@wentorai/research-plugins 1.0.0 → 1.2.0

package/curated/tools/README.md

@@ -1,87 +1,107 @@
-# Curated Research Productivity Tools
-
-> Hand-picked tools for academic researchers covering diagrams, documents, code execution, scraping, knowledge graphs, and OCR/translation.
-
-## Diagrams & Visualization
-
-### Tools & Software
-- **[Mermaid](https://mermaid.js.org/)** — Text-based diagramming tool that renders flowcharts, sequence diagrams, Gantt charts, and more from Markdown-like syntax.
-- **[PlantUML](https://plantuml.com/)** — Open-source tool for creating UML diagrams from plain text; supports sequence, class, activity, and many other diagram types.
-- **[draw.io (diagrams.net)](https://www.drawio.com/)** — Free, open-source diagramming tool with desktop and browser versions; exports to SVG, PNG, PDF.
-- **[Excalidraw](https://excalidraw.com/)** — Virtual whiteboard with a hand-drawn aesthetic; great for informal research diagrams and brainstorming.
-- **[Graphviz](https://graphviz.org/)** — Open-source graph visualization software; the DOT language is a standard for rendering directed and undirected graphs.
-- **[TikZ/PGF (LaTeX)](https://tikz.dev/)** — Programmatic figure drawing in LaTeX; unmatched precision for publication-ready technical diagrams.
-
-### Key References
-- **[Mermaid Live Editor](https://mermaid.live/)** — Browser-based editor for writing and previewing Mermaid diagrams in real time.
-- **[D2 Language](https://d2lang.com/)** — Modern declarative diagramming language; generates clean, readable diagrams from text.
-
-## Document Processing
-
-### PDF Tools
-- **[GROBID](https://github.com/kermitt2/grobid)** — ML library for extracting structured metadata and full text from scholarly PDFs; powers many academic tools.
-- **[PyMuPDF (fitz)](https://pymupdf.readthedocs.io/)** — Fast Python binding for MuPDF; extracts text, images, and annotations from PDFs.
-- **[pdfplumber](https://github.com/jsvine/pdfplumber)** — Python library for extracting text, tables, and metadata from PDFs with precise positional data.
-- **[Marker](https://github.com/VikParuchuri/marker)** — Converts PDF to Markdown with high accuracy; handles academic papers, books, and slides.
-- **[Nougat (Meta)](https://github.com/facebookresearch/nougat)** — Neural OCR for academic PDFs; converts scanned papers to structured Markdown with math.
-
-### Format Converters
-- **[Pandoc](https://pandoc.org/)** — Universal document converter: Markdown, LaTeX, DOCX, HTML, EPUB, and 40+ other formats.
-- **[Quarto](https://quarto.org/)** — Next-generation scientific publishing system; combines Jupyter, R Markdown, and Pandoc into one tool.
-- **[nbconvert](https://nbconvert.readthedocs.io/)** — Convert Jupyter notebooks to HTML, PDF, LaTeX, Markdown, and slides.
-
-## Code Execution & Notebooks
-
-### Notebook Environments
-- **[Jupyter](https://jupyter.org/)** — The standard interactive computing environment; supports Python, R, Julia, and 100+ kernels.
-- **[Google Colab](https://colab.research.google.com/)** — Free cloud-hosted Jupyter notebooks with GPU/TPU access; zero setup required.
-- **[Observable](https://observablehq.com/)** — Reactive JavaScript notebooks for data visualization and exploratory analysis.
-- **[Deepnote](https://deepnote.com/)** — Collaborative data science notebook with real-time editing, SQL integration, and scheduling.
-
-### Sandboxes & Reproducibility
-- **[Binder (mybinder.org)](https://mybinder.org/)** — Turn any Git repo into a collection of interactive notebooks; one-click reproducible environments.
-- **[Docker](https://www.docker.com/)** — Containerization platform for creating reproducible computational environments.
-- **[Pixi](https://pixi.sh/)** — Fast, cross-platform package manager built on conda-forge; reproducible environments from a single lockfile.
-- **[renv (R)](https://rstudio.github.io/renv/)** — Reproducible R environments; records and restores exact package versions per project.
-
-## Web Scraping & APIs
-
-### Scraping Tools
-- **[Scrapy](https://scrapy.org/)** — Fast, high-level Python web crawling and scraping framework.
-- **[Beautiful Soup](https://www.crummy.com/software/BeautifulSoup/)** — Python library for parsing HTML and XML; simple API for navigating and searching parse trees.
-- **[Playwright](https://playwright.dev/)** — Browser automation library from Microsoft; handles JavaScript-rendered pages in Python, Node, and .NET.
-- **[Selenium](https://www.selenium.dev/)** — Browser automation framework; the established tool for dynamic page scraping and testing.
-
-### API Clients & Wrappers
-- **[httpx](https://www.python-httpx.org/)** — Modern async-capable HTTP client for Python; successor to requests.
-- **[Crossref API](https://api.crossref.org/)** — Free REST API for querying 140M+ scholarly metadata records.
-- **[OpenAlex API](https://docs.openalex.org/)** — Fully open API for the global research graph; works, authors, institutions, topics.
-- **[Unpaywall API](https://unpaywall.org/products/api)** — REST API to find open-access copies of papers by DOI.
-
-## Knowledge Graph & RAG
-
-### Knowledge Graph Tools
-- **[Neo4j](https://neo4j.com/)** — Leading graph database; Cypher query language, free Community Edition.
-- **[NetworkX](https://networkx.org/)** — Python package for creating, manipulating, and analyzing complex networks.
-- **[Gephi](https://gephi.org/)** — Open-source network visualization and analysis platform; handles large graphs with interactive exploration.
-- **[VOSviewer](https://www.vosviewer.com/)** — Free tool for constructing and visualizing bibliometric networks (co-citation, co-authorship, keyword co-occurrence).
-
-### RAG Frameworks
-- **[LlamaIndex](https://www.llamaindex.ai/)** — Data framework for building RAG applications; connects LLMs to external data sources.
-- **[LangChain](https://www.langchain.com/)** — Framework for developing LLM-powered applications with retrieval, agents, and chains.
-- **[ChromaDB](https://www.trychroma.com/)** — Open-source embedding database for building AI applications with semantic search.
-- **[PaperQA2](https://github.com/Future-House/paper-qa)** — Purpose-built RAG for scientific literature; retrieves, reads, and cites full-text papers.
-
-## OCR & Translation
-
-### OCR Tools
-- **[Tesseract OCR](https://github.com/tesseract-ocr/tesseract)** — Open-source OCR engine maintained by Google; supports 100+ languages.
-- **[EasyOCR](https://github.com/JaidedAI/EasyOCR)** — Python OCR library with ready-to-use models for 80+ languages; simple API.
-- **[PaddleOCR](https://github.com/PaddlePaddle/PaddleOCR)** — High-accuracy multilingual OCR toolkit from Baidu; excels at CJK text and table recognition.
-- **[Mathpix](https://mathpix.com/)** — AI-powered tool for converting handwritten or printed math equations to LaTeX; also handles tables and chemistry.
-
-### Translation Services
-- **[DeepL](https://www.deepl.com/)** — AI translator known for high-quality European and Asian language translations; API available.
-- **[Google Cloud Translation](https://cloud.google.com/translate)** — Neural machine translation supporting 130+ languages; free tier available.
-- **[Argos Translate](https://www.argosopentech.com/)** — Open-source offline translation library built on OpenNMT; fully self-hostable.
-- **[GT4Sci (Google Translate for Science)](https://translate.google.com/)** — While not science-specific, Google Translate with domain glossary uploads handles technical text reasonably well.
+# Tools — Curated Skills
+
+
+> 60 recommended skills for productivity tools for diagrams, documents, code execution, and more.
+
+
+
+## Code Exec
+
+
+| Skill | Description |
+|-------|-------------|
+| [contextplus-mcp-guide](../../skills/tools/code-exec/contextplus-mcp-guide/) | Semantic code search MCP with Tree-sitter AST and RAG |
+| [google-colab-guide](../../skills/tools/code-exec/google-colab-guide/) | Run and manage Google Colab notebooks for Python and ML research |
+| [jupyter-notebook-guide](../../skills/tools/code-exec/jupyter-notebook-guide/) | Best practices for computational research notebooks with reproducible workflows |
+| [kaggle-api-guide](../../skills/tools/code-exec/kaggle-api-guide/) | Download datasets, manage competitions and notebooks via Kaggle API |
+| [overleaf-cli-guide](../../skills/tools/code-exec/overleaf-cli-guide/) | Sync and manage Overleaf LaTeX projects from the command line |
+| [python-reproducibility-guide](../../skills/tools/code-exec/python-reproducibility-guide/) | Reproducible Python environments, notebooks, and literate programming |
+| [r-reproducibility-guide](../../skills/tools/code-exec/r-reproducibility-guide/) | Create reproducible research workflows with R and RMarkdown/Quarto |
+| [sandbox-execution-guide](../../skills/tools/code-exec/sandbox-execution-guide/) | Secure sandboxed code execution environments for reproducible research computing |
+
+
+## Diagram
+
+
+| Skill | Description |
+|-------|-------------|
+| [clawphd-guide](../../skills/tools/diagram/clawphd-guide/) | Agent for converting papers to diagrams, posters, and videos |
+| [code-flow-visualizer](../../skills/tools/diagram/code-flow-visualizer/) | Convert Python, JavaScript, and TypeScript functions into Mermaid flowcharts |
+| [excalidraw-diagram-guide](../../skills/tools/diagram/excalidraw-diagram-guide/) | Generate hand-drawn style Excalidraw diagrams from text descriptions |
+| [json-data-visualizer](../../skills/tools/diagram/json-data-visualizer/) | Guide to JSON Crack for visualizing complex JSON data structures |
+| [kroki-diagram-api](../../skills/tools/diagram/kroki-diagram-api/) | Generate diagrams from text via Kroki's multi-format rendering API |
+| [mermaid-architect-guide](../../skills/tools/diagram/mermaid-architect-guide/) | Design complex multi-diagram architectures using advanced Mermaid syntax |
+| [mermaid-diagram-guide](../../skills/tools/diagram/mermaid-diagram-guide/) | Create flowcharts, sequence diagrams, and architecture diagrams with Mermaid |
+| [plantuml-guide](../../skills/tools/diagram/plantuml-guide/) | Create UML diagrams and architecture visualizations with PlantUML |
+| [scientific-graphical-abstract](../../skills/tools/diagram/scientific-graphical-abstract/) | Design effective graphical abstracts and scientific figures for papers |
+| [scientific-illustration-guide](../../skills/tools/diagram/scientific-illustration-guide/) | Create graphical abstracts, schematic diagrams, and scientific illustrations |
+| [tldraw-whiteboard-guide](../../skills/tools/diagram/tldraw-whiteboard-guide/) | Guide to tldraw for infinite canvas whiteboarding and diagram creation |
+
+
+## Document
+
+
+| Skill | Description |
+|-------|-------------|
+| [anystyle-api](../../skills/tools/document/anystyle-api/) | Citation reference parser using machine learning |
+| [docsgpt-guide](../../skills/tools/document/docsgpt-guide/) | Deploy DocsGPT for private document analysis and research knowledge bases |
+| [grobid-pdf-parsing](../../skills/tools/document/grobid-pdf-parsing/) | Extract structured text, metadata, and references from academic PDFs |
+| [large-document-reader](../../skills/tools/document/large-document-reader/) | Split and read long documents chapter-by-chapter for structured analysis |
+| [markdown-academic-guide](../../skills/tools/document/markdown-academic-guide/) | Write academic papers in Markdown with Pandoc for multi-format output |
+| [md2pdf-xelatex](../../skills/tools/document/md2pdf-xelatex/) | Convert Markdown to publication-ready PDF with LaTeX math and CJK support |
+| [openpaper-guide](../../skills/tools/document/openpaper-guide/) | Open-source tool for organizing and annotating research papers |
+| [paper-parse-guide](../../skills/tools/document/paper-parse-guide/) | Deep dual-mode reading of academic papers from PDF or URL sources |
+| [pdf-extraction-guide](../../skills/tools/document/pdf-extraction-guide/) | PDF parsing, text extraction, and document format conversion |
+| [weknora-guide](../../skills/tools/document/weknora-guide/) | Tencent document understanding engine with RAG capabilities |
+| [zotero-addon-market-guide](../../skills/tools/document/zotero-addon-market-guide/) | Plugin marketplace and discovery platform for Zotero |
+| [zotero-night-theme-guide](../../skills/tools/document/zotero-night-theme-guide/) | Dark mode theme plugin for Zotero reference manager |
+| [zotero-style-guide](../../skills/tools/document/zotero-style-guide/) | Feature-rich Zotero plugin for UI customization and styling |
+
+
+## Knowledge Graph
+
+
+| Skill | Description |
+|-------|-------------|
+| [citation-network-builder](../../skills/tools/knowledge-graph/citation-network-builder/) | Build and analyze citation networks from academic reference data |
+| [concept-map-generator](../../skills/tools/knowledge-graph/concept-map-generator/) | Generate structured concept maps from academic texts automatically |
+| [graphiti-guide](../../skills/tools/knowledge-graph/graphiti-guide/) | Build real-time knowledge graphs for AI agents using Graphiti by Zep |
+| [knowledge-graph-construction](../../skills/tools/knowledge-graph/knowledge-graph-construction/) | Build research knowledge graphs for literature synthesis and RAG systems |
+| [mimir-memory-guide](../../skills/tools/knowledge-graph/mimir-memory-guide/) | Semantic vector search memory bank for AI agents |
+| [notero-zotero-notion-guide](../../skills/tools/knowledge-graph/notero-zotero-notion-guide/) | Sync Zotero references and annotations to Notion databases |
+| [ontology-design-guide](../../skills/tools/knowledge-graph/ontology-design-guide/) | Design ontologies and knowledge graphs for research data modeling |
+| [open-webui-tools-guide](../../skills/tools/knowledge-graph/open-webui-tools-guide/) | Academic research tools for Open WebUI chat interface |
+| [openspg-guide](../../skills/tools/knowledge-graph/openspg-guide/) | Ant Group knowledge graph engine with SPG and KAG framework |
+| [paperpile-notion-guide](../../skills/tools/knowledge-graph/paperpile-notion-guide/) | Sync Paperpile references and annotations to Notion |
+| [rag-methodology-guide](../../skills/tools/knowledge-graph/rag-methodology-guide/) | RAG architecture for academic knowledge retrieval and synthesis |
+| [zotero-markdb-connect-guide](../../skills/tools/knowledge-graph/zotero-markdb-connect-guide/) | Sync Zotero references to Obsidian and Logseq markdown |
+
+
+## Ocr Translate
+
+
+| Skill | Description |
+|-------|-------------|
+| [formula-recognition-guide](../../skills/tools/ocr-translate/formula-recognition-guide/) | Math OCR and formula recognition to LaTeX conversion |
+| [handwriting-recognition-guide](../../skills/tools/ocr-translate/handwriting-recognition-guide/) | Apply handwriting OCR to digitize historical and archival documents |
+| [latex-ocr-guide](../../skills/tools/ocr-translate/latex-ocr-guide/) | Extract and convert mathematical formulas from images and PDFs to LaTeX code |
+| [latex-translation-guide](../../skills/tools/ocr-translate/latex-translation-guide/) | Translate LaTeX documents preserving math formulas and structure |
+| [math-equation-renderer](../../skills/tools/ocr-translate/math-equation-renderer/) | Render LaTeX math equations as publication-ready PNG and SVG images |
+| [multilingual-research-guide](../../skills/tools/ocr-translate/multilingual-research-guide/) | Strategies for translating academic papers while preserving technical accuracy |
+| [pdf-math-translate-guide](../../skills/tools/ocr-translate/pdf-math-translate-guide/) | Translate scientific PDFs with preserved math formatting via PDFMathTranslate |
+| [zotero-pdf-translate-guide](../../skills/tools/ocr-translate/zotero-pdf-translate-guide/) | Guide to Zotero PDF Translate for multilingual PDF and annotation translation |
+| [zotero-pdf2zh-guide](../../skills/tools/ocr-translate/zotero-pdf2zh-guide/) | PDF Chinese translation plugin for Zotero reference manager |
+
+
+## Scraping
+
+
+| Skill | Description |
+|-------|-------------|
+| [academic-web-scraping](../../skills/tools/scraping/academic-web-scraping/) | Ethical web scraping and API-based data collection for research |
+| [api-data-collection-guide](../../skills/tools/scraping/api-data-collection-guide/) | API-based data collection and web scraping for research |
+| [dataset-finder-guide](../../skills/tools/scraping/dataset-finder-guide/) | Search and download research datasets from Kaggle, HuggingFace, and repos |
+| [easy-spider-guide](../../skills/tools/scraping/easy-spider-guide/) | Guide to EasySpider for visual no-code web data collection |
+| [google-scholar-scraper](../../skills/tools/scraping/google-scholar-scraper/) | Ethical Google Scholar data collection techniques and best practices |
+| [repository-harvesting-guide](../../skills/tools/scraping/repository-harvesting-guide/) | Harvest metadata from open repositories using OAI-PMH protocol |
+| [web-scraping-ethics-guide](../../skills/tools/scraping/web-scraping-ethics-guide/) | Scrape web data ethically and legally for research purposes |

package/curated/writing/README.md

@@ -1,61 +1,108 @@
-# Curated Writing Resources
+# Writing — Curated Skills
+
+
+> 68 recommended skills for academic writing, citation management, and document preparation.
+
+
+
+## Citation
+
+
+| Skill | Description |
+|-------|-------------|
+| [academic-citation-manager](../../skills/writing/citation/academic-citation-manager/) | Manage academic citations across BibTeX, APA, MLA, and Chicago formats |
+| [academic-citation-manager-guide](../../skills/writing/citation/academic-citation-manager-guide/) | Comparison and workflow guide for academic citation management tools |
+| [bibtex-management-guide](../../skills/writing/citation/bibtex-management-guide/) | Clean, format, deduplicate, and manage BibTeX bibliography files for LaTeX |
+| [citation-assistant-skill](../../skills/writing/citation/citation-assistant-skill/) | Claude Code skill for citation workflow via Semantic Scholar |
+| [citation-style-guide](../../skills/writing/citation/citation-style-guide/) | APA, MLA, Chicago citation format guide with CSL configuration |
+| [jabref-reference-guide](../../skills/writing/citation/jabref-reference-guide/) | Guide to JabRef open-source BibTeX and BibLaTeX reference manager |
+| [jasminum-zotero-guide](../../skills/writing/citation/jasminum-zotero-guide/) | Guide to Jasminum for retrieving CNKI Chinese academic metadata in Zotero |
+| [mendeley-api](../../skills/writing/citation/mendeley-api/) | Manage references and search Mendeley's catalog via REST API |
+| [obsidian-citation-guide](../../skills/writing/citation/obsidian-citation-guide/) | Citation plugin for Obsidian note-taking with BibTeX support |
+| [obsidian-zotero-guide](../../skills/writing/citation/obsidian-zotero-guide/) | Insert citations and notes from Zotero into Obsidian knowledge bases |
+| [onecite-reference-guide](../../skills/writing/citation/onecite-reference-guide/) | AI toolkit to parse, complete, and format academic references |
+| [papersgpt-zotero-guide](../../skills/writing/citation/papersgpt-zotero-guide/) | AI plugin for Zotero with ChatGPT, Claude, and DeepSeek support |
+| [papis-cli-guide](../../skills/writing/citation/papis-cli-guide/) | Guide to Papis command-line document and bibliography manager for researchers |
+| [reference-manager-comparison](../../skills/writing/citation/reference-manager-comparison/) | Compare Zotero, Mendeley, EndNote, and Paperpile for research use |
+| [zotero-api](../../skills/writing/citation/zotero-api/) | Reference management library and collections API |
+| [zotero-better-bibtex-guide](../../skills/writing/citation/zotero-better-bibtex-guide/) | Guide to Better BibTeX for Zotero for LaTeX and BibTeX workflows |
+| [zotero-better-notes-guide](../../skills/writing/citation/zotero-better-notes-guide/) | Guide to Zotero Better Notes for comprehensive note-taking in research |
+| [zotero-gpt-guide](../../skills/writing/citation/zotero-gpt-guide/) | Guide to Zotero GPT for AI-powered research assistance within Zotero |
+| [zotero-mcp-guide](../../skills/writing/citation/zotero-mcp-guide/) | Guide to Zotero MCP for connecting Zotero library with AI assistants |
+| [zotero-mdnotes-guide](../../skills/writing/citation/zotero-mdnotes-guide/) | Export Zotero items and annotations to Markdown note files |
+| [zotero-reference-guide](../../skills/writing/citation/zotero-reference-guide/) | PDF references add-on for enriching Zotero library metadata |
+| [zotero-scholar-guide](../../skills/writing/citation/zotero-scholar-guide/) | Save papers with metadata to Zotero via its API programmatically |
+| [zotfile-attachment-guide](../../skills/writing/citation/zotfile-attachment-guide/) | Guide to ZotFile for Zotero attachment management, renaming, and syncing |
 
-> Hand-picked resources for academic researchers working on composition, polishing, formatting, and citation management.
 
 ## Composition
 
-### Writing Guides
-- **[Writing Your Journal Article in Twelve Weeks (Belcher)](https://www.uchicago.edu/research/)** — Step-by-step workbook for turning a draft into a publishable paper; widely used in writing groups.
-- **[The Craft of Research (Booth, Colomb, Williams)](https://press.uchicago.edu/ucp/books/book/chicago/C/bo23521678.html)** — Classic guide to planning, drafting, and revising research writing.
-- **[How to Write a Great Research Paper (Simon Peyton Jones)](https://www.microsoft.com/en-us/research/academic-program/write-great-research-paper/)** — Concise advice from an experienced CS researcher; accompanying video talk is essential viewing.
-- **[Explorations of Style (blog)](https://explorationsofstyle.com/)** — Rachael Cayley's blog on graduate-level academic writing; practical and discipline-agnostic.
 
-### Structure Templates
-- **[IMRaD Structure Guide (NCBI)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC442179/)** — Standard Introduction-Methods-Results-Discussion structure explained for biomedical papers.
-- **[Heilmeier Catechism](https://www.darpa.mil/about/heilmeier-catechism)** — DARPA's framework for articulating research goals; excellent for proposal introductions.
+| Skill | Description |
+|-------|-------------|
+| [abstract-writing-guide](../../skills/writing/composition/abstract-writing-guide/) | Craft structured research abstracts that maximize clarity and journal acceptance |
+| [discussion-writing-guide](../../skills/writing/composition/discussion-writing-guide/) | Write effective discussion sections that interpret results and impact |
+| [introduction-writing-guide](../../skills/writing/composition/introduction-writing-guide/) | Guide to writing effective research paper introductions |
+| [literature-review-writing](../../skills/writing/composition/literature-review-writing/) | Structure and write comprehensive literature reviews for any field |
+| [methods-section-guide](../../skills/writing/composition/methods-section-guide/) | Guide to writing clear and reproducible methodology sections |
+| [ml-paper-writing](../../skills/writing/composition/ml-paper-writing/) | Write ML/AI research papers targeting NeurIPS, ICML, and ICLR venues |
+| [opendraft-thesis-guide](../../skills/writing/composition/opendraft-thesis-guide/) | AI thesis writer with specialized agents and verified citations |
+| [paper-debugger-guide](../../skills/writing/composition/paper-debugger-guide/) | Multi-agent system for academic writing review and improvement |
+| [paperforge-guide](../../skills/writing/composition/paperforge-guide/) | AI-assisted academic paper drafting and structuring tool |
+| [research-paper-writer](../../skills/writing/composition/research-paper-writer/) | Guide for writing formal academic papers following IEEE and ACM standards |
+| [response-to-reviewers](../../skills/writing/composition/response-to-reviewers/) | Write effective point-by-point responses to peer reviewer comments for revisions |
+| [scientific-writing-guide](../../skills/writing/composition/scientific-writing-guide/) | Curated tools and techniques for scientific writing beyond LaTeX |
+| [scientific-writing-resources](../../skills/writing/composition/scientific-writing-resources/) | Curated tools and resources for effective scientific writing |
+| [scientific-writing-wrapper](../../skills/writing/composition/scientific-writing-wrapper/) | AI-powered scientific writing workflow from outline to polished draft |
 
-## Polish
 
-### Tools & Software
-- **[Grammarly](https://www.grammarly.com/)** — AI writing assistant for grammar, clarity, tone, and plagiarism detection.
-- **[Writefull](https://www.writefull.com/)** — Language feedback tool trained specifically on published academic text; integrates with Overleaf and Word.
-- **[LanguageTool](https://languagetool.org/)** — Open-source grammar checker supporting 30+ languages; self-hostable.
-- **[Hemingway Editor](https://hemingwayapp.com/)** — Highlights complex sentences, passive voice, and readability issues; forces concision.
+## Latex
+
 
-### Style Guides
-- **[APA Style (7th ed.)](https://apastyle.apa.org/)** — Official APA manual; standard for social sciences, education, and psychology.
-- **[Chicago Manual of Style](https://www.chicagomanualofstyle.org/)** — Comprehensive guide for humanities writing and publishing.
-- **[IEEE Editorial Style Manual](https://journals.ieeeauthorcenter.ieee.org/your-role-in-article-production/ieee-editorial-style-manual/)** — Required style reference for all IEEE publications.
+| Skill | Description |
+|-------|-------------|
+| [academic-writing-latex](../../skills/writing/latex/academic-writing-latex/) | LaTeX-based academic writing assistant for thesis and paper templates |
+| [bibliography-management-guide](../../skills/writing/latex/bibliography-management-guide/) | Manage references with BibLaTeX, natbib, and LaTeX bibliography styles |
+| [latex-drawing-collection](../../skills/writing/latex/latex-drawing-collection/) | LaTeX drawing examples for Bayesian networks, tensors, and diagrams |
+| [latex-drawing-guide](../../skills/writing/latex/latex-drawing-guide/) | TikZ and PGFPlots techniques for publication-quality scientific figures |
+| [latex-ecosystem-guide](../../skills/writing/latex/latex-ecosystem-guide/) | Comprehensive guide to LaTeX editors, packages, and typesetting workflows |
+| [latex-templates-collection](../../skills/writing/latex/latex-templates-collection/) | Collection of LaTeX templates for papers, presentations, and CVs |
+| [math-typesetting-guide](../../skills/writing/latex/math-typesetting-guide/) | LaTeX math typesetting, equation formatting, and cross-referencing |
+| [md-to-pdf-academic](../../skills/writing/latex/md-to-pdf-academic/) | Convert Markdown to publication-quality PDF with LaTeX math rendering |
+| [overleaf-collaboration-guide](../../skills/writing/latex/overleaf-collaboration-guide/) | Guide to collaborative LaTeX editing with Overleaf |
+| [tex-render-guide](../../skills/writing/latex/tex-render-guide/) | Render LaTeX math expressions to images in PNG, JPEG, and SVG |
+| [tikz-diagrams-guide](../../skills/writing/latex/tikz-diagrams-guide/) | Create publication-quality scientific diagrams with TikZ in LaTeX |
 
-## LaTeX
 
-### Editors & Environments
-- **[Overleaf](https://www.overleaf.com/)** — Collaborative online LaTeX editor; 1-click submission to journals; free tier available.
-- **[TeXstudio](https://www.texstudio.org/)** — Feature-rich open-source desktop LaTeX editor with inline preview.
-- **[Typst](https://typst.app/)** — Modern typesetting system designed as a simpler alternative to LaTeX; growing fast.
+## Polish
 
-### Packages & References
-- **[CTAN](https://ctan.org/)** — Comprehensive TeX Archive Network; the canonical package repository.
-- **[LaTeX Wikibook](https://en.wikibooks.org/wiki/LaTeX)** — Community-maintained, beginner-friendly LaTeX reference.
-- **[TikZ/PGF Manual](https://tikz.dev/)** — The standard for programmatic figure drawing in LaTeX.
 
-## Templates
+| Skill | Description |
+|-------|-------------|
+| [academic-tone-guide](../../skills/writing/polish/academic-tone-guide/) | Adjust writing tone and register for academic audiences and venues |
+| [academic-translation-guide](../../skills/writing/polish/academic-translation-guide/) | Academic translation, post-editing, and Chinglish correction guide |
+| [academic-writing-refiner](../../skills/writing/polish/academic-writing-refiner/) | Checklist-driven academic English polishing and Chinglish correction |
+| [ai-writing-humanizer](../../skills/writing/polish/ai-writing-humanizer/) | Remove AI-generated patterns to produce natural, authentic academic writing |
+| [chinese-text-humanizer](../../skills/writing/polish/chinese-text-humanizer/) | Transform AI-generated Chinese text into natural academic writing style |
+| [conciseness-editing-guide](../../skills/writing/polish/conciseness-editing-guide/) | Eliminate wordiness and redundancy in academic prose for clarity |
+| [grammar-checker-guide](../../skills/writing/polish/grammar-checker-guide/) | Use grammar and style checking tools to polish academic manuscripts |
+| [paper-polish-guide](../../skills/writing/polish/paper-polish-guide/) | Review and polish LaTeX research papers for clarity and style |
+| [plagiarism-detection-guide](../../skills/writing/polish/plagiarism-detection-guide/) | Use plagiarism detection tools and ensure manuscript originality |
 
-### Journal & Conference Templates
-- **[Overleaf Templates Gallery](https://www.overleaf.com/latex/templates)** — Thousands of publisher-official and community LaTeX templates.
-- **[IEEE Template Selector](https://template-selector.ieee.org/)** — Official tool to find the correct IEEE template for your target publication.
-- **[Springer LaTeX Templates](https://www.springer.com/gp/authors-editors/book-authors-editors/your-publication-journey/manuscript-preparation)** — Official Springer Nature templates for books and journals.
-- **[Elsevier LaTeX Templates](https://www.elsevier.com/researcher/author/policies-and-guidelines/latex-instructions)** — elsarticle class and documentation for all Elsevier journals.
 
-## Citation Management
+## Templates
 
-### Reference Managers
-- **[Zotero](https://www.zotero.org/)** — Free, open-source reference manager with browser connector, PDF annotation, and Word/LibreOffice plugins.
-- **[Paperpile](https://paperpile.com/)** — Fast, clean reference manager with tight Google Docs and Overleaf integration.
-- **[Mendeley](https://www.mendeley.com/)** — Free reference manager and academic social network by Elsevier; good PDF reader.
-- **[JabRef](https://www.jabref.org/)** — Open-source BibTeX/BibLaTeX manager; ideal for LaTeX-centric workflows.
 
-### Format & Conversion Tools
-- **[Citation Style Language (CSL)](https://citationstyles.org/)** — Open repository of 10,000+ citation styles used by Zotero, Mendeley, and Pandoc.
-- **[doi2bib](https://www.doi2bib.org/)** — Paste a DOI, get a BibTeX entry instantly.
-- **[AnyStyle](https://anystyle.io/)** — AI-powered parser that extracts structured references from plain-text bibliographies.
+| Skill | Description |
+|-------|-------------|
+| [arxiv-preprint-template](../../skills/writing/templates/arxiv-preprint-template/) | LaTeX template for arXiv preprints in NIPS/NeurIPS style format |
+| [beamer-presentation-guide](../../skills/writing/templates/beamer-presentation-guide/) | Guide to creating academic presentations with LaTeX Beamer |
+| [conference-paper-template](../../skills/writing/templates/conference-paper-template/) | Templates and formatting guides for major academic conference submissions |
+| [elegant-paper-template](../../skills/writing/templates/elegant-paper-template/) | Beautiful LaTeX template for working papers and technical reports |
+| [graphical-abstract-guide](../../skills/writing/templates/graphical-abstract-guide/) | Create SVG graphical abstracts for journal paper submissions |
+| [novathesis-guide](../../skills/writing/templates/novathesis-guide/) | LaTeX thesis template supporting multiple universities and formats |
+| [scientific-article-pdf](../../skills/writing/templates/scientific-article-pdf/) | Generate publication-ready scientific article PDFs from templates |
+| [sjtuthesis-guide](../../skills/writing/templates/sjtuthesis-guide/) | Write SJTU theses using the SJTUThesis LaTeX template with full compliance |
+| [thesis-template-guide](../../skills/writing/templates/thesis-template-guide/) | Set up LaTeX templates for PhD and Master's thesis documents |
+| [thesis-writing-guide](../../skills/writing/templates/thesis-writing-guide/) | Templates, formatting rules, and strategies for thesis and dissertation writing |
+| [thuthesis-guide](../../skills/writing/templates/thuthesis-guide/) | Write Tsinghua University theses using the ThuThesis LaTeX template |

package/mcp-configs/academic-db/alphafold-mcp.json

@@ -0,0 +1,20 @@
+{
+  "id": "alphafold-mcp",
+  "name": "AlphaFold MCP",
+  "description": "AlphaFold Protein Structure Database for structure prediction",
+  "category": "academic-db",
+  "install": {
+    "runtime": "node",
+    "package": "alphafold-mcp-server",
+    "command": "npm install -g alphafold-mcp-server"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "get_structure",
+    "search_protein"
+  ],
+  "verified": false,
+  "source": "https://github.com/ac3xx/AlphaFold-MCP-Server"
+}

package/mcp-configs/academic-db/brightspace-mcp.json

@@ -0,0 +1,21 @@
+{
+  "id": "brightspace-mcp",
+  "name": "Brightspace LMS MCP",
+  "description": "D2L Brightspace LMS: grades, assignments, announcements",
+  "category": "academic-db",
+  "install": {
+    "runtime": "node",
+    "package": "brightspace-mcp-server",
+    "command": "npm install -g brightspace-mcp-server"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "get_grades",
+    "get_assignments",
+    "get_announcements"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/brightspace-mcp-server"
+}

package/mcp-configs/academic-db/climatiq-mcp.json

@@ -0,0 +1,20 @@
+{
+  "id": "climatiq-mcp",
+  "name": "Climatiq Carbon MCP",
+  "description": "Carbon emissions calculations via Climatiq API",
+  "category": "academic-db",
+  "install": {
+    "runtime": "node",
+    "package": "climatiq-mcp-server",
+    "command": "npm install -g climatiq-mcp-server"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "estimate",
+    "get_factors"
+  ],
+  "verified": false,
+  "source": "https://github.com/Climatiq/climatiq-mcp-server"
+}

package/mcp-configs/academic-db/gibs-mcp.json

@@ -0,0 +1,20 @@
+{
+  "id": "gibs-mcp",
+  "name": "GIBS Regulatory MCP",
+  "description": "Regulatory compliance search (AI Act, GDPR, DORA) with citations",
+  "category": "academic-db",
+  "install": {
+    "runtime": "node",
+    "package": "gibs-mcp",
+    "command": "npm install -g gibs-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search_regulation",
+    "get_article"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/gibs-mcp"
+}

package/mcp-configs/academic-db/gis-mcp-server.json

@@ -0,0 +1,22 @@
+{
+  "id": "gis-mcp-server",
+  "name": "GIS MCP Server",
+  "description": "Geocoding, routing, elevation, spatial analysis, Shapefile/GeoJSON",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "gis-mcp-server",
+    "command": "pip install gis-mcp-server"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "geocode",
+    "route",
+    "elevation",
+    "spatial_analysis"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/gis-mcp-server"
+}

package/mcp-configs/academic-db/google-earth-engine-mcp.json

@@ -0,0 +1,21 @@
+{
+  "id": "google-earth-engine-mcp",
+  "name": "Google Earth Engine MCP",
+  "description": "Query Google Earth Engine with natural language",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "google-earth-engine-mcp",
+    "command": "pip install google-earth-engine-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "query",
+    "get_dataset",
+    "analyze"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/google-earth-engine-mcp"
+}

package/mcp-configs/academic-db/m4-clinical-mcp.json

@@ -0,0 +1,21 @@
+{
+  "id": "m4-clinical-mcp",
+  "name": "M4 Clinical Database MCP",
+  "description": "MIMIC-IV and eICU clinical database with domain knowledge",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "m4",
+    "command": "pip install m4"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "query",
+    "get_patient",
+    "analyze"
+  ],
+  "verified": false,
+  "source": "https://github.com/derrickmo/m4"
+}

package/mcp-configs/academic-db/medical-mcp.json

@@ -0,0 +1,21 @@
+{
+  "id": "medical-mcp",
+  "name": "Medical MCP",
+  "description": "Medical information from FDA, WHO, PubMed drug databases",
+  "category": "academic-db",
+  "install": {
+    "runtime": "node",
+    "package": "medical-mcp",
+    "command": "npm install -g medical-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search_drugs",
+    "get_interactions",
+    "search_conditions"
+  ],
+  "verified": false,
+  "source": "https://github.com/Cicatriiz/medical-mcp"
+}

package/mcp-configs/academic-db/nexonco-mcp.json

@@ -0,0 +1,20 @@
+{
+  "id": "nexonco-mcp",
+  "name": "NexOnco MCP",
+  "description": "Clinical evidence data for precision medicine and oncology",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "nexonco-mcp",
+    "command": "pip install nexonco-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search_evidence",
+    "get_treatment"
+  ],
+  "verified": false,
+  "source": "https://github.com/nicosantos-mcp/nexonco-mcp"
+}

package/mcp-configs/academic-db/omop-mcp.json

@@ -0,0 +1,20 @@
+{
+  "id": "omop-mcp",
+  "name": "OMOP Concept MCP",
+  "description": "Map clinical terminology to OMOP concepts for healthcare data",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "omop-mcp",
+    "command": "pip install omop-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search_concepts",
+    "map_terms"
+  ],
+  "verified": false,
+  "source": "https://github.com/nicosantos-mcp/omop_mcp"
+}