methods-mcp
Structured methods extraction for academic papers, designed for the Worldwide AI Science Fellowship build challenge. Exposes eight tools that resolve paper URLs (arXiv, DOI) into canonical metadata, full text with section splits, Pydantic-validated methods objects (steps, reagents, equipment, analyses), and associated code repositories discovered via Papers With Code. The assess_repo_reproducibility tool scores GitHub repos without cloning by analyzing README presence, dependency files, notebooks, figure scripts, and maintenance signals through the GitHub REST API. The composite methods_repro_review tool runs the full pipeline in one call and returns a plain-English narrative alongside structured data. Uses Claude Sonnet 4 for extraction via tool-use validation with one repair attempt on schema failures. Reach for this when you need on-demand reproducibility verdicts that return in seconds rather than the 30-minute runtimes of execution-based pipelines.
- tools
- 8
- auth
- Secret needed
- transport
- STDIO
- env vars
- 3
- last updated
- Apr 15, 2026
Tools
8 toolsPublic tool metadata for what this MCP can expose to an agent.
healthServer liveness + config check.
Server liveness + config check.
No parameter schema in public metadata yet.
get_paper_metadataResolve URL / arXiv ID / DOI to canonical metadata.
Resolve URL / arXiv ID / DOI to canonical metadata.
No parameter schema in public metadata yet.
fetch_paper_textFull text + section split. Defaults to ar5iv HTML for arXiv papers (cheap, structured), PDF fallback otherwise.
Full text + section split. Defaults to ar5iv HTML for arXiv papers (cheap, structured), PDF fallback otherwise.
No parameter schema in public metadata yet.
extract_methodsLLM-driven, Pydantic-validated structured methods extraction.
LLM-driven, Pydantic-validated structured methods extraction.
No parameter schema in public metadata yet.
find_code_repoDiscover the paper's code repo via paper text → abstract → Papers With Code.
Discover the paper's code repo via paper text → abstract → Papers With Code.
No parameter schema in public metadata yet.
assess_repo_reproducibilityHeuristic, no-clone reproducibility assessment via the GitHub REST API.
Heuristic, no-clone reproducibility assessment via the GitHub REST API.
No parameter schema in public metadata yet.
summarize_paperLLM summary in three depths.
LLM summary in three depths.
No parameter schema in public metadata yet.
methods_repro_reviewComposite — metadata + methods + repo + repro in one call.
Composite — metadata + methods + repo + repro in one call.
No parameter schema in public metadata yet.
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ANTHROPIC_API_KEY*secretRequired for LLM-driven extraction tools (extract_methods, summarize_paper, methods_repro_review).
GITHUB_TOKENsecretOptional. Raises the GitHub REST API rate limit used by reproducibility assessment.
METHODS_MCP_MODELOverride the default Claude model (default: claude-sonnet-4-6).
Readme
methods-mcp
Lightweight, on-demand MCP server for structured methods extraction + reproducibility heuristics on academic papers. Built for the Worldwide AI Science Fellowship build challenge.
⚠️ Status: alpha (0.1.x). The tool surface and output shapes may shift between minor versions. Pin to an exact version in production. Bug reports very welcome via GitHub Issues.
Quick demo
$ uvx --from methods-mcp methods-mcp --version
methods-mcp 0.1.6
# In a Claude Code session:
> /mcp add methods-mcp methods-mcp
> Run methods_repro_review on https://arxiv.org/abs/2509.06917
→ tool: methods_repro_review({"input_str":"https://arxiv.org/abs/2509.06917"})
Details
- Repository
- github.com/flynnlachendro/methods-mcp
- Website
- github.com/FlynnLachendro/methods-mcp
- Package
methods-mcp- Transport
- STDIO
- Auth
- Required
- Registry
- MCP registry, active