https://github.com/shzhao27208/aut_sci_write
Academic research skills suite for AI Agent — literature search/download (WoS+Elsevier+Springer), PDF extraction, figure cropping, review writing, Zotero sync, and PPT/Html generation.
https://github.com/shzhao27208/aut_sci_write
academic-research agent claude-code codex llm-tools openclaw opencode pptx skills zotero
Last synced: about 23 hours ago
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Academic research skills suite for AI Agent — literature search/download (WoS+Elsevier+Springer), PDF extraction, figure cropping, review writing, Zotero sync, and PPT/Html generation.
- Host: GitHub
- URL: https://github.com/shzhao27208/aut_sci_write
- Owner: ShZhao27208
- License: other
- Created: 2026-04-06T05:47:16.000Z (4 months ago)
- Default Branch: main
- Last Pushed: 2026-07-14T16:15:55.000Z (13 days ago)
- Last Synced: 2026-07-14T16:32:56.622Z (13 days ago)
- Topics: academic-research, agent, claude-code, codex, llm-tools, openclaw, opencode, pptx, skills, zotero
- Language: Python
- Homepage: https://shzhao27208.github.io/Aut_Sci_Write/
- Size: 56.5 MB
- Stars: 162
- Watchers: 4
- Forks: 22
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-academic-skills - aut_sci_write - lifecycle suite: literature search across arXiv/PubMed/Web of Science, PDF and figure extraction, review/meta-analysis writing, Zotero sync and slides. Broad and well-adopted; a do-everything suite, not a best-in-one-stage tool | `net` | (Suites, Systems & Meta / Skill Suites)
README
# Aut_Sci_Write
**Autonomous Scientific Writer**
*A modular Agent Skills suite for the full academic research lifecycle*
[](package.json)
[](#-what-it-does)
[](#-what-it-does)
[](#-what-it-does)
[](https://www.python.org/)
[](https://nodejs.org/)
[](#-what-it-does)
[](#-what-it-does)
[](LICENSE)
[](https://github.com/ShZhao27208/Aut_Sci_Write)
[🌐 Live Demo](https://shzhao27208.github.io/Aut_Sci_Write/) · [📦 Install](#-installation) · [📖 中文说明](#中文说明)
---
## English
**Aut_Sci_Write** is a modular collection of **AI Agent Skills** that automates the entire academic research and writing lifecycle — from literature discovery and deep PDF analysis to figure extraction, review writing, and professional PPT generation.
> Install once, use anywhere. Just talk to AI Agent naturally — the skills activate automatically based on what you say.
### ✨ What It Does
| Skill | Description | Example Trigger |
|:------|:------------|:----------------|
| `sci-search` | Search arXiv + PubMed + **Web of Science** + **Elsevier** +**Springer** + Semantic Scholar + OpenAlex simultaneously with JCR tier & impact factor data | /sci-search *Find high-IF papers on perovskite solar cells* |
| `sci-download` | Download paper PDFs with intelligent DOI routing across 8 sources: **Elsevier**, **Springer**, IEEE, arXiv, Unpaywall, Semantic Scholar, PubMed Central, CNKI | /sci-download *Download 10.1038/s41586-023-06600-9* |
| `sci-extract` | Extract core insights, experimental parameters, and conclusions from PDFs | /sci-extract *Analyze the key findings of paper.pdf* |
| `sci-figure` | Auto-detect and crop figures from PDFs at 600 DPI, with subfigure splitting | /sci-figure *Extract Figure 3c from this paper* |
| `sci-review` | Draft literature reviews and professional peer-review rebuttals (NeurIPS/ICLR standard) | /sci-figure *Write a literature review on GNNs for drug discovery* |
| `sci-zotero` | Sync Zotero library, add citations by DOI/ISBN/PMID, fetch open-access PDFs | /sci-zotero *Connect to my Zotero database* |
| `sci-ppt` | Generate professional academic PPTX from paper PDFs or structured text, with LaTeX formula rendering | /sci-zotero *Turn this paper into a seminar presentation* |
| `sci-html` | Convert PDFs, Markdown, outlines, or summaries into interactive academic HTML slide decks and browser reports. | /sci-html Turn this paper into an interactive HTML report |
| `sci-polish` | Two-stage academic paper polishing: AI detection reduction + 8-dimension quality improvement (grammar, tone, coherence, conciseness, terminology, structure, clarity, journal compliance) | /sci-polish *Polish this paper for NeurIPS submission* |
#### 🔌 API
| Data Source | API Endpoint | Auth |
|:------------|:-------------|:-----|
| Web of Science | `https://developer.clarivate.com/apis/wos` | `WOS_API_KEY` |
| Springer (Meta) | `https://dev.springernature.com/#api` | `SPRINGER_API_KEY` |
| Springer (OA) | `https://dev.springernature.com/#api` | `SPRINGER_OA_API_KEY` |
| Scopus (Elsevier) | `https://api.elsevier.com/content/search/scopus` | `SCOPUS_API_KEY` |
| Semantic Scholar | `https://www.semanticscholar.org/product/api` | Optional |
| PubMed (E-utilities) | `https://pmc.ncbi.nlm.nih.gov/tools/developers/` | Optional `NCBI_API_KEY` |
| Zotero | `https://www.zotero.org/settings/keys` | `ZOTERO_API_KEY` |
### 🚀 Installation
**Prerequisites**
Before installation, make sure the following environments are available:
- **Python 3.10+**: required for Python-based skills such as `sci-search`, `sci-extract`, `sci-figure`, `sci-review`, and `sci-ppt`
- **Node.js 18+**: required for `npx skills add ...` installation and CLI-based skill registration
- **pip**: used to install Python dependencies from `requirements.txt`
### ***Then*** choose **one** of the following methods:
#### Method 1: Claude Code Plugin (Recommended)
No prerequisites needed — the plugin system handles everything.
```bash
# Add the marketplace (one-time)
/plugin marketplace add ShZhao27208/Aut_Sci_Write
# Install the plugin
/plugin install academic-skills@shuozhao
```
Update to latest version:
```bash
/plugin update academic-skills@shuozhao
```
#### Method 2: npx CLI
**One-line install** (***Recommended*** — installs all 9 skills globally):
```bash
npx skills add ShZhao27208/Aut_Sci_Write -g -y
```
**Update to latest version:**
```bash
npx skills add ShZhao27208/Aut_Sci_Write -g -y
```
> After npx install, you still need Python dependencies for the skills to run:
> ```bash
> pip install -r requirements.txt
> ```
#### Method 3: Manual Install (Download/Clone to local)
```bash
git clone https://github.com/ShZhao27208/Aut_Sci_Write.git
cd Aut_Sci_Write
npx skills add . -g -y
pip install -r requirements.txt
```
#### Method 4: Docker (Isolated Environment)
Requires: **Docker** — no Python/Node.js needed locally.
```bash
git clone https://github.com/ShZhao27208/Aut_Sci_Write.git
cd Aut_Sci_Write
docker-compose build
docker-compose up -d
```
See [DOCKER.md](DOCKER.md) for detailed Docker deployment guide.
> **⚠️ Troubleshooting: PromptScript error**
>
> If you see errors like `✗ sci-extract → PromptScript: PromptScript does not support global skill installation` after a recent `skills` CLI update, **don't worry — the installation has already completed successfully**. This error only affects PromptScript (an unsupported target platform) and does not impact Claude Code or other AI agents.
>
> To avoid this message, simply remove the `-g` flag:
>
> ```bash
> npx skills add ShZhao27208/Aut_Sci_Write -y
> ```
>
> Or for local installs:
>
> ```bash
> npx skills add . -y
> ```
### ⚙️ Configuration
On first use, any skill will automatically create `~/.aut_sci_write/.env` with a template of all supported keys. Open it and fill in the ones you need:
```bash
# ~/.aut_sci_write/.env — unified config for all skills
# For sci-zotero (optional)
ZOTERO_API_KEY=your_personal_api_key
ZOTERO_USER_ID=your_numeric_user_id
# For sci-search — Web of Science (optional but recommended)
# Apply for a free key at: https://developer.clarivate.com/apis/wos-starter
WOS_API_KEY=your_wos_api_key
# For sci-ppt PDF workflow (choose one)
ANTHROPIC_API_KEY=sk-ant-... # Claude API
MOONSHOT_API_KEY=sk-... # Moonshot API
# For sci-figure subfigure OCR (optional, Windows example)
TESSERACT_CMD="C:\Program Files\Tesseract-OCR\tesseract.exe"
```
All skills share this single `.env` file — fill a key once, every skill that needs it will read from here. Do not commit or publish this file.
### 💬 Usage Examples
Once installed, just type naturally in AI Agent — no commands to memorize:
```
# Literature search
"/sci-search Search for recent papers on solid-state electrolytes for lithium batteries"
# Paper download
"/sci-download Download the PDF for DOI 10.1038/s41586-023-06600-9"
# Deep paper analysis
"/sci-extract Extract the core findings and experimental parameters from paper.pdf"
# Figure extraction
"/sci-figure Extract Figure 3 from paper.pdf and split subfigures a, b, c"
# Literature review
"/sci-review Write a literature review on graph neural networks in drug discovery"
# Rebuttal writing
"/sci-review Help me respond to Reviewer 2's comment about missing baselines"
# Zotero sync
"/sci-zotero List the paper items from my Zotero 'Materials' collection"
# PPT generation
"/sci-ppt Convert paper.pdf into a group meeting presentation, save as seminar.pptx"
# HTML report generation
"/sci-html Convert paper.pdf into an interactive browser-based academic report"
# Paper polishing (de-AI + 8-dimension quality)
"/sci-polish Polish this paper for NeurIPS submission, reduce AI detection rate"
```
### 📁 Repository Structure
```
Aut_Sci_Write/
├── skills/
│ ├── _shared/ # Unified env config module (env_config.py)
│ ├── sci-search/ # Literature search with journal metrics (7 sources)
│ ├── sci-download/ # Paper PDF download with intelligent DOI routing (8 sources)
│ ├── sci-extract/ # Paper analysis and structured insight extraction
│ ├── sci-figure/ # PDF figure and subfigure extraction
│ ├── sci-review/ # Literature review and rebuttal writing
│ ├── sci-ppt/ # Academic PPTX generation
│ ├── sci-html/ # Interactive HTML reports and browser slide decks
│ ├── sci-polish/ # Academic paper polishing: de-AI + 8-dimension quality
│ └── sci-zotero/ # Zotero library integration
├── scripts/
│ ├── extract_core_insights.py # Compatibility wrapper for sci-extract CLI
│ ├── zotero.py # Compatibility wrapper for sci-zotero CLI
│ └── journal_db.json # Journal metrics database (independently updatable)
├── examples/ # Sample outputs (PDF + Markdown + PPT)
├── docs/ # GitHub Pages site
├── skills-cli.js # Local skill discovery helper
└── requirements.txt # Shared Python dependencies
```
### 🤝 Contributing
Contributions welcome! Priority areas:
- Add journal metrics to `scripts/journal_db.json`
- Add writing templates to `skills/sci-review/templates/`
- Add new PPT slide types to `skills/Aut_Sci_PPt/src/aut_sci_ppt/templates/`
- Post problems you encounter when using it to `issue`
---
## 中文说明
**Aut_Sci_Write** 是一套专为科研工作者设计的 **AI Agent Skills 技能包**，将科研写作的各个环节自动化，覆盖从文献发现到成果输出的完整链路。
> 安装一次，随处可用。直接用自然语言和 AI Agent 对话，技能会根据你说的内容自动激活。
### ✨ 功能概览
| 技能 | 功能描述 | 触发词示例 |
|------|----------|:----------|
| `sci-search` | arXiv + PubMed + **Web of Science** + **Elsevier** +**Springer** + Semantic Scholar + OpenAlex 七源检索，自动附加 JCR 分区和影响因子 | /sci-search *搜索钙钛矿太阳能电池最新论文* |
| `sci-download` | 论文 PDF 智能下载，根据 DOI 前缀自动路由到 **Elsevier**、**Springer**、IEEE、arXiv、Unpaywall、Semantic Scholar、PubMed Central,、知网 8 个数据源 | /sci-download *下载 10.1038/s41586-023-06600-9* |
| `sci-extract` | 从 PDF 提取核心发现、实验参数、数值对比和主要结论 | /sci-extract *分析 paper.pdf 的核心结论* |
| `sci-figure` | 自动检测并裁剪论文图片（600 DPI），支持复合图拆分为子图 | /sci-figure *提取论文第3张图的子图* |
| `sci-review` | 文献综述写作 + 专业审稿回复，对标 NeurIPS/ICLR 标准 | /sci-review *帮我写图神经网络在药物发现中的综述* |
| `sci-zotero` | Zotero 文献库同步，支持 DOI/ISBN/PMID 添加引用，自动获取 PDF | /sci-zotero *连接我的zotero数据库* |
| `sci-ppt` | 从论文 PDF 或结构化文本一键生成学术 PPT，支持 LaTeX 公式渲染 | /sci-ppt *把这篇文献做成组会汇报PPT* |
| `sci-html` | 将论文 PDF、Markdown、大纲或总结转换为可交互的 HTML 学术报告或浏览器幻灯片。 | /sci-html 把这篇论文做成网页版交互报告 |
| `sci-polish` | 两阶段学术论文润色：降低 AI 检测率 + 八维质量提升（语法、语调、连贯性、简洁性、术语、结构、论证、期刊合规） | /sci-polish *帮我润色这篇论文，目标投 NeurIPS* |
#### 🔌 API
| 数据源 | API 地址 | 认证方式 |
| :------------------- | :----------------------------------------------- | :---------------------- |
| Web of Science | `https://developer.clarivate.com/apis/wos` | `WOS_API_KEY` |
| Springer (Meta) | `https://dev.springernature.com/#api` | `SPRINGER_API_KEY` |
| Springer (OA) | `https://dev.springernature.com/#api` | `SPRINGER_OA_API_KEY` |
| Scopus (Elsevier) | `https://api.elsevier.com/content/search/scopus` | `SCOPUS_API_KEY` |
| Semantic Scholar | `https://www.semanticscholar.org/product/api` | Optional |
| PubMed (E-utilities) | `https://pmc.ncbi.nlm.nih.gov/tools/developers/` | Optional `NCBI_API_KEY` |
| Zotero | `https://www.zotero.org/settings/keys` | `ZOTERO_API_KEY` |
### 🚀 安装方法
**安装前提**
安装前请先确保本机已具备以下环境：
- **Python 3.10 及以上**：用于运行 `sci-search`、`sci-extract`、`sci-figure`、`sci-review`、`sci-ppt` 等基于 Python 的技能
- **Node.js 18 及以上**：用于执行 `npx skills add ...` 安装命令，以及完成 CLI 方式的技能注册
- **pip**：用于安装 `requirements.txt` 中的 Python 依赖
### 随后选择以下 **任一** 方式安装：
#### 方式 1：Claude Code 插件安装（推荐）
无需预装环境，插件系统自动处理依赖。
```bash
# 添加 marketplace（仅需一次）
/plugin marketplace add ShZhao27208/Aut_Sci_Write
# 安装插件
/plugin install academic-skills@shuozhao
```
更新到最新版本：
```bash
/plugin update academic-skills@shuozhao
```
#### 方式 2：npx 命令安装
**一行命令安装**（***推荐***，将全部 9 个技能进行全局安装）：
```bash
npx skills add ShZhao27208/Aut_Sci_Write -g -y
```
**更新到最新版本**（重新运行安装命令即可覆盖更新）：
```bash
npx skills add ShZhao27208/Aut_Sci_Write -g -y
```
> npx 安装后仍需安装 Python 依赖才能运行技能：
> ```bash
> pip install -r requirements.txt
> ```
#### 方式 3：手动安装（克隆/下载仓库到本地）
```bash
git clone https://github.com/ShZhao27208/Aut_Sci_Write.git
cd Aut_Sci_Write
npx skills add . -g -y
pip install -r requirements.txt
```
#### 方式 4：Docker 安装（隔离环境）
需要：**Docker** — 本地无需 Python/Node.js。
```bash
git clone https://github.com/ShZhao27208/Aut_Sci_Write.git
cd Aut_Sci_Write
docker-compose build
docker-compose up -d
```
详细的 Docker 部署指南请参考 [DOCKER.md](DOCKER.md)。
> **⚠️ 常见问题：PromptScript 报错**
>
> 如果安装后出现 `✗ sci-extract → PromptScript: PromptScript does not support global skill installation` 等错误，**无需担心，skills 已经安装成功**。此错误仅影响 PromptScript（一个不支持全局安装的目标平台），不影响 Claude Code 或其他 AI Agent 的正常使用。
>
> 如需消除此提示，去掉 `-g` 参数即可：
>
> ```bash
> npx skills add ShZhao27208/Aut_Sci_Write -y
> ```
>
> 或本地安装时：
>
> ```bash
> npx skills add . -y
> ```
### ⚙️ 配置说明
首次使用任意技能时，会自动创建 `~/.aut_sci_write/.env` 并写入所有支持的 API key 模板。打开该文件，按需填入：
```bash
# ~/.aut_sci_write/.env — 所有技能共用的统一配置文件
# sci-zotero 文献管理（可选）
ZOTERO_API_KEY=你的个人API密钥
ZOTERO_USER_ID=你的Zotero数字用户ID
# sci-search Web of Science 检索（可选，强烈推荐）
# 免费申请地址：https://developer.clarivate.com/apis/wos-starter
WOS_API_KEY=你的WoS_API密钥
# sci-ppt 论文工作流（选择其一）
ANTHROPIC_API_KEY=sk-ant-... # Claude API
MOONSHOT_API_KEY=sk-... # Moonshot API（国内推荐）
# sci-figure 子图 OCR 识别（可选）
# Windows 示例：
TESSERACT_CMD="C:\Program Files\Tesseract-OCR\tesseract.exe"
```
所有技能共享这一个 `.env` 文件 — 填写一次，所有需要该密钥的技能都会自动读取。请勿提交或公开此文件。
### 💬 使用示例
安装后直接在AI Agent 中用自然语言对话，无需记忆命令：
```
# 文献检索
"/sci-search 搜索关于锂离子电池固态电解质的高影响因子论文"
# 论文下载
"/sci-download 下载这篇论文 10.1038/s41586-023-06600-9"
# 深度论文解析
"/sci-extract 分析 paper.pdf 的核心发现，提取实验参数和主要结论"
# 图表提取
"/sci-figure 从 paper.pdf 中提取 Figure 3 并拆分子图 a、b、c"
# 文献综述
"/sci-review 帮我写一篇关于图神经网络在药物发现中应用的文献综述"
# 审稿回复
"/sci-review 帮我回复审稿人2关于缺少基线对比实验的意见"
# Zotero 同步
"/sci-zotero 列出我 Zotero 中 Materials 文件夹的文献条目"
# 生成 PPT
"/sci-ppt 把 paper.pdf 做成组会汇报PPT，输出到 seminar.pptx"
# 生成 HTML汇报
"/sci-html 将 paper.pdf 转换成交互式 HTML 学术报告"
# 论文润色（降AI率 + 八维提升）
"/sci-polish 帮我润色这篇论文，目标期刊是 IEEE TPAMI"
```
### 📁 项目结构
```
Aut_Sci_Write/
├── skills/
│ ├── _shared/ # 统一环境配置模块 (env_config.py)
│ ├── sci-search/ # 文献检索与期刊指标（7 源）
│ ├── sci-download/ # 论文 PDF 智能下载（8 源）
│ ├── sci-extract/ # 文献核心内容提取
│ ├── sci-figure/ # 论文图表检测与裁剪
│ ├── sci-review/ # 综述写作与审稿回复
│ ├── sci-ppt/ # PPT 生成引擎（模板、布局、解析器）
│ ├── sci-html/ # html交互式报告生成
│ ├── sci-polish/ # 论文润色：降AI率 + 八维质量提升
│ └── sci-zotero/ # Zotero 文献库集成
├── scripts/
│ ├── extract_core_insights.py # sci-extract CLI 兼容包装
│ ├── zotero.py # sci-zotero CLI 兼容包装
│ └── journal_db.json # 期刊指标数据库（可独立更新）
├── examples/ # 示例输出（PDF + Markdown + PPT）
├── docs/ # GitHub Pages 展示页
├── skills-cli.js # 本地技能发现助手
└── requirements.txt
```
### 🤝 贡献指南
欢迎贡献！优先方向：
- 在 `scripts/journal_db.json` 中补充期刊指标数据
- 在 `skills/sci-review/templates/` 中添加新的写作模板
- 在 `skills/Aut_Sci_PPt/src/aut_sci_ppt/templates/` 中新增 PPT 页面类型
- 在`issue`中提出自己遇到的问题
---
## 📄 License
MIT License — see [LICENSE](LICENSE)