wehub-resource-sync
84 lines
4.2 KiB
Markdown
84 lines
4.2 KiB
Markdown
# Bio-Research Plugin
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Connect to preclinical research tools and databases (literature search, genomics analysis, target prioritization) to accelerate early-stage life sciences R&D. Use with [Cowork](https://claude.com/product/cowork) or install directly in Claude Code.
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This plugin consolidates 11 MCP server integrations and 5 analysis skills into a single package for life science researchers.
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## What's Included
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### MCP Servers (Data Sources & Tools)
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> If you see unfamiliar placeholders or need to check which tools are connected, see [CONNECTORS.md](CONNECTORS.md).
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| Provider | What It Does | Category/Placeholder |
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|----------|-------------|---------------------|
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| U.S. National Library of Medicine | Search biomedical literature and research articles | `~~literature` |
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| deepsense.ai | Access preprints from bioRxiv and medRxiv | `~~literature` |
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| Consensus | AI-powered search and synthesis of peer-reviewed research | `~~literature` |
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| John Wiley & Sons | Access academic research and publications | `~~journal access` |
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| Sage Bionetworks | Collaborative research data management | `~~data repository` |
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| deepsense.ai | Bioactive drug-like compound database | `~~chemical database` |
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| OpenTargets | Drug target discovery and prioritization | `~~drug targets` |
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| deepsense.ai | NIH/NLM clinical trial registry | `~~clinical trials` |
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| BioRender | Scientific illustration creation | `~~scientific illustration` |
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| Owkin | AI for biology — histopathology and drug discovery | `~~AI research` |
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| Benchling\* | Lab data management platform | `~~lab platform` |
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### Optional Binary MCP Servers
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These require a separate binary download:
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- **10X Genomics txg-mcp** (`~~genomics platform`) — Cloud analysis data and workflows ([GitHub](https://github.com/10XGenomics/txg-mcp/releases))
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- **ToolUniverse** (`~~tool database`) — AI tools for scientific discovery from Harvard MIMS ([GitHub](https://github.com/mims-harvard/ToolUniverse/releases))
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### Skills (Analysis Workflows)
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#### Single-Cell RNA QC
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Automated quality control for scRNA-seq data following scverse best practices. Supports `.h5ad` and `.h5` files with MAD-based filtering and comprehensive visualizations.
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#### scvi-tools
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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.
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#### Nextflow Pipelines
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Run nf-core bioinformatics pipelines on local or public GEO/SRA sequencing data:
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- **rnaseq** — Gene expression and differential expression
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- **sarek** — Germline and somatic variant calling (WGS/WES)
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- **atacseq** — Chromatin accessibility analysis
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#### Instrument Data to Allotrope
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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.
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#### Scientific Problem Selection
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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.
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## Getting Started
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```bash
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# Install the plugin
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/install anthropics/knowledge-work-plugins bio-research
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# Run the start command to see available tools
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/start
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```
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## Common Workflows
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**Literature Review**
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Search ~~literature database for papers, access full-text through ~~journal access, and create figures with ~~scientific illustration.
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**Single-Cell Analysis**
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Run QC on scRNA-seq data, then use scvi-tools for integration, batch correction, and cell type annotation.
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**Sequencing Pipeline**
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Download public data from GEO/SRA, run nf-core pipelines (RNA-seq, variant calling, ATAC-seq), and verify outputs.
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**Drug Discovery**
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Search ~~chemical database for bioactive compounds, use ~~drug target database for target prioritization, and review clinical trial data.
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**Research Strategy**
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Pitch a new idea, troubleshoot a stuck project, or evaluate strategic decisions using the scientific problem selection framework.
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## License
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Skills are licensed under Apache 2.0. MCP servers are provided by their respective authors — see individual server documentation for terms.
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