Bio Research

Bio-Research Plugin

Connect to preclinical research tools and databases (literature search, genomics analysis, target prioritization) to accelerate early-stage life sciences R&D. Use with Cowork or install directly in Claude Code.

This plugin consolidates 11 MCP server integrations and 5 analysis skills into a single package for life science researchers.

What's Included

MCP Servers (Data Sources & Tools)

If you see unfamiliar placeholders or need to check which tools are connected, see CONNECTORS.md.

Provider	What It Does	Category/Placeholder
U.S. National Library of Medicine	Search biomedical literature and research articles	~~literature
deepsense.ai	Access preprints from bioRxiv and medRxiv	~~literature
Consensus	AI-powered search and synthesis of peer-reviewed research	~~literature
John Wiley & Sons	Access academic research and publications	~~journal access
Sage Bionetworks	Collaborative research data management	~~data repository
deepsense.ai	Bioactive drug-like compound database	~~chemical database
OpenTargets	Drug target discovery and prioritization	~~drug targets
deepsense.ai	NIH/NLM clinical trial registry	~~clinical trials
BioRender	Scientific illustration creation	~~scientific illustration
Owkin	AI for biology — histopathology and drug discovery	~~AI research
Benchling*	Lab data management platform	~~lab platform

Optional Binary MCP Servers

These require a separate binary download:

• 10X Genomics txg-mcp (~~genomics platform) — Cloud analysis data and workflows (GitHub)
• ToolUniverse (~~tool database) — AI tools for scientific discovery from Harvard MIMS (GitHub)

Skills (Analysis Workflows)

Single-Cell RNA QC

Automated quality control for scRNA-seq data following scverse best practices. Supports .h5ad and .h5 files with MAD-based filtering and comprehensive visualizations.

scvi-tools

Deep learning toolkit for single-cell omics. Covers scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, and sysVI models for integration, batch correction, label transfer, and multi-modal analysis.

Nextflow Pipelines

Run nf-core bioinformatics pipelines on local or public GEO/SRA sequencing data:

• rnaseq — Gene expression and differential expression
• sarek — Germline and somatic variant calling (WGS/WES)
• atacseq — Chromatin accessibility analysis

Instrument Data to Allotrope

Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) format. Supports 40+ instrument types including cell counters, spectrophotometers, plate readers, qPCR, and chromatography systems.

Scientific Problem Selection

Systematic framework for research problem selection based on Fischbach & Walsh's framework. Includes 9 skills covering ideation, risk assessment, optimization, decision trees, adversity planning, and synthesis.

Getting Started

# Install the plugin
/install anthropics/knowledge-work-plugins bio-research

# Run the start command to see available tools
/start

Common Workflows

Literature Review Search ~~literature database for papers, access full-text through ~~journal access, and create figures with ~~scientific illustration.

Single-Cell Analysis Run QC on scRNA-seq data, then use scvi-tools for integration, batch correction, and cell type annotation.

Sequencing Pipeline Download public data from GEO/SRA, run nf-core pipelines (RNA-seq, variant calling, ATAC-seq), and verify outputs.

Drug Discovery Search ~~chemical database for bioactive compounds, use ~~drug target database for target prioritization, and review clinical trial data.

Research Strategy Pitch a new idea, troubleshoot a stuck project, or evaluate strategic decisions using the scientific problem selection framework.

License

Skills are licensed under Apache 2.0. MCP servers are provided by their respective authors — see individual server documentation for terms.