# Biorxiv Search

Search bioRxiv biology preprints with natural language queries.

- Repository: https://github.com/beita6969/ScienceClaw (1024 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-10-31
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add beita6969/ScienceClaw --skill biorxiv-search -g -a claude-code -y`
Codex: `npx skills add beita6969/ScienceClaw --skill biorxiv-search -g -a codex -y`
Cursor: `npx skills add beita6969/ScienceClaw --skill biorxiv-search -g -a cursor -y`
Gemini CLI: `npx skills add beita6969/ScienceClaw --skill biorxiv-search -g -a gemini-cli -y`

## Description

Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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

1. Node.js 18+ (uses built-in fetch)
2. 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:

1. **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"

2. **Once the user provides the key, run:**
   ```bash
   scripts/search setup <api-key>
   ```

3. **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

The rest: https://github.com/beita6969/ScienceClaw/blob/HEAD/skills/biorxiv-search/SKILL.md