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SKILL verified MIT Self-run

General Biorxiv Search

skill-learningmatter-mit-atomisticskills-general-biorxiv-search · by learningmatter-mit

Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.

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Install

$ agentstack add skill-learningmatter-mit-atomisticskills-general-biorxiv-search

✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

View the full security report →

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Reliability & compatibility

✓ Security review passed
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Declared compatibility

Claude CodeClaude Desktop

Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.

Preview Execution monitoring

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About

bioRxiv / medRxiv Search

Goal

Search and retrieve preprint metadata (title, authors, abstract, DOI, category, etc.) from bioRxiv and medRxiv using the official REST API. Supports keyword filtering, subject category filtering, date-range search, and DOI lookup.

Instructions

1. Keyword Search (Recent Papers)

Search last 30 days for papers matching keywords in title/abstract.

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "protein folding" --max_results 5 --output protein_folding.json

2. Date Range Search

Retrieve preprints posted in a specific date range, with optional keyword/category filter.

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "CRISPR" --start 2025-01-01 --end 2025-06-01 --max_results 10 --output crispr_2025.json

3. Category Filter

Filter by subject category (use shortcuts or full names).

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --category neuroscience --days 14 --max_results 10

Supported Category Shortcuts:

  • biochemistry, bioinformatics, biophysics
  • cancer → cancer_biology
  • cell-bio → cell_biology
  • dev-bio → developmental_biology
  • ecology, epidemiology, evolution
  • genetics, genomics, immunology
  • microbiology, molecular-bio → molecular_biology
  • neuroscience, pharmacology, physiology
  • plant-bio → plant_biology
  • synthetic-bio → synthetic_biology
  • systems-bio → systems_biology

4. Search medRxiv

Use --server medrxiv for medical preprints.

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "COVID vaccine efficacy" --server medrxiv --max_results 5 --output covid_vaccine.json

5. DOI Lookup

Retrieve metadata for a specific preprint by DOI.

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --doi 10.1101/2021.01.01.000000 --output paper.json

Examples

Recent Neuroscience Papers

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --category neuroscience --days 7 --max_results 5

Genomics Papers with Keyword Filter

# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "single cell sequencing" --category genomics --start 2024-01-01 --end 2024-12-31 --max_results 10 --output scrna_2024.json

Constraints

  • No official rate limit specified by bioRxiv API; script includes 0.5s delay per request as courtesy.
  • Pagination: API returns 30 results per page; script paginates automatically up to --max_results.
  • Keyword filtering: Done client-side (API lacks full-text search); date range must be broad enough to surface relevant papers.
  • Environment: Requires base-agent conda environment.
  • Dependencies: Uses requests.
  • Metadata fields: DOI, URL, title, authors, abstract, date, category, server, version, license, published journal (if available).

Author: mlederbauer Contact: GitHub @learningmatter-mit

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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