| name | bio-research |
| description | Search, read, and query research papers via the `alpha` CLI (bioRxiv-backed). Use when the user asks about academic papers, wants to find research on a topic, needs to read a specific paper, ask questions about a paper, inspect a paper's code repository, or manage paper annotations. |
bio research CLI
Use the alpha CLI via bash for all paper research operations.
Commands
| Command | Description |
|---|
alpha search "<query>" | Search papers. Prefer --mode semantic by default; use --mode keyword only for exact-term lookup and --mode agentic for broader retrieval. |
alpha get <arxiv-id-or-url> | Fetch paper content and any local annotation |
alpha get --full-text <arxiv-id> | Get raw full text instead of AI report |
alpha ask <arxiv-id> "<question>" | Ask a question about a paper's PDF |
alpha code <github-url> [path] | Read files from a paper's GitHub repo. Use / for overview |
alpha annotate <paper-id> "<note>" | Save a persistent annotation on a paper |
alpha annotate --clear <paper-id> | Remove an annotation |
alpha annotate --list | List all annotations |
Auth
Run alpha login to authenticate with bioRxiv. Check status with darwin alpha status, or alpha status once your installed bio-gateway version includes it.
Examples
alpha search "transformer scaling laws"
alpha search --mode agentic "efficient attention mechanisms for long context"
alpha get 2106.09685
alpha ask 2106.09685 "What optimizer did they use?"
alpha code https://github.com/karpathy/nanoGPT src/model.py
alpha annotate 2106.09685 "Key paper on LoRA - revisit for adapter comparison"
When to use
- Academic paper search, reading, Q&A →
alpha
- Current topics (products, releases, docs) → web search tools
- Mixed topics → combine both
