A side-by-side look at the Noodle Biomedical Literature Discovery MCP and Cbioportal MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Noodle Biomedical Literature Discovery MCP for biology & bioinformatics work over a hosted endpoint; choose for biology & bioinformatics as a local process. You can also run both side by side in one block.
mcpServerssearch_biomedical_literature, get_publication_details, get_work_details.search_studies, get_study, get_gene.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 78/100 · Great | 51/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Remote HTTP/SSE | Local subprocess (stdio) |
| Auth | No auth required | Not declared |
| Pricing | Free | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Verified | Community listing |
| GitHub stars | 0 | 0 |
| Directory activity | 6 views 0 installs 0 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 7 | 4 |
| Full listing | View Noodle Biomedical Literature Discovery MCP | View Cbioportal |
search_biomedical_literatureSemantically search Noodle's public PubMed-derived biomedical corpus. Include known PMID, DOI, or PMCID identifiers in the query so they can act as exact anchors. Results are for literature discovery and professional review, not diagnosis or treatment.get_publication_detailsRetrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.get_work_detailsRetrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.get_publication_neighborhoodRetrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.get_work_neighborhoodRetrieve the bounded citation and semantic neighborhood around one Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.get_corpus_summaryReturn public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.support_helenaLearn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.search_studiesSearch public cancer genomics studies in cBioPortal (TCGA, CPTAC, MSK, etc.) by keyword. Matches study name, study id, or cancer-type id (case-insensitive). Returns study ids, names, cancer types, and sample counts. Keyless, open data.get_studyGet full details for one cBioPortal cancer study by its study id (e.g. "brca_tcga_pub", "glioma_mskcc_2019"), including description, cancer type, sample count, PMID, and citation.get_geneResolve a gene to its Entrez gene id and canonical info via cBioPortal. Accepts a HUGO symbol (e.g. "TP53", "BRCA1") or an Entrez gene id. Returns entrez_gene_id, symbol, and type.list_cancer_typesList cancer types defined in cBioPortal (id, display name, parent type). Useful for resolving cancer-type ids used by studies.Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
{
"mcpServers": {
"noodle-biomedical-literature-discovery-mcp": {
"url": "https://api.helena.bio/noodle/v1/mcp"
}
}
}
{
"mcpServers": {
"cbioportal": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-cbioportal"
]
}
}
}