methods-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
| logging | {} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| extensions | {
"io.modelcontextprotocol/ui": {}
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| healthA | Return a small health report — confirms the server is alive and configured. |
| get_paper_metadataA | Resolve an arXiv ID/URL, bioRxiv URL, DOI, or generic URL to canonical metadata. For arXiv inputs this hits the arXiv export API to fetch title/authors/abstract. Other sources return the resolved URL with empty bibliographic fields (cheap by design). |
| fetch_paper_textB | Return best-effort full text + section split for a paper. prefer: one of "auto" (default), "html" (force ar5iv HTML — arXiv only), or "pdf". Sections are normalised to lowercase canonical names: abstract, introduction, methods, experiments, results, discussion, conclusion, limitations, related_work. |
| extract_methodsA | Extract a structured methods object from a paper. Pulls full text, isolates the methods-relevant section(s), then asks Claude (default: claude-sonnet-4-6) to fill out a Pydantic schema with steps, reagents, equipment, and analyses. Validation-enforced — invalid responses trigger one repair attempt before raising. Requires ANTHROPIC_API_KEY in the server's environment. |
| find_code_repoA | Discover the code repo (if any) associated with a paper. Strategy: scan the paper's full text and abstract for github.com URLs; fall back to Papers With Code lookup for arXiv papers. |
| assess_repo_reproducibilityA | Heuristic, no-clone reproducibility assessment of a GitHub repo. Returns a verdict (likely-reproducible / partial / unlikely / insufficient-info) plus weighted signals: README quality, dependency files, fixture data, notebooks, figure-generating scripts, recent maintenance, license. No code is downloaded or executed. Set GITHUB_TOKEN to raise the API rate limit. |
| summarize_paperA | Generate an LLM summary of a paper in one of three modes. abstract = 2-3 sentences close to the authors' framing. tldr = one-line takeaway. exec = executive summary (what / found / why-it-matters). |
| methods_repro_reviewA | Resolve a paper + extract methods + find its code repo + assess reproducibility — in one call. Returns a
For the meaning of numeric scores and verdict buckets, see the "Scores & verdicts explained" section of the README. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 8 tools
Each tool has a clearly distinct purpose: health check, metadata resolution, text fetching, methods extraction, code repo discovery, reproducibility assessment, summarization, and a combined orchestration tool. The composite tool is explicitly described as a one-call pipeline, so no confusion with individual steps.
Most tools follow a verb_noun pattern (get, fetch, extract, find, assess, summarize), but 'health' is a bare noun and 'methods_repro_review' is a noun phrase without a verb. These deviations break the otherwise consistent snake_case convention.
8 tools is well within the ideal range, and each tool maps to a specific stage in the paper analysis pipeline. No redundancy or unnecessary duplication, and the count feels appropriately scoped for the server's reproducibility-focused purpose.
The tool surface covers the entire workflow from paper resolution to reproducibility assessment, including a composite endpoint. Minor gaps like search or fine-grained section access are absent but not essential to the stated domain, making the set largely complete.