synapse

This marketplace provides MCP (Model Context Protocol) servers and skills for life sciences tools. Install these plugins to access specialized research and analysis tools directly within Claude Code.

What's included:

• •MCP Servers: Connect to external services like PubMed, BioRender, Synapse, and more
• •Skills: Domain-specific workflows and analysis capabilities that extend Claude's expertise

Quick Start

# Add the marketplace
/plugin marketplace add anthropics/life-sciences

# Install MCP servers
/plugin install pubmed@life-sciences
/plugin install biorender@life-sciences
/plugin install synapse@life-sciences
/plugin install wiley-scholar-gateway@life-sciences
/plugin install 10x-genomics@life-sciences

# Install skills
/plugin install single-cell-rna-qc@life-sciences
/plugin install instrument-data-to-allotrope@life-sciences
/plugin install nextflow-development@life-sciences
/plugin install scvi-tools@life-sciences
/plugin install scientific-problem-selection@life-sciences

For servers requiring authentication (all except PubMed), configure credentials after installation:

1. Type /plugin in Claude Code
2. Select "Manage plugins"
3. Find your installed server
4. Select "Configure"
5. Enter required credentials
6. Restart Claude Code

Available Plugins

Remote MCP Servers

Plugin ID: pubmed@life-sciences

Search and access biomedical literature and research articles from PubMed.

Requirements: None - accessible to all users

Plugin ID: biorender@life-sciences

Create and access scientific illustrations and diagrams.

Requirements: Free BioRender account (https://www.biorender.com)

Plugin ID: synapse@life-sciences

Collaborative research data management platform by Sage Bionetworks.

Requirements: Free Synapse account (https://www.synapse.org)

Plugin ID: wiley-scholar-gateway@life-sciences

Access academic research and publications from Wiley's Scholar Gateway.

Requirements: Free Scholar Gateway account

Plugin ID: consensus@life-sciences

AI-powered search across 200M+ peer-reviewed scientific research papers, with evidence synthesis.

Requirements: Consensus account (https://consensus.app)

Plugin ID: cortellis@life-sciences

Global drug regulatory intelligence covering submissions, approvals, and guidance documents.

Requirements: Cortellis subscription (https://clarivate.com/cortellis)

Plugin ID: adisinsight@life-sciences

Drug development pipeline, clinical trials, safety, and deals intelligence.

Requirements: AdisInsight subscription (https://adisinsight.springer.com)

Local MCP Servers (MCPB)

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

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.

Plugin ID: instrument-data-to-allotrope@life-sciences

Convert instrument data to Allotrope Simple Model (ASM) format for standardized data exchange and analysis.

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

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.

Plugin ID: scientific-problem-selection@life-sciences

Systematic framework for scientific problem selection and strategic research decisions. Based on Fischbach & Walsh's methodology from Cell (2024), this skill helps researchers with project ideation, risk assessment, troubleshooting stuck projects, and strategic scientific planning.

Use cases:

• •Pitch and refine new research ideas
• •Evaluate project risks and feasibility
• •Navigate decision trees in active projects
• •Strategic research planning and problem choice

Detailed Installation

1. Add the marketplace (one time)

/plugin marketplace add https://github.com/anthropics/life-sciences.git

2. Install specific plugins

# Remote MCP servers (no configuration needed for PubMed)
/plugin install pubmed@life-sciences
/plugin install biorender@life-sciences
/plugin install synapse@life-sciences
/plugin install wiley-scholar-gateway@life-sciences

# Local MCP servers (require configuration)
/plugin install 10x-genomics@life-sciences

# Skills (no configuration needed)
/plugin install single-cell-rna-qc@life-sciences
/plugin install instrument-data-to-allotrope@life-sciences
/plugin install nextflow-development@life-sciences
/plugin install scvi-tools@life-sciences
/plugin install scientific-problem-selection@life-sciences

3. Configure credentials (if needed)

For servers requiring authentication, use the /plugin menu:

1. Type /plugin in Claude Code
2. Select "Manage plugins"
3. Find your installed server
4. Select "Configure" (if available)
5. Enter your API credentials

Or authenticate through the server's web interface when prompted.

4. Restart Claude Code

Restart to activate the MCP servers.

Authentication Requirements

• •No authentication: PubMed
• •Free account required: BioRender, Synapse, Wiley Scholar Gateway, Consensus
• •Paid/institutional account: 10x Genomics (requires data in account to be useful), Cortellis, AdisInsight

Support

For issues with:

• •Claude Code plugin system: Report in #claude-cli-feedback on Anthropic Slack
• •Individual MCP servers: Contact the respective provider's support

License

Individual MCP servers are licensed by their respective providers. See each provider's terms of service for details.

Removed Plugins

• •Benchling: Removed because Benchling uses tenant-specific URLs which are not supported by the plugin system.