Side-by-Side Model Context Protocol Comparison
Biosamples vs Biostudies
In-depth architectural comparison of the Biosamples and Biostudies MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.
At a Glance & Executive Verdict
Biosamples
Developer Tools · Remote HTTP/SSE
Quality: 45/100 (Fair) | Auth: No auth required
Biostudies
Developer Tools · Remote HTTP/SSE
Quality: 45/100 (Fair) | Auth: No auth required
Verdict Summary: Choose Biosamples if you need specialized Developer Tools tools running via a hosted cloud SSE transport. Choose Biostudies if your workspace requires Developer Tools integration with remote web transport. Both servers can be configured concurrently in your client's
mcpServers manifest.Which MCP Server Should You Choose?
B
Choose Biosamples when:
- You need dedicated capabilities in the Developer Tools domain.
- You prefer remote streaming HTTP/SSE transport architecture.
- Your security boundary fits: No auth required (Free / Open Source).
- Primary tools included: search_samples, get_sample.
B
Choose Biostudies when:
- You need dedicated capabilities in the Developer Tools domain.
- You prefer remote streaming HTTP/SSE transport architecture.
- Your security boundary fits: No auth required (Free / Open Source).
- Primary tools included: search_studies, get_study.
Feature & Specification Comparison
Tools & Capabilities Breakdown
Biosamples Tools (2)
search_samples
Search EBI BioSamples — metadata for biological samples (cell lines, tissues, organisms) referenced across EBI archives. Free-text search by organism, tissue, or keyword; returns matching samples with accession, name, organism, and release date. Keyless.
get_sample
Fetch a single EBI BioSamples record by accession. Returns the sample name, dates, taxId, organism, and a flattened map of its characteristics (organism, tissue, sex, cell type, etc.). Keyless.
Biostudies Tools (2)
search_studies
Search EBI BioStudies — a keyless database of biological study descriptions that links across EBI archives (ArrayExpress, PRIDE, etc.). Find studies by keyword and get accession, title, authors, type, release date, and link/file counts.
get_study
Get the metadata for a single EBI BioStudies study by accession (e.g. "S-EPMC6010251"). Returns the title, flattened attributes (abstract, release date, data source, etc.), and counts of links and subsections. EBI BioStudies links across EBI archives. Keyless.
Ready-to-Paste Client Configurations
Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).
Biosamples Configuration
Biostudies Configuration