aut-sci-write

Aut_Sci_Write

Autonomous Scientific Writer

A modular Agent Skills suite for the full academic research lifecycle

🌐 Live Demo · 📦 Install · 📖 中文说明

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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 from PDFs; Paper Harvester fetches full text + figures from DOI/PMID/arXiv with multi-source fallthrough, degraded capture handling, and extraction status badges	/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	Doc
Web of Science	https://api.clarivate.com/apis/wos-starter/v1/documents	WOS_API_KEY (header X-ApiKey)	developer.clarivate.com
Springer Nature (Meta)	https://api.springernature.com/meta/v2/json	SPRINGER_API_KEY (query param api_key)	dev.springernature.com
Springer Nature (OA)	https://api.springernature.com/openaccess/json	SPRINGER_OA_API_KEY (query param api_key)	dev.springernature.com
Scopus (Elsevier)	https://api.elsevier.com/content/search/scopus	SCOPUS_API_KEY (header X-ELS-APIKey)	dev.elsevier.com
Elsevier Article	https://api.elsevier.com/content/article/doi/{doi}	ELSEVIER_API_KEY + optional ELSEVIER_INSTTOKEN	dev.elsevier.com
Semantic Scholar	https://api.semanticscholar.org/graph/v1/paper/search	Optional SEMANTIC_SCHOLAR_API_KEY (header x-api-key)	semanticscholar.org/product/api
OpenAlex	https://api.openalex.org/works	Optional OPENALEX_EMAIL (query param mailto)	docs.openalex.org
PubMed (NCBI E-utils)	https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi	Optional NCBI_API_KEY + NCBI_EMAIL	ncbi.nlm.nih.gov
Europe PMC	https://www.ebi.ac.uk/europepmc/webservices/rest/search	None	europepmc.org/RestfulWebService
CrossRef	https://api.crossref.org/works	None (optional mailto for polite pool)	crossref.org/documentation
Unpaywall	https://api.unpaywall.org/v2/{doi}	UNPAYWALL_EMAIL (query param email)	unpaywall.org/products/api
IEEE Xplore	https://ieeexploreapi.ieee.org/api/v1/search/articles	IEEE_API_KEY (query param apikey)	developer.ieee.org
arXiv	https://export.arxiv.org/api/query	None	info.arxiv.org/help/api
Zotero	https://api.zotero.org	ZOTERO_API_KEY (header Zotero-API-Key, v3)	zotero.org/support/dev/web_api

🚀 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.

# Add the marketplace (one-time)
/plugin marketplace add ShZhao27208/Aut_Sci_Write

# Install the plugin
/plugin install academic-skills@shuozhao

Update to latest version:

/plugin update academic-skills@shuozhao

Method 2: npx CLI

One-line install (Recommended — installs all 9 skills globally):

npx skills add ShZhao27208/Aut_Sci_Write -g -y

Update to latest version:

npx skills add ShZhao27208/Aut_Sci_Write -g -y

After npx install, you still need Python dependencies for the skills to run:

pip install -r requirements.txt

Method 3: Manual Install (Download/Clone to local)

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.

git clone https://github.com/ShZhao27208/Aut_Sci_Write.git
cd Aut_Sci_Write
docker-compose build
docker-compose up -d

See 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:

npx skills add ShZhao27208/Aut_Sci_Write -y

Or for local installs:

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:

# ~/.aut_sci_write/.env — unified config for all skills

# ─── sci-search ───────────────────────────────────────────────
# Web of Science Starter API (free): https://developer.clarivate.com/apis/wos-starter
WOS_API_KEY=
# Elsevier Scopus API (free): https://dev.elsevier.com/
SCOPUS_API_KEY=
# Springer Nature Metadata API (free): https://dev.springernature.com/
SPRINGER_API_KEY=
# Springer Nature Open Access API (falls back to SPRINGER_API_KEY)
SPRINGER_OA_API_KEY=
# Semantic Scholar (optional, for higher rate limits): https://www.semanticscholar.org/product/api#api-key
SEMANTIC_SCHOLAR_API_KEY=
# OpenAlex polite pool (optional, just your email)
OPENALEX_EMAIL=

# ─── sci-download ─────────────────────────────────────────────
# Elsevier Article Retrieval API (free): https://dev.elsevier.com/
ELSEVIER_API_KEY=
ELSEVIER_INSTTOKEN=
# IEEE Xplore API (free tier): https://developer.ieee.org/
IEEE_API_KEY=
# Unpaywall (just your email): https://unpaywall.org/products/api
UNPAYWALL_EMAIL=

# ─── sci-search & sci-download (shared) ──────────────────────
# NCBI/PubMed E-utilities (free): https://www.ncbi.nlm.nih.gov/account/settings/
NCBI_API_KEY=
NCBI_EMAIL=

# ─── sci-zotero ──────────────────────────────────────────────
# Zotero API key: https://www.zotero.org/settings/keys/new
ZOTERO_API_KEY=
# Numeric user ID (for personal library)
ZOTERO_USER_ID=
# Numeric group ID (for group library, use instead of USER_ID)
ZOTERO_GROUP_ID=

# ─── sci-ppt (optional AI parser) ────────────────────────────
ANTHROPIC_API_KEY=sk-ant-...    # Claude API
OPENAI_API_KEY=sk-...           # OpenAI fallback

# ─── sci-figure (optional subfigure OCR, Windows example) ────
TESSERACT_CMD="C:\Program Files\Tesseract-OCR\tesseract.exe"

Everything except sci-ppt and sci-figure works without any key — CrossRef, OpenAlex, Europe PMC, arXiv, and Semantic Scholar's anonymous tier need no credentials. Keys mainly unlock publisher-side full text and raise rate limits.

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: