@wentorai/research-plugins 1.1.0 → 1.2.0

package/curated/tools/README.md

@@ -1,7 +1,8 @@
 # Tools — Curated Skills
 
 
-> 42 recommended skills for productivity tools for diagrams, documents, code execution, and more.
+> 60 recommended skills for productivity tools for diagrams, documents, code execution, and more.
+
 
 
 ## Code Exec
@@ -9,6 +10,7 @@
 
 | 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 |
@@ -23,12 +25,15 @@
 
 | 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 |
 
@@ -43,8 +48,14 @@
 | [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
@@ -56,8 +67,14 @@
 | [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
@@ -68,6 +85,8 @@
 | [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 |

package/curated/writing/README.md

@@ -1,7 +1,8 @@
 # Writing — Curated Skills
 
 
-> 57 recommended skills for academic writing, citation management, and document preparation.
+> 68 recommended skills for academic writing, citation management, and document preparation.
+
 
 
 ## Citation
@@ -10,12 +11,16 @@
 | 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 |
@@ -41,7 +46,10 @@
 | [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 |
@@ -53,6 +61,7 @@
 
 | 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 |
@@ -74,6 +83,7 @@
 | [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 |
@@ -85,8 +95,10 @@
 
 | 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 |

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"
+}

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

@@ -0,0 +1,20 @@
+{
+  "id": "onekgpd-mcp",
+  "name": "1000 Genomes MCP",
+  "description": "Real-time access to 1000 Genomes Project dataset",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "onekgpd-mcp",
+    "command": "pip install onekgpd-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search_variants",
+    "get_population"
+  ],
+  "verified": false,
+  "source": "https://github.com/nicosantos-mcp/onekgpd-mcp"
+}

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

@@ -0,0 +1,20 @@
+{
+  "id": "openedu-mcp",
+  "name": "OpenEdu MCP",
+  "description": "Educational resources from OpenLibrary, Wikipedia, arXiv",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "openedu-mcp",
+    "command": "pip install openedu-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search",
+    "get_resource"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/openedu-mcp"
+}

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

@@ -0,0 +1,20 @@
+{
+  "id": "opengenes-mcp",
+  "name": "OpenGenes MCP",
+  "description": "Aging and longevity research gene database",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "opengenes-mcp",
+    "command": "pip install opengenes-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search_genes",
+    "get_gene_info"
+  ],
+  "verified": false,
+  "source": "https://github.com/nicosantos-mcp/opengenes-mcp"
+}

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

@@ -0,0 +1,21 @@
+{
+  "id": "openstax-mcp",
+  "name": "OpenStax Textbooks MCP",
+  "description": "OpenStax textbooks with semantic search and practice problems",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "openstax-mcp-server",
+    "command": "pip install openstax-mcp-server"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search",
+    "get_chapter",
+    "generate_problems"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/openstax-mcp-server"
+}

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

@@ -0,0 +1,21 @@
+{
+  "id": "openstreetmap-mcp",
+  "name": "OpenStreetMap MCP",
+  "description": "OpenStreetMap location services and geospatial data",
+  "category": "academic-db",
+  "install": {
+    "runtime": "node",
+    "package": "open-streetmap-mcp",
+    "command": "npm install -g open-streetmap-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search",
+    "geocode",
+    "get_map"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/open-streetmap-mcp"
+}

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

@@ -0,0 +1,21 @@
+{
+  "id": "opentargets-mcp",
+  "name": "Open Targets MCP",
+  "description": "Open Targets Platform GraphQL for drug target discovery",
+  "category": "academic-db",
+  "install": {
+    "runtime": "python",
+    "package": "opentargets-mcp",
+    "command": "pip install opentargets-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search_targets",
+    "get_associations",
+    "get_drugs"
+  ],
+  "verified": false,
+  "source": "https://github.com/nicosantos-mcp/opentargets-mcp"
+}

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

@@ -0,0 +1,21 @@
+{
+  "id": "pdb-mcp",
+  "name": "Protein Data Bank MCP",
+  "description": "PDB worldwide 3D protein structure repository",
+  "category": "academic-db",
+  "install": {
+    "runtime": "node",
+    "package": "pdb-mcp-server",
+    "command": "npm install -g pdb-mcp-server"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search",
+    "get_structure",
+    "get_sequence"
+  ],
+  "verified": false,
+  "source": "https://github.com/ac3xx/PDB-MCP-Server"
+}

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

@@ -0,0 +1,20 @@
+{
+  "id": "smithsonian-mcp",
+  "name": "Smithsonian Open Access MCP",
+  "description": "Smithsonian Institution Open Access museum collections",
+  "category": "academic-db",
+  "install": {
+    "runtime": "node",
+    "package": "smithsonian-mcp",
+    "command": "npm install -g smithsonian-mcp"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search",
+    "get_item"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/smithsonian-mcp"
+}

package/mcp-configs/ai-platform/magi-researchers.json

@@ -0,0 +1,21 @@
+{
+  "id": "magi-researchers",
+  "name": "MAGI Researchers MCP",
+  "description": "Three AI models cross-verify for multi-perspective research",
+  "category": "ai-platform",
+  "install": {
+    "runtime": "python",
+    "package": "magi-researchers",
+    "command": "pip install magi-researchers"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "research",
+    "verify",
+    "synthesize"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/magi-researchers"
+}

package/mcp-configs/ai-platform/mcp-academic-researcher.json

@@ -0,0 +1,22 @@
+{
+  "id": "mcp-academic-researcher",
+  "name": "Academic Researcher MCP",
+  "description": "Full-stack research assistant with papers, notes, citations",
+  "category": "ai-platform",
+  "install": {
+    "runtime": "python",
+    "package": "mcp-academic-researcher",
+    "command": "pip install mcp-academic-researcher"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search",
+    "take_notes",
+    "cite",
+    "analyze"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/mcp-academic-researcher"
+}

package/mcp-configs/ai-platform/open-paper-machine.json

@@ -0,0 +1,21 @@
+{
+  "id": "open-paper-machine",
+  "name": "Open Paper Machine MCP",
+  "description": "Autonomous agent for full academic paper pipeline",
+  "category": "ai-platform",
+  "install": {
+    "runtime": "python",
+    "package": "open-paper-machine",
+    "command": "pip install open-paper-machine"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "research",
+    "write",
+    "compile"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/open-paper-machine"
+}

package/mcp-configs/ai-platform/paper-intelligence.json

@@ -0,0 +1,21 @@
+{
+  "id": "paper-intelligence",
+  "name": "Paper Intelligence MCP",
+  "description": "PDF management with RAG capabilities",
+  "category": "ai-platform",
+  "install": {
+    "runtime": "python",
+    "package": "paper-intelligence",
+    "command": "pip install paper-intelligence"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "ingest",
+    "search",
+    "summarize"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/paper-intelligence"
+}

package/mcp-configs/ai-platform/paper-reader.json

@@ -0,0 +1,21 @@
+{
+  "id": "paper-reader",
+  "name": "Paper Reader MCP",
+  "description": "Search, read, and summarize arXiv papers",
+  "category": "ai-platform",
+  "install": {
+    "runtime": "python",
+    "package": "paper-reader",
+    "command": "pip install paper-reader"
+  },
+  "config": {
+    "env": {}
+  },
+  "tools": [
+    "search",
+    "read",
+    "summarize"
+  ],
+  "verified": false,
+  "source": "https://github.com/jjohare/paper_reader"
+}