Remote MCP Servers
#### PubMed
Plugin ID: pubmed@life-sciences
Search and access biomedical literature and research articles from PubMed.
Requirements: None - accessible to all users
#### BioRender
Plugin ID: biorender@life-sciences
Create and access scientific illustrations and diagrams.
Requirements: Free BioRender account (https://www.biorender.com)
#### Synapse.org
Plugin ID: synapse@life-sciences
Collaborative research data management platform by Sage Bionetworks.
Requirements: Free Synapse account (https://www.synapse.org)
#### Scholar Gateway (Wiley)
Plugin ID: wiley-scholar-gateway@life-sciences
Access academic research and publications from Wiley's Scholar Gateway.
Requirements: Free Scholar Gateway account
Local MCP Servers (MCPB)
#### 10x Genomics Cloud
Plugin ID: 10x-genomics@life-sciences
Access 10x Genomics Cloud analysis data and workflows.
Requirements:
- 10x Genomics Cloud account (https://www.10xgenomics.com/products/cloud-analysis)
- Access token (generate from: https://cloud.10xgenomics.com/account/security)
- Note: Only useful if you have analysis data in your account
Skills
#### Single-Cell RNA-seq Quality Control
Plugin ID: single-cell-rna-qc@life-sciences
Automated quality control workflow for single-cell RNA-seq data following scverse best practices. Performs MAD-based filtering with comprehensive visualizations.
#### Instrument Data to Allotrope
Plugin ID: instrument-data-to-allotrope@life-sciences
Convert instrument data to Allotrope Simple Model (ASM) format for standardized data exchange and analysis.
#### Nextflow Development
Plugin ID: nextflow-development@life-sciences
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on local or public GEO/SRA sequencing data. Designed for bench scientists who need to run large-scale omics analyses without specialized bioinformatics training.
Supported pipelines:
- rnaseq: Gene expression and differential expression analysis
- sarek: Germline and somatic variant calling (WGS/WES)
- atacseq: Chromatin accessibility analysis
Features:
- Download public datasets from GEO/SRA
- Auto-detect data types and suggest appropriate pipelines
- Generate pipeline-compatible samplesheets
- Environment validation and troubleshooting guidance
Requirements: Docker and Nextflow installed locally
#### scvi-tools
Plugin ID: scvi-tools@life-sciences
Deep learning toolkit for single-cell omics analysis using scvi-tools. Includes model selection guidance, training workflows, and integration pipelines for scVI, scANVI, totalVI, PeakVI, MultiVI, and more.
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