Agent skill

Biorxiv Search

Search bioRxiv biology preprints with natural language queries.

Install Biorxiv Search

skills CLI

$ npx skills add wu-yc/LabClaw --skill biorxiv-search -a claude-code

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

GitHub CLI

$ gh skill install wu-yc/LabClaw 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/wu-yc/LabClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/literature/biorxiv-search .claude/skills/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/

Paste into Claude Code

Install the "biorxiv-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/literature/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

$skill-installer install https://github.com/wu-yc/LabClaw/tree/main/skills/literature/biorxiv-search

Type 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.

skills CLI

$ npx skills add wu-yc/LabClaw --skill biorxiv-search -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw biorxiv-search --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/literature/biorxiv-search .agents/skills/biorxiv-search && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "biorxiv-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/literature/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.

skills CLI

$ npx skills add wu-yc/LabClaw --skill biorxiv-search -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw biorxiv-search --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/literature/biorxiv-search .cursor/skills/biorxiv-search && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "biorxiv-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/literature/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

$ gemini skills install https://github.com/wu-yc/LabClaw.git --path skills/literature/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.

skills CLI

$ npx skills add wu-yc/LabClaw --skill biorxiv-search -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw biorxiv-search --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/literature/biorxiv-search .gemini/skills/biorxiv-search && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "biorxiv-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/literature/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.

GitHub CLI

$ gh skill install wu-yc/LabClaw biorxiv-search

Installs 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).

skills CLI

$ npx skills add wu-yc/LabClaw --skill biorxiv-search -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/literature/biorxiv-search .github/skills/biorxiv-search && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "biorxiv-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/literature/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.

skills CLI

$ npx skills add wu-yc/LabClaw --skill biorxiv-search -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install wu-yc/LabClaw biorxiv-search --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/literature/biorxiv-search .opencode/skills/biorxiv-search && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "biorxiv-search" agent skill from https://github.com/wu-yc/LabClaw/tree/main/skills/literature/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: 1.1k
Token cost: ~1.3k tokens
SKILL.md length: 316 words
Files: 1
Skills in repo: 68
Repo updated: Mar 19, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Search bioRxiv biology preprints with natural language queries.

Works in 2 steps: Node.js 18+ (uses built-in fetch) → Valyu API key from…
Tasks that involve Academic paper search
SKILL.md covers Why This Skill is Powerful, Requirements, CRITICAL: Script Path Resolution and API Key Setup Flow, plus 8 more sections
Calls jq; reaches platform.valyu.ai and api.valyu.ai

What it does

Biorxiv Search is an agent skill from wu-yc/LabClaw. Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.

Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Academic paper search. The repository describes itself as: LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists). The licence is MIT.

When your agent uses it

Tasks that involve Academic paper search

Example prompts

“/biorxiv-search”

Requirements

Python 3
Node.js

Workflow steps

2 steps, taken from the first numbered list in SKILL.md.

Node.js 18+ (uses built-in fetch)
Valyu API key from https://platform.valyu.ai ($10 free credits)

What it can do on your machine

Read from SKILL.md and the folder at commit df37802. 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
Shell commands in SKILL.md call:
- jq
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:
- platform.valyu.ai
- api.valyu.ai
- biorxiv.org
Also links to:
- docs.valyu.ai
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 1.3k tokens when it runs. Until then it costs about 28 tokens; SKILL.md has 316 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~28
When it runs · the whole SKILL.md, loaded when a task matches: ~1.3k

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); files beside SKILL.md are not scanned.

SKILL.md

The full file from wu-yc/LabClaw at commit df37802, republished under its MIT licence (© wu-yc). 316 words, ~1,334 tokens.

Download SKILL.mdSave it as .claude/skills/biorxiv-search/SKILL.md (or your agent's skills folder).

name: biorxiv-search
description: Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.
keywords: biorxiv, biology-preprints, molecular-biology, genetics, life-sciences, semantic-search
license: MIT

bioRxiv Search

Search the complete bioRxiv database of biological sciences preprints using natural language queries powered by Valyu's semantic search API.

Why This Skill is Powerful

No API Parameter Parsing: Just pass natural language queries directly - no need to construct complex search parameters
Semantic Search: Understands the meaning of your query, not just keyword matching
Full-Text Access: Returns complete article content, not just abstracts
Image Links: Includes figures and images from papers
Comprehensive Coverage: Access to all bioRxiv preprints in biological sciences

Requirements

Node.js 18+ (uses built-in fetch)
Valyu API key from https://platform.valyu.ai ($10 free credits)

CRITICAL: Script Path Resolution

The scripts/search commands in this documentation are relative to this skill's installation directory.

Before running any command, locate the script using:

bash

BIORXIV_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/biorxiv-search/*/scripts/*" -type f 2>/dev/null | head -1)

Then use the full path for all commands:

bash

$BIORXIV_SCRIPT "CRISPR gene editing" 15

API Key Setup Flow

When you run a search and receive "setup_required": true, follow this flow:

Ask the user for their API key: "To search bioRxiv, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"
Once the user provides the key, run:
bash
```
scripts/search setup <api-key>
```
Retry the original search.

Example Flow:

User: Search bioRxiv for CRISPR advances
→ Response: {"success": false, "setup_required": true, ...}
→ Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai"
→ User: "val_abc123..."
→ Claude runs: scripts/search setup val_abc123...
→ Response: {"success": true, "type": "setup", ...}
→ Claude retries: scripts/search "CRISPR advances" 10
→ Success!

When to Use This Skill

Finding biology research not yet published in journals
Cross-disciplinary life sciences research
Rapid access to unpublished experimental data
Disease mechanism research
Evolutionary and developmental biology studies
Ecological research and conservation biology

Output Format

json

{
  "success": true,
  "type": "biorxiv_search",
  "query": "CRISPR gene editing",
  "result_count": 10,
  "results": [
    {
      "title": "Article Title",
      "url": "https://biorxiv.org/content/...",
      "content": "Full article text with figures...",
      "source": "biorxiv",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.025
}

Processing Results

With jq

bash

# Get article titles
scripts/search "query" 10 | jq -r '.results[].title'

# Get URLs
scripts/search "query" 10 | jq -r '.results[].url'

# Extract full content
scripts/search "query" 10 | jq -r '.results[].content'

Common Use Cases

Molecular Biology

bash

# Find recent molecular biology papers
scripts/search "protein-protein interaction networks" 50

Neuroscience

bash

# Search for neuroscience research
scripts/search "optogenetics in behavior studies" 20

Genomics

bash

# Find genomics papers
scripts/search "single cell RNA sequencing analysis" 15

Developmental Biology

bash

# Search for developmental biology papers
scripts/search "embryonic stem cell differentiation" 25

Error Handling

All commands return JSON with success field:

json

{
  "success": false,
  "error": "Error message"
}

Exit codes:

0 - Success
1 - Error (check JSON for details)

API Endpoint

Base URL: https://api.valyu.ai/v1
Endpoint: /search
Authentication: X-API-Key header

Architecture

scripts/
├── search          # Bash wrapper
└── search.mjs      # Node.js CLI

Direct API calls using Node.js built-in fetch(), zero external dependencies.

Adding to Your Project

If you're building an AI project and want to integrate bioRxiv Search directly into your application, use the Valyu SDK:

Python Integration

python

from valyu import Valyu

client = Valyu(api_key="your-api-key")

response = client.search(
    query="your search query here",
    included_sources=["valyu/valyu-biorxiv"],
    max_results=20
)

for result in response["results"]:
    print(f"Title: {result['title']}")
    print(f"URL: {result['url']}")
    print(f"Content: {result['content'][:500]}...")

TypeScript Integration

typescript

import { Valyu } from "valyu-js";

const client = new Valyu("your-api-key");

const response = await client.search({
  query: "your search query here",
  includedSources: ["valyu/valyu-biorxiv"],
  maxResults: 20
});

response.results.forEach((result) => {
  console.log(`Title: ${result.title}`);
  console.log(`URL: ${result.url}`);
  console.log(`Content: ${result.content.substring(0, 500)}...`);
});

See the Valyu docs for full integration examples and SDK reference.

Files

Just SKILL.md in skills/literature/biorxiv-search of wu-yc/LabClaw.

Open the folder on GitHubat commit df37802

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.

Biorxiv Search compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Biorxiv Search this skillwu-yc/LabClaw	1.1k	—	~1.3k	Automated safety check: Pass	MIT	6 mo ago
Read arXiv Paperkarpathy/nanochat	59k	1 repos	~494	Automated safety check: Pass	MIT	1 mo ago
Perplexity Web Searchdavila7/claude-code-templates	33k	11 repos	~3.5k	Automated safety check: Notes	MIT	today
Literature Reviewneflibata-feng/MyArxiv-Agent	126	20 repos	~5.9k	Automated safety check: Notes	MIT	today
Openalex Databaseneflibata-feng/MyArxiv-Agent	126	12 repos	~3k	Automated safety check: Pass	Custom licence	today
Citation ManagementK-Dense-AI/claude-scientific-writer	2.4k	2 repos	~3.9k	Automated safety check: Notes	MIT	2 days ago

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Questions about Biorxiv Search

What does Biorxiv Search do?

Search bioRxiv biology preprints with natural language queries. Biorxiv Search is an agent skill from wu-yc/LabClaw. Search bioRxiv biology preprints with natural language queries.

When should I use Biorxiv Search?

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

How do I install Biorxiv Search in Claude Code?

Run `npx skills add wu-yc/LabClaw --skill biorxiv-search -a claude-code`. Or copy the skill folder (skills/literature/biorxiv-search in wu-yc/LabClaw) 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 wu-yc/LabClaw --skill biorxiv-search -a codex`. Or copy the skill folder (skills/literature/biorxiv-search in wu-yc/LabClaw) 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 wu-yc/LabClaw --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 the command-line tools its instructions call (jq). Our summary lists: Python 3; Node.js.

Does Biorxiv Search access the network?

SKILL.md names 4 domains. In commands or code: platform.valyu.ai, api.valyu.ai and biorxiv.org; the agent is likely to contact these when it follows the instructions. As links in the text: docs.valyu.ai. 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. Review the folder before installing.

What licence does Biorxiv Search use?

Biorxiv Search is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Biorxiv Search use?

About 1.3k tokens (SKILL.md is roughly 5.3k 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?

wu-yc (a GitHub user) maintains it in wu-yc/LabClaw, which has 1,055 GitHub stars. The repository holds 68 skills in this directory. The repository was last updated on March 19, 2026.

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

Install Biorxiv Search

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

bioRxiv Search

Why This Skill is Powerful

Requirements

CRITICAL: Script Path Resolution

API Key Setup Flow

Example Flow:

When to Use This Skill

Output Format

Processing Results

With jq

Common Use Cases

Molecular Biology

Neuroscience

Genomics

Developmental Biology

Error Handling

API Endpoint

Architecture

Adding to Your Project

Python Integration

TypeScript Integration

Files

Compare with similar skills

Similar skills

More from wu-yc/LabClaw

Related

Questions about Biorxiv Search