A side-by-side look at the Noodle Biomedical Literature Discovery MCP and Codeindex 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.status, search, find_symbol.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 78/100 · Great | 57/100 · 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 | 3 |
| Directory activity | 6 views 0 installs 0 upvotes | 2 views 0 installs 0 upvotes |
| Tools | 7 | 16 |
| Full listing | View Noodle Biomedical Literature Discovery MCP | View Codeindex |
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.statusIndex stats: file count, symbol count, indexing state, token savings %, the indexed `workspace` and whether a `watcher` is livesearchTrigram-accelerated full-text search across all indexed filesfind_symbolFind symbol definitions (functions, structs, classes…) by namefind_wordExact word/identifier lookup in the inverted word indexfind_callersCall sites of a symbol, each with the function that holds it. Matched by name, so a same-named definition elsewhere is includedget_outlineStructural outline of a file (symbols, line counts)get_treeDirectory tree with file metadataget_importsWhat files does a given file import/depend onget_imported_byReverse dependencies — who imports this fileget_change_impactTransitive blast radius: what breaks if a file changesplan_changeFull refactor plan for a symbol or file — definitions, callers, file role, literals, blast radiusget_hot_filesRecently changed files sorted by recencyPaste 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": {
"codeindex": {
"command": "npx",
"args": [
"-y",
"@munhq/codeindex"
]
}
}
}