lobster-ai 1.1.3

Multi-Agent Bioinformatics Analysis System powered by LangGraph

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

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🧑‍🔬 Human Quickstart

1. Install Lobster AI (macOS/Linux):

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

(Windows users: irm https://install.lobsterbio.com/windows | iex)

2. Configure your LLM (Anthropic, Gemini, local Ollama, etc.):

lobster init

3. Start an interactive session and run a full pipeline:

lobster chat

Then describe your analysis:

> Search PubMed for single-cell CRISPR screens in T cells from 2023–2024,
  download the most cited dataset, run QC, integrate batches with Harmony,
  cluster the cells, annotate cell types, and export a reproducible notebook.

Watch: installation & init walkthrough

🤖 For AI Coding Agents

Teach your coding agent (Claude Code, Cursor, Gemini) to use and extend Lobster AI instantly:

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

Installs the lobster-use and lobster-dev skills so your AI knows our entire 10-package architecture.

Real-World Use Cases

See Lobster AI applied end-to-end across omics domains:

Domain	Case Study
Single-Cell Transcriptomics	Cell clustering, annotation & trajectory inference
CML Drug Resistance	Resistance mechanism discovery from scRNA-seq
Drug Discovery	Target identification & compound prioritization
Clinical Genomics	Variant annotation & GWAS analysis
Mass Spec Proteomics	Biomarker panel selection from DIA-NN data
Literature Mining	Automated dataset discovery from PubMed
Multi-Omics ML	Feature selection & survival analysis

🧠 The Architecture

Lobster isn't just a chatbot; it's a modular ecosystem of 22 specialist agents across 10 packages.

• Your machine, your data: Patient data never leaves your hardware.
• Tool calls, not token dreams: Agents execute real, validated Python packages (Scanpy, PyDESeq2).
• 100% Reproducible: W3C-PROV tracking and automatic Jupyter notebook exports.

🛠️ Build Your Own Agent

The lobster-dev skill gives your coding assistant (Claude Code, Gemini CLI, Cursor) deep knowledge of how Lobster agents are structured. Describe the biological domain you need — it scaffolds the package, wires the tools, writes the tests, and registers the agent.

1. The Request

2. The Result

❓ Deep Dives & FAQ

What omics domains are supported?

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

Which LLMs can I use?

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

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

Advanced installation (Windows, pip)

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

How do I build my 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.

Built to accelerate multi-omics research.

Omics-OS  ·  Lobster AI  ·  Docs