell RNA-seq, bulk RNA-seq, proteomics, genomics, literature mining, and machine learning. Results are reproducible (W3C-PROV), exportable as Jupyter notebooks, and backed by the same open-source tools researchers already trust (Scanpy, PyDESeq2, AnnData).

Built for bioinformaticians, computational biologists, and research teams who need intelligent workflows without writing code.

---

Quick Start

macOS / Linux (recommended):

curl -fsSL https://install.lobsterbio.com | bash

Windows (PowerShell):

irm https://install.lobsterbio.com/windows | iex

Manual (any platform):

uv tool install 'lobster-ai[full,anthropic]'
lobster init
lobster chat

Or with pip:

pip install 'lobster-ai[full]'
lobster init
lobster chat

---

Agent Packages

Lobster AI uses a modular architecture. Install exactly the agents you need.

Package	Agents	Status
lobster-ai	Supervisor, Core infrastructure	Beta
lobster-transcriptomics	Transcriptomics, Annotation, DE Analysis	Beta
lobster-research	Research, Data Expert	Beta
lobster-visualization	Visualization Expert	Beta
lobster-metadata	Metadata Assistant	Beta
lobster-structural-viz	Protein Structure Visualization	Beta
lobster-genomics	Genomics Expert	Alpha
lobster-proteomics	Proteomics Expert	Alpha
lobster-ml	ML, Feature Selection, Survival Analysis	Alpha

Add individual agents (uv tool installs):

uv tool install lobster-ai --with lobster-proteomics --with lobster-genomics

Or run lobster init --force to interactively select agents — it generates the command for you.

Install everything:

uv tool install 'lobster-ai[full,anthropic]'   # uv tool (recommended)
pip install 'lobster-ai[full]'                  # pip

Upgrade:

uv tool upgrade lobster-ai                      # uv tool
pip install --upgrade lobster-ai                 # pip

Build your own agent: Use the lobster-agent-template to create custom analysis agents.

---

Coding Agent Skills

Teach your coding agents (Claude Code, Codex, Gemini CLI, OpenClaw) to use Lobster:

curl -fsSL https://skills.lobsterbio.com | bash

Installs two skills:

• lobster-use — End-user workflows (search PubMed, analyze cells, RNA-seq)
• lobster-dev — Developer guide (create agents, extend services, testing)

---

LLM Providers

Lobster supports 5 LLM providers. Choose based on your needs:

Provider	Type	Setup	Use Case
Ollama	Local	ollama pull gpt-oss:20b	Privacy, zero cost, offline
Anthropic	Cloud	API key	Fastest, best quality
AWS Bedrock	Cloud	AWS credentials	Enterprise, compliance
Google Gemini	Cloud	Google API key	Multimodal, long context
Azure AI	Cloud	Endpoint + credential	Enterprise Azure

Configure via lobster init or set environment variables manually.

---

Features

Multi-Omics Analysis

• Single-cell RNA-seq (QC, clustering, cell type annotation, trajectory)
• Bulk RNA-seq (Kallisto/Salmon import, DE with PyDESeq2)
• Proteomics (DDA/DIA, missing values, normalization)
• Genomics (VCF/PLINK, GWAS, PCA, variant annotation)
• Multi-omics integration (MOFA, pathway enrichment)

Machine Learning

• Feature selection (stability selection, LASSO, variance filter)
• Survival analysis (Cox models, Kaplan-Meier, risk stratification)
• Cross-validation (stratified k-fold, nested CV)
• Interpretability (SHAP, feature importance)

Research & Metadata

• Literature discovery (PubMed, PMC, GEO)
• Dataset downloads (GEO, SRA, PRIDE)
• Metadata harmonization and validation
• Sample grouping and filtering

Reproducibility

• W3C-PROV provenance tracking
• Jupyter notebook export
• Parameter schemas for all analyses

---

Usage Examples

Interactive chat:

lobster chat

Single-turn queries:

lobster query "Search PubMed for CRISPR studies in 2024"
lobster query "Download GSE109564 and cluster cells"

Session continuity:

lobster query --session-id project1 "Search for Alzheimer's scRNA-seq datasets"
lobster query --session-id project1 "Download the top 3 results"
lobster query --session-id latest "Cluster the first dataset"

Export pipelines:

lobster chat
> /pipeline export
> /pipeline list
> /pipeline run analysis.ipynb geo_gse109564

---

Development

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

# Install with dev dependencies (editable)
make dev-install

# Run tests
make test

# Format and lint
make format && make lint

# Activate environment
source .venv/bin/activate

# Test as end user (uv tool install)
uv tool install 'lobster-ai[full,anthropic]'

Environment variables (will be created during init):

• ANTHROPIC_API_KEY — Anthropic Direct
• AWS_BEDROCK_ACCESS_KEY, AWS_BEDROCK_SECRET_ACCESS_KEY — AWS Bedrock
• GOOGLE_API_KEY — Google Gemini
• OLLAMA_BASE_URL — Ollama server (default: http://localhost:11434)
• LOBSTER_LLM_PROVIDER — Explicit provider selection
• LOBSTER_WORKSPACE — Workspace directory

---

Documentation

For detailed documentation, see README_FULL.md or visit docs.omics-os.com.

Key topics:

• Platform-specific installation (macOS, Linux, Windows)
• One-line installers (install.lobsterbio.com)
• uv tool install and upgrade workflows
• Docker deployment
• LLM provider configuration
• Premium features
• Troubleshooting

---

Ecosystem

Project	Description	Link
Lobster AI	Open-source multi-agent bioinformatics engine	lobsterbio.com
Omics-OS Cloud	Managed cloud platform	app.omics-os.com
Documentation	Guides, API reference, tutorials	docs.omics-os.com
Agent Template	Create your own Lobster agent	GitHub

---

Contributing

Contributions are welcome. See CONTRIBUTING.md for guidelines.

Ways to contribute:

• Report bugs and request features via GitHub Issues
• Submit pull requests for bug fixes or new features
• Improve documentation
• Create custom agent packages

---

License

Code: AGPL-3.0-or-later Documentation: CC BY 4.0

See LICENSE for details.

---

Built by Omics-OS to accelerate multi-omics research
Omics-OS · Lobster AI · Docs