/` and can be exported with one command: `/export word`, `/export pptx`, or `/export latex`.
[Browse all 6 Research Recipes →](#research-recipes)
---
## Quick Start
```bash
git clone https://github.com/Zaoqu-Liu/ScienceClaw.git && cd ScienceClaw
bash scripts/setup.sh # installs deps, configures API key (interactive)
./scienceclaw run # starts gateway + opens TUI — done
```
> **China users:** setup will ask for an API key. Use [DeepSeek](https://platform.deepseek.com/) — direct access, no proxy, ¥1/M tokens. Or use [OpenRouter](https://openrouter.ai/) as a relay for all providers.
Prerequisites
| Requirement | Version | Notes |
|-------------|---------|-------|
| Node.js | >= 22 | [nodejs.org](https://nodejs.org/) |
| Python | >= 3.10 | For code execution (R, Julia optional) |
| Docker | Latest | Optional — sandboxed execution |
Troubleshooting
```bash
./scienceclaw models # which models work? diagnose 404/403/429
./scienceclaw doctor # full system health check
```
One-shot mode & channels
```bash
./scienceclaw ask "分析 BRCA1 在乳腺癌中的作用" # one-shot, no TUI
./scienceclaw add telegram # or discord, slack, whatsapp, feishu, wechat
./scienceclaw channels # list configured channels
```
---
## What It Can Do
| Capability | Details |
|------------|---------|
| **Search literature** | 15+ sources — PubMed, Semantic Scholar, OpenAlex, Europe PMC, and more |
| **Query databases** | 77+ databases — UniProt, PDB, NCBI, ChEMBL, STRING, GTEx, ClinicalTrials.gov, and more |
| **Run code** | Python, R, Julia via bash — install packages on the fly |
| **Generate figures** | Journal-spec palettes (NPG, Lancet, JCO, NEJM), publication-ready sizing |
| **Write reports** | Real citations from search results, never fabricated |
| **Review research** | 8-dimension ScholarEval rubric for systematic quality assessment |
| **Research Recipes** | 6 pre-built workflows — gene landscape, target validation, literature review, and more |
| **Export deliverables** | One command to Word, PowerPoint, or LaTeX from project results |
| **Monitor literature** | `/watch` tracks topics on PubMed, alerts on new papers at session start |
---
## Research Recipes
Six pre-built research workflows that execute complete multi-step analyses from a single prompt. ScienceClaw auto-detects which Recipe matches and runs the full pipeline autonomously.
| Recipe | Trigger Examples | What It Does |
|--------|-----------------|-------------|
| **gene-landscape** | "分析 TP53 在肝癌中的作用" | Literature → TCGA expression → survival → immune → pathway → report |
| **target-validation** | "评估 EGFR 的成药性" | Literature → STRING → ChEMBL → DrugBank → trials → patents → report |
| **literature-review** | "综述 CRISPR 在基因治疗中的应用" | Multi-source 50+ → filter → full text → trend chart → structured review |
| **diff-expression** | "分析这个表达矩阵" | QC → DESeq2/limma → volcano + heatmap → GO/KEGG → report |
| **clinical-query** | "NSCLC 的最新治疗方案" | ClinicalTrials → guidelines → drugs → summary table |
| **person-research** | "调研张三教授" | OpenAlex → PubMed → citations → themes → profile report |
```bash
./scienceclaw recipes # list all Recipes
./scienceclaw ask "分析 TP53 在肝癌中的作用" # auto-matches gene-landscape
```
---
## New in This Release
| Feature | Description |
|---------|------------|
| **Research Recipes** | 6 one-liner-to-full-workflow templates (see above) |
| **Export to Word/PPT/LaTeX** | `/export word`, `/export pptx`, `/export latex` — generate formatted deliverables from project results |
| **Literature Monitoring** | `/watch TOPIC` — track new publications on PubMed, alerts at session start |
| **Research Memory** | Structured findings stored in JSONL — cross-session, cross-project recall via `/recall` |
| **METHODS.md** | Auto-generated Methods section after deep analyses, ready for paper insertion |
| **Smart Task Routing** | Quick tasks (single lookup) stay in chat; deep tasks get project directories |
| **Follow-up Suggestions** | Data-driven next-step suggestions after every multi-step analysis |
| **Session Greeting** | Context-aware greeting — returning users see recent project status + pending alerts |
| **First-run Welcome** | Guided onboarding for new users with actionable examples |
| **CLI `recipes` / `ask`** | `./scienceclaw recipes` to browse, `./scienceclaw ask "..."` for one-shot queries |
---
## Channel Integrations
ScienceClaw inherits all channel integrations from OpenClaw. Connect your preferred interface:
| Channel | How to use |
|---------|-----------|
| **Terminal UI** | `scienceclaw tui` |
| **Web Dashboard** | `scienceclaw dashboard` |
| **Telegram** | [Setup guide](docs/channels/telegram.md) |
| **Discord** | [Setup guide](docs/channels/discord.md) |
| **Slack** | [Setup guide](docs/channels/slack.md) |
| **Feishu / Lark** | [Setup guide](docs/channels/feishu.md) |
| **WeChat** | [Setup guide](docs/channels/wechat.md) |
| **WhatsApp** | [Setup guide](docs/channels/whatsapp.md) |
| **Matrix** | [Setup guide](docs/channels/matrix.md) |
| + more | `scienceclaw channels --help` |
---
## Architecture
```
ScienceClaw = OpenClaw engine + SCIENCE.md (~600 lines) + 266 Skills (markdown)
= 0 lines of custom code
```
No TypeScript. No Python servers. No MCP. No plugins. No middleware. The `scienceclaw` bash wrapper (~130 lines) manages the gateway lifecycle. Everything else is markdown that teaches the model how to be a scientist.
| Layer | Components |
|-------|-----------|
| **User** | Terminal UI, Web Dashboard, Telegram, Discord, Slack, Feishu, WeChat, WhatsApp, Matrix |
| **Gateway** | OpenClaw gateway — routes messages, manages sessions, handles tool calls (port 18789) |
| **Agent** | `SCIENCE.md` (identity + research discipline) + 266 domain skills (loaded on demand) |
| **Tools** | `web_search` (Brave), `bash` (Python/R/Julia + curl to REST APIs) — two tools do everything |
When models get smarter, ScienceClaw gets smarter — no code to update, no integrations to fix. See [Architecture docs](docs/architecture/ARCHITECTURE.md) for the full design rationale.
---
## 🔍 Deep Research
ScienceClaw searches across 15+ sources, cross-references results, and verifies citations before including them in reports.
| Category | Sources |
|----------|---------|
| **Biomedical literature** | PubMed, PubMed Central, Europe PMC |
| **Broad academic** | Semantic Scholar, OpenAlex, CrossRef, CORE |
| **Preprints** | bioRxiv, medRxiv, arXiv |
| **Clinical** | ClinicalTrials.gov, WHO ICTRP |
| **Patents & grants** | Google Patents, NIH RePORTER |
| **General** | Google Scholar, Web search |
---
## 🗄 Database Access
77+ databases across 9 disciplines, all accessed through their public REST APIs via `bash` + `curl`.
| Discipline | Databases | Count |
|------------|-----------|-------|
| **Genomics & Transcriptomics** | NCBI Gene, Ensembl, UCSC Genome Browser, GEO, TCGA, GTEx, ENCODE | 10+ |
| **Proteomics & Structure** | UniProt, PDB, AlphaFold DB, InterPro, Pfam, SWISS-MODEL | 8+ |
| **Pathways & Interactions** | STRING, BioGRID, KEGG, Reactome, WikiPathways, IntAct | 8+ |
| **Pharmacology & Drug Discovery** | ChEMBL, DrugBank, PubChem, PharmGKB, DGIdb, TTD | 8+ |
| **Disease & Phenotype** | OMIM, DisGeNET, ClinVar, GWAS Catalog, HPO, Orphanet | 8+ |
| **Immunology** | IEDB, IMGT, ImmPort, TIMER2.0, TCIA | 6+ |
| **Microbiome** | GMrepo, gutMDisorder, BugBase, MicrobiomeDB | 5+ |
| **Clinical & Epidemiology** | ClinicalTrials.gov, GBD, WHO GHO, SEER, cBioPortal | 7+ |
| **Model Organisms** | MGI, FlyBase, WormBase, ZFIN, RGD, SGD | 7+ |
---
## 📚 266 Domain Skills
Each skill is a markdown file that teaches the model *how* to perform a specific analysis — complete with API patterns, code templates, and validation steps.
| Domain | Count | Skills |
|--------|-------|--------|
| **Bioinformatics** | 30+ | `scanpy`, `anndata`, `pydeseq2`, `arboreto`, `biopython`, `deeptools`, `pysam` |
| **Visualization** | 35+ | `matplotlib`, `seaborn`, `plotly`, `visualization`, `networkx` |
| **Drug Discovery** | 20+ | `chembl-database`, `rdkit`, `zinc-database`, `alphafold-database`, `adaptyv`, `medchem` |
| **Clinical & Survival** | 15+ | `clinicaltrials-database`, `scikit-survival`, `clinical`, `fda-database` |
| **Single-cell** | 10+ | `scanpy`, `scvi-tools`, `cellxgene-census`, `anndata` |
| **Genomics** | 15+ | `gene-database`, `ensembl-database`, `gwas-database`, `clinvar-database`, `geo-database` |
| **Databases** | 20+ | `uniprot-database`, `pdb-database`, `string-database`, `opentargets-database`, `reactome-database` |
| **Machine Learning** | 10+ | `scikit-learn`, `shap`, `aeon`, `statistics`, `exploratory-data-analysis` |
| **Scientific Writing** | 15+ | `academic-literature-search`, `writing`, `review-writing`, `peer-review`, `venue-templates` |
```bash
./scienceclaw skills # browse all 266 skills by domain
./scienceclaw skills search "survival" # search by keyword
```
---
## Deployment
**Local** — already covered in [Quick Start](#quick-start).
**Docker** — sandboxed Python/R/Julia execution:
```bash
docker compose -f docker/docker-compose.yml up
```
See [Deployment Guide](docs/guides/deployment.md) for production options including autostart, reverse proxy, and cloud deployment.
---
## Contributing
Contributions are welcome. Please read [CONTRIBUTING.md](CONTRIBUTING.md) before submitting a pull request.
---
## Author
**LIU Zaoqu**
International Academy of Phronesis Medicine (Guangdong) · π-HuB infrastructure
Contact: [liuzaoqu@163.com](mailto:liuzaoqu@163.com)
---
## License
This project is licensed under the [MIT License](LICENSE).
---
**ScienceClaw** — Your AI Research Colleague.
