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Agent skill

General Biorxiv Search

by learningmatter-mit in learningmatter-mit/AtomisticSkills

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

MITAuto-check passedResearch & Science

Install General Biorxiv Search

skills CLI
$ npx skills add learningmatter-mit/AtomisticSkills --skill general-biorxiv-search -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install learningmatter-mit/AtomisticSkills general-biorxiv-search --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/general-biorxiv-search .claude/skills/general-biorxiv-search && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
general-biorxiv-search
GitHub stars
176
Token cost
~854 tokens
SKILL.md length
215 words
Files
2 (incl. scripts)
Skills in repo
129
Repo updated
First seen
Licence
MIT

At a glance

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

  • Works in 5 steps: Keyword Search (Recent Papers) → Date Range Search → Category Filter → …
  • Tasks that involve Academic paper search
  • SKILL.md covers Goal, Instructions, Examples and Constraints
  • Runs Python scripts from its folder

What it does

General Biorxiv Search is an agent skill from learningmatter-mit/AtomisticSkills. Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.

Its SKILL.md is about 850 tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including scripts (for example `scripts/biorxiv_search.py`).

It sits in Research & Science, covering Academic paper search. The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.

When your agent uses it

  • Tasks that involve Academic paper search

Example prompts

  • “/general-biorxiv-search”

Requirements

  • Python 3

Workflow steps

5 steps, taken from the step headings in SKILL.md.

  1. Keyword Search (Recent Papers)
  2. Date Range Search
  3. Category Filter
  4. Search medRxiv
  5. DOI Lookup

What it can do on your machine

Read from SKILL.md and the folder at commit 6257444. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • github.com

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

General Biorxiv Search loads about 854 tokens when it runs. Until then it costs about 32 tokens; SKILL.md has 215 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~32
When it runs · the whole SKILL.md, loaded when a task matches
~854

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 215 words, ~854 tokens.

Download SKILL.mdSave it as .claude/skills/general-biorxiv-search/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.
name
general-biorxiv-search
description
Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.
metadata.category
general
metadata.venv
cpu

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.

bash
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/biorxiv_search.py "protein folding" --max_results 5 --output protein_folding.json

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

bash
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/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).

bash
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/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.

bash
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/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.

bash
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/biorxiv_search.py --doi 10.1101/2021.01.01.000000 --output paper.json

Examples

Recent Neuroscience Papers
bash
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/biorxiv_search.py --category neuroscience --days 7 --max_results 5
Genomics Papers with Keyword Filter
bash
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/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 the cpu 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

© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 1 other file (scripts) in skills/general-biorxiv-search of learningmatter-mit/AtomisticSkills.

  • SKILL.md
  • scripts/biorxiv_search.py

Open the folder on GitHubat commit 6257444

Compare with similar skills

General Biorxiv Search next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

General Biorxiv Search compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
General Biorxiv Search this skilllearningmatter-mit/AtomisticSkills176—~854Automated safety check: PassMIT
Read arXiv Paperkarpathy/nanochat59k1 repos~494Automated safety check: PassMIT
Perplexity Web Searchdavila7/claude-code-templates32k11 repos~3.5kAutomated safety check: NotesMIT
Literature Reviewneflibata-feng/MyArxiv-Agent12620 repos~5.9kAutomated safety check: NotesMIT
Openalex Databaseneflibata-feng/MyArxiv-Agent12612 repos~3kAutomated safety check: PassCustom licence
Citation ManagementK-Dense-AI/claude-scientific-writer2.4k2 repos~3.9kAutomated safety check: NotesMIT

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Categories

Questions about General Biorxiv Search

What does General Biorxiv Search do?

Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research. General Biorxiv Search is an agent skill from learningmatter-mit/AtomisticSkills. Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.

When should I use General Biorxiv Search?

General Biorxiv Search fits situations like: tasks that involve Academic paper search.

How do I install General Biorxiv Search in Claude Code?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill general-biorxiv-search -a claude-code`. Or copy the skill folder (skills/general-biorxiv-search in learningmatter-mit/AtomisticSkills) into .claude/skills/general-biorxiv-search in your project. Claude Code loads it when a task matches its description.

How do I install General Biorxiv Search in Codex?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill general-biorxiv-search -a codex`. Or copy the skill folder (skills/general-biorxiv-search in learningmatter-mit/AtomisticSkills) into .agents/skills/general-biorxiv-search in your project. Codex loads it when a task matches its description.

Can I use General Biorxiv Search in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add learningmatter-mit/AtomisticSkills --skill general-biorxiv-search -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/general-biorxiv-search, .gemini/skills/general-biorxiv-search, .github/skills/general-biorxiv-search and .opencode/skills/general-biorxiv-search in your project.

What does General Biorxiv Search need to run?

Going by SKILL.md and its folder, General Biorxiv Search needs Python for the scripts in its folder. Our summary lists: Python 3.

Does General Biorxiv Search access the network?

SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.

Is General Biorxiv Search safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does General Biorxiv Search use?

General Biorxiv Search is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does General Biorxiv Search use?

About 854 tokens (SKILL.md is roughly 3.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to General Biorxiv Search?

Skills that share tags, products or a category with General Biorxiv Search: Read arXiv Paper (karpathy/nanochat, 59k stars), Perplexity Web Search (davila7/claude-code-templates, 32k stars), Literature Review (neflibata-feng/MyArxiv-Agent, 126 stars) and Openalex Database (neflibata-feng/MyArxiv-Agent, 126 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains General Biorxiv Search?

learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.

Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.