How do I install the General Biorxiv Search skill?

Run npx skillmds@latest add learningmatter-mit/general-biorxiv-search in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is General Biorxiv Search safe to use?

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Which AI agents work with General Biorxiv Search?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is General Biorxiv Search free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published General Biorxiv Search?

learningmatter-mit (@learningmatter-mit) published this skill. Their other Agent Skills are listed on their SkillMD profile.

General Biorxiv Search by learningmatter-mit

Name: General Biorxiv Search
Rating: 4.5 (4 reviews)
Author: learningmatter-mit

File contents

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

---name: general-biorxiv-searchdescription: Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.---# bioRxiv / medRxiv Search## GoalSearch 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.```bash# Env: base-agentpython .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "protein folding" --max_results 5 --output protein_folding.json```### 2. Date Range SearchRetrieve preprints posted in a specific date range, with optional keyword/category filter.```bash# Env: base-agentpython .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 FilterFilter by subject category (use shortcuts or full names).```bash# Env: base-agentpython .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 medRxivUse `--server medrxiv` for medical preprints.```bash# Env: base-agentpython .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "COVID vaccine efficacy" --server medrxiv --max_results 5 --output covid_vaccine.json```### 5. DOI LookupRetrieve metadata for a specific preprint by DOI.```bash# Env: base-agentpython .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --doi 10.1101/2021.01.01.000000 --output paper.json```## Examples### Recent Neuroscience Papers```bash# Env: base-agentpython .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --category neuroscience --days 7 --max_results 5```### Genomics Papers with Keyword Filter```bash# Env: base-agentpython .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](https://github.com/learningmatter-mit)

Frequently asked questions

General Biorxiv Search