bio-research

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SKILL.md (first lines)

# 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

```bash
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

From yejunbin/darwin, MIT.

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