Data & ReproScientific VisualizationFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

lobster-bioinformatics

Maintainer FreedomIntelligence · Last updated April 1, 2026

Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. Use when analyzing genomics data, searching for papers/datasets, or working with H5AD, CSV, GEO/SRA accessions, or biological data. Requires lobster-ai package installed.

OpenClawNanoClawAnalysisWritinglobster-bioinformatics🧠 bioos extended suiteresearch infrastructure & agentsrun

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/lobster-bioinformatics

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Lobster AI is a bioinformatics platform that combines specialized AI agents with open-source tools to analyze multi-omics data through natural language.
uv pip install lobster-ai lobster init --help #to see non-interactive.
Lobster requires an LLM provider (Ollama, Anthropic, or AWS Bedrock).

Source Doc

Excerpt From SKILL.md

When to use this Skill

Use Lobster when the user asks to:

Analyze single-cell RNA-seq data (QC, clustering, annotation, markers)
Perform bulk RNA-seq analysis (differential expression, complex designs)
Search scientific literature (PubMed, PMC, full-text retrieval)
Discover datasets (GEO, SRA, ENA (free) and PRIDE, MASSive (cloud))
Run quality control on biological data
Generate bioinformatics visualizations (UMAP, volcano plots, heatmaps)
Download and process biological datasets
Work with H5AD, CSV, Excel, 10X formats
Extract methods or metadata from papers

Requirements

Lobster must be installed and configured:


## Pre-flight check (IMPORTANT)

**Before running any analysis, always verify Lobster is ready:**

Returns structured JSON:

This command validates:
- **LLM provider** - Ollama server running + models installed, or Anthropic/Bedrock API keys valid
- **NCBI API** - PubMed/GEO access (optional but recommended)
- **Workspace** - Directory writable for output files

**Expected output for a working setup:**

**If config-test fails:**

| Error | Solution |
|-------|----------|
| No LLM provider configured | Run `lobster init` |
| Ollama server not accessible | Start Ollama: `ollama serve` |
| Ollama: No models installed | After asking user - Install a model: `ollama pull gpt-oss:20b` |
| Anthropic/Bedrock API error | Check API key validity in `.env` |
| NCBI API not configured | Add `NCBI_API_KEY` to `.env` (optional) |
| Workspace not writable | Check directory permissions |

**Quick status checks:**
```bash