Read arXiv Paper
karpathy/nanochat
Fetches the TeX source of an arXiv paper from its URL, reads it and writes a markdown summary tied to the nanochat project.
Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries.
Install Biorxiv Search
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill biorxiv-search -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills biorxiv-search --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/omics/biorxiv-search .claude/skills/biorxiv-search && rm -rf skills-srcUse ~/.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/
Install the "biorxiv-search" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/biorxiv-search into .claude/skills/biorxiv-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biorxiv-search", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/biorxiv-searchType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill biorxiv-search -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills biorxiv-search --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/omics/biorxiv-search .agents/skills/biorxiv-search && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "biorxiv-search" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/biorxiv-search into .agents/skills/biorxiv-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biorxiv-search", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill biorxiv-search -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills biorxiv-search --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/omics/biorxiv-search .cursor/skills/biorxiv-search && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "biorxiv-search" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/biorxiv-search into .cursor/skills/biorxiv-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biorxiv-search", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/BioTender-max/awesome-bio-agent-skills.git --path skills/omics/biorxiv-search--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill biorxiv-search -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills biorxiv-search --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/omics/biorxiv-search .gemini/skills/biorxiv-search && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "biorxiv-search" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/biorxiv-search into .gemini/skills/biorxiv-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biorxiv-search", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install BioTender-max/awesome-bio-agent-skills biorxiv-searchInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill biorxiv-search -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/omics/biorxiv-search .github/skills/biorxiv-search && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "biorxiv-search" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/biorxiv-search into .github/skills/biorxiv-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biorxiv-search", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill biorxiv-search -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills biorxiv-search --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/omics/biorxiv-search .opencode/skills/biorxiv-search && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "biorxiv-search" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/biorxiv-search into .opencode/skills/biorxiv-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biorxiv-search", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
biorxiv-search- GitHub stars
- 200
- Token cost
- ~2.4k tokens
- SKILL.md length
- 1,123 words
- Files
- 4 (incl. scripts)
- Skills in repo
- 23
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries.
- Works in 11 steps: Prefer this skill when the request is… → Use the bundled CLI → The official bioRxiv API does not… → …
- You need recent biology preprints
- SKILL.md covers Instructions, Quick Reference, Input Requirements and Search Semantics, plus 5 more sections
- Runs Python scripts from its folder; reaches api.biorxiv.org
What it does
Biorxiv Search is an agent skill from BioTender-max/awesome-bio-agent-skills. Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries. Use when you need recent biology preprints, bioRxiv-native metadata, date-range scans, DOI lookups, or author shortlists that may not yet appear in peer-reviewed literature indexes.
Its SKILL.md is about 2.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts (for example `agents/openai.yaml` and `scripts/search.py`).
It sits in Research & Science, covering Academic paper search. The repository describes itself as: A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
When your agent uses it
- You need recent biology preprints
- BioRxiv-native metadata
- Date-range scans
- Author shortlists that may not yet appear in peer-reviewed literature indexes
Example prompts
- “/biorxiv-search”
Requirements
- Python 3
Workflow steps
11 steps, taken from the first numbered list in SKILL.md.
- Prefer this skill when the request is about bioRxiv-native preprints, recent biology submissions, or preprint metadata that may lag in…
- Use the bundled CLI
- The official bioRxiv API does not provide a general server-side keyword search endpoint.
- When keywords are provided, search title, abstract, and authors by default.
- Keep the search window bounded.
- Use --category when the topic should stay narrow.
- Use --author for author-specific requests.
- The API paginates 100 records at a time.
- By default, the CLI collapses multiple versions of the same preprint and keeps the latest version for each DOI.
- Treat the API output as discovery metadata.
- If the user wants peer-reviewed biomedical literature or PMC full text rather than bioRxiv preprints, use polars-dovmed instead.
What it can do on your machine
Read from SKILL.md and the folder at commit 8cbdd18. 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 2 files in scripts/ (Python), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
api.biorxiv.org
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
Biorxiv Search loads about 2.4k tokens when it runs. Until then it costs about 81 tokens; SKILL.md has 1,123 words of instructions outside code blocks.
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
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 1,123 words (~2,380 tokens).
“Search bioRxiv through its official API for recent-preprint discovery, date-range scans, DOI lookups, author shortlisting, and local keyword filtering over title, abstract, and author metadata.”
- name
- biorxiv-search
Files
SKILL.md and 3 other files (scripts) in skills/omics/biorxiv-search of BioTender-max/awesome-bio-agent-skills.
- SKILL.md
- agents/openai.yaml
- scripts/search
- scripts/search.py
Open the folder on GitHubat commit 8cbdd18
Compare with similar skills
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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Biorxiv Search this skillBioTender-max/awesome-bio-agent-skills | 200 | — | ~2.4k | Automated safety check: Pass | Custom licence | |
| Read arXiv Paperkarpathy/nanochat | 59k | 1 repos | ~494 | Automated safety check: Pass | MIT | |
| Perplexity Web Searchdavila7/claude-code-templates | 33k | 11 repos | ~3.5k | Automated safety check: Notes | MIT | |
| Literature Reviewneflibata-feng/MyArxiv-Agent | 126 | 20 repos | ~5.9k | Automated safety check: Notes | MIT | |
| Openalex Databaseneflibata-feng/MyArxiv-Agent | 126 | 12 repos | ~3k | Automated safety check: Pass | Custom licence | |
| Citation ManagementK-Dense-AI/claude-scientific-writer | 2.4k | 2 repos | ~3.9k | Automated safety check: Notes | MIT |
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Categories
Questions about Biorxiv Search
What does Biorxiv Search do?
Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries. Biorxiv Search is an agent skill from BioTender-max/awesome-bio-agent-skills. Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries.
When should I use Biorxiv Search?
Biorxiv Search fits situations like: you need recent biology preprints; bioRxiv-native metadata; date-range scans; author shortlists that may not yet appear in peer-reviewed literature indexes.
How do I install Biorxiv Search in Claude Code?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill biorxiv-search -a claude-code`. Or copy the skill folder (skills/omics/biorxiv-search in BioTender-max/awesome-bio-agent-skills) into .claude/skills/biorxiv-search in your project. Claude Code loads it when a task matches its description.
How do I install Biorxiv Search in Codex?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill biorxiv-search -a codex`. Or copy the skill folder (skills/omics/biorxiv-search in BioTender-max/awesome-bio-agent-skills) into .agents/skills/biorxiv-search in your project. Codex loads it when a task matches its description.
Can I use 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 BioTender-max/awesome-bio-agent-skills --skill 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/biorxiv-search, .gemini/skills/biorxiv-search, .github/skills/biorxiv-search and .opencode/skills/biorxiv-search in your project.
What does Biorxiv Search need to run?
Going by SKILL.md and its folder, Biorxiv Search needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Biorxiv Search access the network?
SKILL.md names 1 domain. In commands or code: api.biorxiv.org; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.
Is 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 Biorxiv Search use?
Biorxiv Search has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Biorxiv Search use?
About 2.4k tokens (SKILL.md is roughly 9.5k 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 Biorxiv Search?
Skills that share tags, products or a category with Biorxiv Search: Read arXiv Paper (karpathy/nanochat, 59k stars), Perplexity Web Search (davila7/claude-code-templates, 33k 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 Biorxiv Search?
BioTender-max (a GitHub user) maintains it in BioTender-max/awesome-bio-agent-skills, which has 200 GitHub stars. The repository holds 23 skills in this directory. The repository was last updated on July 1, 2026.
Source: BioTender-max/awesome-bio-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.