lobster-ai 1.0.13

Multi-Agent Bioinformatics Analysis System powered by LangGraph

Lobster AI

Open-source multi-agent bioinformatics engine. Describe your analysis in natural language.

Documentation · PyPI · Omics-OS Cloud

Quick Start

#installs only core lobster
curl -fsSL https://install.lobsterbio.com | bash

Then:

# Define LLM provider and domain expert installation
lobster init

Finaly:

lobster chat 
# or non-interactive
lobster query "Hi, what can you do?"

Windows, pip, and other install methods

Windows (PowerShell):

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

uv (recommended manual install):

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

pip:

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

Upgrade:

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

Why Lobster AI

Your machine, your data. No uploads, no third-party cloud. Patient data and unpublished results stay on your hardware.

Tool calls, not token dreams. Agents execute real bioinformatics tools: Scanpy, PyDESeq2, AnnData. Every result is traceable to a function call with validated inputs and outputs.

Reproducible by design. W3C-PROV provenance tracking, Jupyter notebook export, and parameter schemas for every analysis. The same question produces the same pipeline.

Agents

18 specialist agents across 9 packages. Install exactly what you need.

Package	Domain	Status
lobster-ai	Core engine, supervisor, infrastructure	Stable
lobster-transcriptomics	Single-cell & bulk RNA-seq, DE analysis, cell type annotation	Stable
lobster-research	PubMed, GEO, Pride, and more.. dataset discovery	Stable
lobster-visualization	Publication-quality Plotly plots	Stable
lobster-metadata	ID mapping, sample filtering, metadata validation	Stable
lobster-genomics	GWAS pipeline, clinical variant analysis	Beta
lobster-proteomics	Mass spec & affinity proteomics, biomarker discovery	Beta
lobster-metabolomics	LC-MS, GC-MS, NMR analysis	Beta
lobster-structural-viz	Protein structure visualization	Beta
lobster-ml	Feature selection, survival analysis, MOFA integration	Beta

Install individual agents

# Pick agents interactively
lobster init --force

# Or install specific packages
uv tool install lobster-ai --with lobster-proteomics --with lobster-genomics

# Install everything
uv tool install 'lobster-ai[full,anthropic]'

Build your own agent

Create custom agents for any domain. Agents plug in via Python entry points — discovered automatically, no core changes needed.

Install the lobster-dev skill to teach your coding agent the full architecture:

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

Then ask your coding agent: "Create a Lobster agent for [your domain]" — it knows the package structure, AGENT_CONFIG pattern, factory function, tool design, testing, and the 28-step checklist.

Usage

# Interactive chat
lobster chat

# Single-turn queries
lobster query "Download GSE109564 and cluster cells"
lobster query "Search PubMed for CRISPR studies in 2024"

# 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"

Pipeline export and slash commands

lobster chat
> /pipeline export         # Export reproducible Jupyter notebook
> /pipeline list           # List exported pipelines
> /pipeline run analysis.ipynb geo_gse109564
> /data                    # Show loaded datasets
> /status                  # Session info
> /help                    # All commands

Capabilities by domain

Transcriptomics

• Single-cell RNA-seq: QC, doublet detection (Scrublet), batch integration (Harmony/scVI), clustering, cell type annotation, trajectory inference (DPT/PAGA)
• Bulk RNA-seq: Salmon/kallisto/featureCounts import, sample QC, batch detection, normalization (DESeq2/VST/CPM), DE with PyDESeq2, GSEA, publication-ready export

Genomics

• GWAS: VCF/PLINK import, LD pruning, kinship, association testing, result clumping
• Clinical: variant annotation (VEP), gnomAD frequencies, ClinVar pathogenicity, variant prioritization

Proteomics

• Mass spec: MaxQuant/DIA-NN/Spectronaut import, PTM analysis, peptide-to-protein rollup, batch correction
• Affinity: Olink NPX/SomaScan ADAT/Luminex MFI import, LOD quality, bridge normalization
• Downstream: GO/Reactome/KEGG enrichment, kinase enrichment (KSEA), STRING PPI, biomarker panel selection

Metabolomics

• LC-MS, GC-MS, NMR with auto-detection
• QC (RSD, TIC), filtering, imputation, normalization (PQN/TIC/IS)
• PCA, PLS-DA, OPLS-DA, m/z annotation (HMDB/KEGG), lipid class analysis

Machine Learning

• Feature selection (stability selection, LASSO, variance filter)
• Survival analysis (Cox models, Kaplan-Meier, risk stratification)
• Cross-validation, SHAP interpretability, multi-omics integration (MOFA)

Research & Metadata

• Literature discovery (PubMed, PMC, GEO, PRIDE, MetaboLights)
• Dataset download orchestration, metadata harmonization, sample filtering

LLM providers

Lobster supports 5 LLM providers. Configure via lobster init or environment variables.

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

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)

Development

git clone https://github.com/the-omics-os/lobster.git
cd lobster
make dev-install    # editable install with dev deps
make test           # run all tests
make format         # black + isort

Environment variables

Set during lobster init or manually:

Variable	Purpose
ANTHROPIC_API_KEY	Anthropic Direct
AWS_BEDROCK_ACCESS_KEY	AWS Bedrock
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

Ecosystem

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

Contributing

Contributions welcome. See CONTRIBUTING.md for guidelines.

License

Code: AGPL-3.0-or-later · Docs: CC BY 4.0 · See LICENSE

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