Skill v1.0.1
currentAutomated scan100/100+3 new
version: "1.0.1" name: lobster-use description: | Runs bioinformatics analysis with Lobster AI -- single-cell RNA-seq, bulk RNA-seq, genomics (VCF/GWAS), proteomics (mass spec/affinity), metabolomics (LC-MS/GC-MS/NMR), machine learning (feature selection, survival analysis), drug discovery, literature search, dataset discovery, and visualization. Use when working with biological data, omics analysis, or bioinformatics tasks. Covers: H5AD, CSV, VCF, PLINK, 10X, mzML formats, GEO/SRA/PRIDE/MetaboLights accessions.
Lobster AI works in two deployment modes:
- LOCAL: agents run on-device, you provide an LLM API key
- CLOUD: agents run on Omics-OS Cloud (ECS Fargate), managed Bedrock, per-user billing
TRIGGER PHRASES: "analyze cells", "search PubMed", "download GEO", "run QC", "cluster", "find markers", "differential expression", "UMAP", "volcano plot", "single-cell", "RNA-seq", "VCF", "GWAS", "proteomics", "mass spec", "metabolomics", "MetaboLights", "LC-MS", "metabolite", "feature selection", "survival analysis", "biomarker", "bioinformatics", "drug discovery", "pharmacogenomics", "variant annotation", "cloud chat", "omics-os cloud", "lobster cloud", "cloud login", "cloud session"
ASSUMES: Lobster is installed and configured. For setup issues, tell user to run lobster config-test (local) or lobster cloud status (cloud) and fix any errors. required_binaries:
- lobster
- python3
primary_credential: LLM_PROVIDER_API_KEY required_env_vars:
- name: ANTHROPIC_API_KEY
required: one_of_provider description: Anthropic Claude API key (local mode)
- name: GOOGLE_API_KEY
required: one_of_provider description: Google Gemini API key (local mode)
- name: OPENAI_API_KEY
required: one_of_provider description: OpenAI API key (local mode)
- name: OPENROUTER_API_KEY
required: one_of_provider description: OpenRouter API key (local mode, 600+ models)
- name: NEBIUS_API_KEY
required: one_of_provider description: Nebius AI Studio API key (local mode, open-weight models)
- name: AWS_ACCESS_KEY_ID
required: one_of_provider description: AWS Bedrock access key (local mode, must pair with SECRET)
- name: AWS_SECRET_ACCESS_KEY
required: one_of_provider description: AWS Bedrock secret key (local mode, must pair with ACCESS_KEY)
- name: AZURE_AI_ENDPOINT
required: one_of_provider description: Azure AI endpoint URL (local mode, must pair with CREDENTIAL)
- name: AZURE_AI_CREDENTIAL
required: one_of_provider description: Azure AI API credential (local mode, must pair with ENDPOINT)
- name: NCBI_API_KEY
required: false description: NCBI API key for faster PubMed/GEO access (recommended) credential_note: | LOCAL MODE: Exactly ONE LLM provider is required. Choose one and set only that provider's env var(s). Paired credentials (AWS, Azure) must both be set. CLOUD MODE: No LLM keys needed. Run lobster cloud login to authenticate via browser OAuth or lobster cloud login --api-key "$OMICS_OS_API_KEY" for headless environments. Credentials stored at ~/.config/omics-os/credentials.json. declared_writes:
- .lobster_workspace/ # Workspace data, session state, outputs
- .lobster_workspace/.env # Provider credential (workspace-scoped, mode 0600)
- .lobster_workspace/provider_config.json # Provider selection config
- ~/.config/lobster/credentials.env # ONLY if --global flag is used (not default)
- ~/.config/lobster/providers.json # ONLY if --global flag is used (not default)
- ~/.config/omics-os/credentials.json # Cloud OAuth/API key credentials
network_access:
- docs.omics-os.com # On-demand documentation fetches
- app.omics-os.com # Omics-OS Cloud REST API (cloud mode)
- stream.omics-os.com # Omics-OS Cloud streaming (cloud mode)
- LLM provider API endpoint # Whichever single provider is configured (local mode)
- eutils.ncbi.nlm.nih.gov # PubMed/GEO search (Research Agent only)
- ftp.ncbi.nlm.nih.gov # GEO/SRA dataset downloads (Data Expert only)
- www.ebi.ac.uk # PRIDE/MetaboLights (Research Agent only)
source: github: https://github.com/the-omics-os/lobster pypi: https://pypi.org/project/lobster-ai/ always: false
Lobster AI Usage Guide
Lobster AI is a multi-agent bioinformatics platform. Users describe analyses in natural language -- Lobster routes to 22 specialist agents across 10 packages automatically.
Requirements
- Binaries:
lobsterCLI (pip install lobster-ai), Python 3.12+ - Local mode (one of):
ANTHROPIC_API_KEY|GOOGLE_API_KEY|OPENAI_API_KEY|OPENROUTER_API_KEY|NEBIUS_API_KEYAWS_ACCESS_KEY_ID+AWS_SECRET_ACCESS_KEY(Bedrock)AZURE_AI_ENDPOINT+AZURE_AI_CREDENTIAL(Azure)- Ollama: no key needed (local models)
- Cloud mode:
lobster cloud login(browser OAuth or--api-key "$KEY"). No LLM keys needed. - Env var:
OMICS_OS_API_KEY(cloud auth alternative to stored credentials) - Optional:
NCBI_API_KEYfor faster PubMed/GEO - Writes:
.lobster_workspace/(local),~/.config/omics-os/credentials.json(cloud) - Network: LLM provider (local) or
app.omics-os.com+stream.omics-os.com(cloud)
Docs Discovery
The docs site at docs.omics-os.com exposes LLM-friendly raw markdown:
| Route | Use | |
|---|---|---|
/llms.txt | Index of all pages (title + URL + description) | |
/llms-full.txt | Full content dump of all free pages | |
/raw/docs/{slug}.md | Raw markdown for a specific page |
Workflow: Fetch /llms.txt first to discover slugs, then fetch individual pages via /raw/docs/{slug}.md.
Example: https://docs.omics-os.com/raw/docs/tutorials/single-cell-rnaseq.md
Three Modes
Local Mode
Agents run on your machine. You provide LLM API key. Data stays local.
lobster init # Configure LLM providerlobster chat # Interactive (Ink or Go TUI)lobster query "Analyze my data" --json # Single-turn
Cloud Mode (Omics-OS Cloud)
Agents run on ECS Fargate. Managed Bedrock. Per-user billing. No LLM keys.
lobster cloud login # Browser OAuth (one-time)lobster cloud chat # Interactive (launches npm TUI)lobster cloud status # Check tier, usage, budgetlobster cloud logout # Clear stored credentials
Orchestrator Mode
Coding agents call lobster query --json programmatically, parse structured output, and chain multi-step analyses. Cloud mode uses lobster cloud chat (interactive npm TUI). See agent-patterns.md.
Quick Start
# Installpip install 'lobster-ai[full]'# or: uv tool install 'lobster-ai[full]'# === Local mode ===lobster init --non-interactive --anthropic-key "$ANTHROPIC_API_KEY" --profile productionlobster query -w ./my_analysis --session-id "proj" --json "Download GSE109564 and run QC"# === Cloud mode ===lobster cloud login # One-time browser OAuthlobster cloud chat # Interactive cloud chat (npm TUI)# Inspect workspace (no tokens, ~300ms, local mode only)lobster command data --json -w ./my_analysis
Source: github.com/the-omics-os/lobster | PyPI: pypi.org/project/lobster-ai
Routing Table
| You want to... | Docs slug | Skill reference | |
|---|---|---|---|
| Install & configure | getting-started/installation | -- | |
| Configuration options | getting-started/configuration | -- | |
| Use the CLI (local + cloud) | guides/cli-commands | cli-reference.md | |
| Orchestrate programmatically | -- | agent-patterns.md | |
| Analyze scRNA-seq | tutorials/single-cell-rnaseq | -- | |
| Analyze bulk RNA-seq | tutorials/bulk-rnaseq | -- | |
| Analyze proteomics | tutorials/proteomics | -- | |
| Understand data formats | guides/data-formats | -- | |
| Search literature / datasets | agents/research | -- | |
| Analyze genomics | agents/genomics | -- | |
| Analyze metabolomics | case-studies/metabolomics | -- | |
| ML / feature selection | agents/ml | -- | |
| Drug discovery | agents/drug-discovery | -- | |
| Visualize results | agents/visualization | -- | |
| Troubleshoot | support/troubleshooting | -- | |
| See case studies | case-studies/{domain} | -- | |
| All agent capabilities | agents | -- | |
| Extend Lobster (dev) | -- | Use lobster-dev skill |
To fetch a docs page: https://docs.omics-os.com/raw/docs/{slug}.md
Hard Rules
- Always use `--session-id` for multi-step local analyses -- loaded data persists across queries
- Use `lobster command --json` for workspace inspection (no tokens, ~300ms, local mode only)
- Research Agent is the ONLY agent with internet access -- all others operate on loaded data
- Never skip QC before analysis -- always assess quality first
- Use `--json` flag when parsing output programmatically (both local and cloud)
- Cloud mode: run
lobster cloud loginbeforelobster cloud chat - Cloud sessions persist server-side -- managed within the npm TUI
- Default workspace:
.lobster_workspace/(local only) -- override with-w <path> - Fetch docs on demand from
docs.omics-os.com/raw/docs/{slug}.md-- don't guess workflows
Local vs Cloud Decision
| Factor | Local | Cloud | |
|---|---|---|---|
| LLM keys | You provide | Managed (Bedrock) | |
| Agent execution | Your machine | ECS Fargate | |
| Data storage | Local .lobster_workspace/ | Cloud workspace | |
| Session persistence | Disk (workspace) | Server-side (UUID) | |
| Billing | Your LLM provider | Omics-OS usage-based | |
| Offline | Yes | No | |
| Multi-device | No | Yes (web + CLI continuity) | |
| Setup | lobster init | lobster cloud login |
Rule: If user has Omics-OS Cloud account, prefer cloud mode. Otherwise local.
Agent Overview
22 agents across 10 packages. Supervisor routes automatically based on natural language.
| Agent | Package | Handles | |
|---|---|---|---|
| Supervisor | lobster-ai | Routes queries, coordinates agents | |
| Research Agent | lobster-research | PubMed, GEO, SRA, PRIDE, MetaboLights search (online) | |
| Data Expert | lobster-research | File loading, downloads, format conversion (offline) | |
| Transcriptomics Expert | lobster-transcriptomics | scRNA-seq + bulk RNA-seq: QC, clustering, trajectory | |
| Annotation Expert | lobster-transcriptomics | Cell type annotation, gene set enrichment (child) | |
| DE Analysis Expert | lobster-transcriptomics | Differential expression, pseudobulk, GSEA (child) | |
| Proteomics Expert | lobster-proteomics | MS + affinity import, QC, normalization, batch correction | |
| Proteomics DE Expert | lobster-proteomics | Protein DE, pathway enrichment, KSEA, STRING PPI (child) | |
| Biomarker Discovery | lobster-proteomics | Panel selection, nested CV, hub proteins (child) | |
| Metabolomics Expert | lobster-metabolomics | LC-MS/GC-MS/NMR: QC, normalization, PCA/PLS-DA, annotation | |
| Genomics Expert | lobster-genomics | VCF/PLINK: QC, GWAS, variant annotation | |
| Variant Analysis Expert | lobster-genomics | VEP annotation, ClinVar, clinical prioritization (child) | |
| ML Expert | lobster-ml | ML prep, scVI embeddings, data export | |
| Feature Selection Expert | lobster-ml | Stability selection, LASSO, variance filtering (child) | |
| Survival Analysis Expert | lobster-ml | Cox models, Kaplan-Meier, risk stratification (child) | |
| Drug Discovery Expert | lobster-drug-discovery | Drug target validation, compound profiling | |
| Cheminformatics Expert | lobster-drug-discovery | Molecular descriptors, fingerprints, similarity (child) | |
| Clinical Dev Expert | lobster-drug-discovery | Trial design, endpoint analysis, safety signals (child) | |
| Pharmacogenomics Expert | lobster-drug-discovery | PGx variants, drug-gene interactions (child) | |
| Visualization Expert | lobster-visualization | UMAP, heatmaps, volcano plots, dot plots (Plotly) | |
| Metadata Assistant | lobster-metadata | ID mapping, metadata standardization (internal) | |
| Protein Structure Viz | lobster-structural-viz | PDB fetch, PyMOL visualization, RMSD |
Per-agent docs: https://docs.omics-os.com/raw/docs/agents/{domain}.md