@wentorai/research-plugins 1.0.0 → 1.2.0

package/skills/tools/diagram/tldraw-whiteboard-guide/SKILL.md

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+---
+name: tldraw-whiteboard-guide
+description: "Guide to tldraw for infinite canvas whiteboarding and diagram creation"
+metadata:
+  openclaw:
+    emoji: "🖊️"
+    category: "tools"
+    subcategory: "diagram"
+    keywords: ["whiteboard", "infinite canvas", "diagram SDK", "collaborative drawing", "research diagrams", "visual thinking"]
+    source: "https://github.com/tldraw/tldraw"
+---
+
+# tldraw Whiteboard Guide
+
+## Overview
+
+tldraw is an open-source infinite canvas whiteboard SDK with over 46K stars on GitHub. It provides a complete whiteboard experience that can be used standalone or embedded into custom applications. The library offers a polished, intuitive drawing interface with shapes, connectors, text, freehand drawing, and image support, all running in the browser with no backend required for basic use.
+
+For academic researchers, tldraw serves multiple roles. It can function as a collaborative brainstorming tool for research ideation sessions, a diagram creation tool for papers and presentations, a visual note-taking surface during literature reviews, and a framework diagramming tool for conceptual models. Unlike traditional diagramming tools that impose rigid structures, tldraw's freeform canvas encourages the kind of fluid visual thinking that drives research innovation.
+
+The SDK architecture makes tldraw particularly interesting for research tool builders. It can be embedded into lab notebooks, research management platforms, and educational tools. The state management system is extensible, allowing developers to add custom shapes, tools, and behaviors for domain-specific diagramming needs such as circuit diagrams, molecular structures, or experimental workflow visualizations.
+
+## Getting Started
+
+### Using tldraw Online
+
+The fastest way to use tldraw is through the hosted version at tldraw.com. Create diagrams immediately with no installation, and share them via links.
+
+### Self-Hosted Deployment
+
+```bash
+# Clone and run locally
+git clone https://github.com/tldraw/tldraw.git
+cd tldraw
+npm install
+npm run dev
+
+# Access at http://localhost:5420
+```
+
+### Embedding in a React Application
+
+```bash
+# Install the tldraw package
+npm install tldraw
+```
+
+```tsx
+import { Tldraw } from 'tldraw';
+import 'tldraw/tldraw.css';
+
+function ResearchWhiteboard() {
+  return (
+    <div style={{ width: '100vw', height: '100vh' }}>
+      <Tldraw />
+    </div>
+  );
+}
+```
+
+## Core Features for Research Work
+
+### Shape Tools
+
+tldraw provides a comprehensive set of shape tools suitable for creating research diagrams:
+
+- **Rectangle** - Process boxes, system components, categories
+- **Ellipse** - States, entities, conceptual groupings
+- **Diamond** - Decision nodes, conditions
+- **Arrow** - Relationships, flows, dependencies, causal links
+- **Line** - Connections, separators, timelines
+- **Text** - Labels, annotations, descriptions
+- **Freehand** - Sketches, handwritten annotations, emphasis marks
+- **Note** - Sticky notes for brainstorming and categorization
+- **Frame** - Grouping related elements into named sections
+- **Star/Heart/Cloud** - Emphasis markers and decorative elements
+
+### Drawing a Research Framework Diagram
+
+A typical research conceptual framework can be constructed using tldraw's shape tools.
+
+```
+Example: Conceptual Framework for Mixed-Methods Study
+
+1. Create a Frame labeled "Research Design"
+2. Add rectangles for each research phase:
+   - "Literature Review" -> "Hypothesis Formation"
+   - "Quantitative Study" -> "Statistical Analysis"
+   - "Qualitative Study" -> "Thematic Analysis"
+   - "Integration" -> "Conclusions"
+3. Connect phases with arrows showing sequence and relationships
+4. Use color coding:
+   - Blue rectangles: quantitative components
+   - Green rectangles: qualitative components
+   - Purple rectangles: integration points
+5. Add text labels for key variables and relationships
+6. Use sticky notes for annotations about methods and tools
+```
+
+### Collaborative Research Sessions
+
+tldraw supports real-time collaboration when deployed with its sync backend, making it ideal for remote research meetings.
+
+```tsx
+import { Tldraw, createTLStore } from 'tldraw';
+import { useSync } from '@tldraw/sync';
+
+function CollaborativeWhiteboard({ roomId }) {
+  const store = useSync({
+    uri: `wss://collaboration-server.lab.internal/connect/${roomId}`,
+    assets: { /* asset configuration */ }
+  });
+
+  return (
+    <div style={{ width: '100%', height: '80vh' }}>
+      <Tldraw store={store} />
+    </div>
+  );
+}
+```
+
+## Custom Shapes for Domain-Specific Diagrams
+
+One of tldraw's most powerful features for research is the ability to define custom shapes. Researchers can create domain-specific visual elements.
+
+### Defining a Custom Research Node Shape
+
+```tsx
+import {
+  ShapeUtil,
+  TLBaseShape,
+  HTMLContainer,
+  BaseBoxShapeUtil,
+} from 'tldraw';
+
+// Define the shape type
+type ResearchNodeShape = TLBaseShape<
+  'research-node',
+  {
+    w: number;
+    h: number;
+    label: string;
+    nodeType: 'hypothesis' | 'method' | 'finding' | 'conclusion';
+    status: 'planned' | 'in-progress' | 'complete';
+  }
+>;
+
+// Color map for node types
+const nodeColors = {
+  hypothesis: '#3B82F6',
+  method: '#10B981',
+  finding: '#F59E0B',
+  conclusion: '#EF4444',
+};
+
+const statusIcons = {
+  planned: '[ ]',
+  'in-progress': '[~]',
+  complete: '[x]',
+};
+
+class ResearchNodeUtil extends BaseBoxShapeUtil<ResearchNodeShape> {
+  static override type = 'research-node' as const;
+
+  getDefaultProps(): ResearchNodeShape['props'] {
+    return {
+      w: 200,
+      h: 80,
+      label: 'New Node',
+      nodeType: 'hypothesis',
+      status: 'planned',
+    };
+  }
+
+  component(shape: ResearchNodeShape) {
+    const { label, nodeType, status } = shape.props;
+    const color = nodeColors[nodeType];
+
+    return (
+      <HTMLContainer>
+        <div style={{
+          width: '100%',
+          height: '100%',
+          backgroundColor: color + '20',
+          border: `2px solid ${color}`,
+          borderRadius: '8px',
+          padding: '8px 12px',
+          display: 'flex',
+          flexDirection: 'column',
+          justifyContent: 'center',
+          fontFamily: 'Inter, sans-serif',
+        }}>
+          <div style={{ fontSize: '10px', color: color, fontWeight: 600 }}>
+            {nodeType.toUpperCase()} {statusIcons[status]}
+          </div>
+          <div style={{ fontSize: '13px', color: '#1F2937', marginTop: '4px' }}>
+            {label}
+          </div>
+        </div>
+      </HTMLContainer>
+    );
+  }
+
+  indicator(shape: ResearchNodeShape) {
+    return (
+      <rect
+        width={shape.props.w}
+        height={shape.props.h}
+        rx={8}
+        ry={8}
+      />
+    );
+  }
+}
+```
+
+### Registering Custom Shapes
+
+```tsx
+import { Tldraw } from 'tldraw';
+
+const customShapeUtils = [ResearchNodeUtil];
+
+function ResearchDiagramEditor() {
+  return (
+    <Tldraw
+      shapeUtils={customShapeUtils}
+      tools={[/* custom tools */]}
+    />
+  );
+}
+```
+
+## Research Diagram Templates
+
+### Literature Review Mind Map
+
+Use tldraw to create a visual literature map during systematic reviews:
+
+```
+Structure:
+- Central node: Research Question
+- Branch 1: Theoretical Frameworks
+  - Sub-nodes for each major theory
+  - Connections showing relationships between theories
+- Branch 2: Key Findings
+  - Grouped by theme or methodology
+  - Color-coded by strength of evidence
+- Branch 3: Research Gaps
+  - Identified gaps linked to existing literature
+  - Arrows pointing to proposed research directions
+```
+
+### Experimental Design Flowchart
+
+```
+Layout:
+1. Start: "Research Question"
+2. Diamond: "Experimental or Observational?"
+3. Branch A (Experimental):
+   - "Control Group Definition"
+   - "Treatment Conditions"
+   - "Randomization Strategy"
+   - "Measurement Protocol"
+4. Branch B (Observational):
+   - "Sampling Frame"
+   - "Data Collection Method"
+   - "Confound Identification"
+5. Merge: "Data Analysis Plan"
+6. End: "Expected Outcomes"
+```
+
+### System Architecture Diagram
+
+For computational research papers that need to illustrate software architecture:
+
+```
+Components arranged in layers:
+- Top: User Interface (web dashboard, CLI)
+- Middle: Application Logic (API server, task scheduler)
+- Bottom: Data Layer (database, file storage, cache)
+- Side: External Services (cloud APIs, instrument interfaces)
+- Arrows showing data flow between components
+- Color coding for different deployment environments
+```
+
+## Exporting Diagrams for Publications
+
+### Export as SVG (Vector)
+
+tldraw supports exporting the canvas or selected shapes as SVG, which is ideal for publication figures.
+
+```tsx
+import { Editor } from 'tldraw';
+
+async function exportDiagram(editor: Editor) {
+  // Export selected shapes or entire page
+  const shapeIds = editor.getSelectedShapeIds();
+  const svg = await editor.getSvg(
+    shapeIds.length > 0 ? shapeIds : undefined,
+    { background: true, padding: 20 }
+  );
+
+  if (svg) {
+    const svgString = new XMLSerializer().serializeToString(svg);
+    const blob = new Blob([svgString], { type: 'image/svg+xml' });
+    const url = URL.createObjectURL(blob);
+
+    const link = document.createElement('a');
+    link.href = url;
+    link.download = 'research-diagram.svg';
+    link.click();
+    URL.revokeObjectURL(url);
+  }
+}
+```
+
+### Export as PNG (Raster)
+
+```tsx
+async function exportAsPng(editor: Editor) {
+  const blob = await editor.toImage(
+    editor.getSelectedShapeIds(),
+    { type: 'png', quality: 1, scale: 3, background: true }
+  );
+
+  const url = URL.createObjectURL(blob);
+  const link = document.createElement('a');
+  link.href = url;
+  link.download = 'research-diagram.png';
+  link.click();
+  URL.revokeObjectURL(url);
+}
+```
+
+## Programmatic Diagram Generation
+
+For reproducible research diagrams, tldraw's API allows programmatic shape creation.
+
+```tsx
+function generateMethodologyDiagram(editor: Editor, steps: string[]) {
+  const startX = 100;
+  const startY = 100;
+  const boxWidth = 200;
+  const boxHeight = 60;
+  const gap = 40;
+
+  steps.forEach((step, index) => {
+    const y = startY + index * (boxHeight + gap);
+
+    // Create a box for each step
+    editor.createShape({
+      type: 'geo',
+      x: startX,
+      y: y,
+      props: {
+        geo: 'rectangle',
+        w: boxWidth,
+        h: boxHeight,
+        text: step,
+        fill: 'semi',
+        color: 'blue',
+      },
+    });
+
+    // Connect to next step with an arrow
+    if (index < steps.length - 1) {
+      editor.createShape({
+        type: 'arrow',
+        props: {
+          start: { x: startX + boxWidth / 2, y: y + boxHeight },
+          end: { x: startX + boxWidth / 2, y: y + boxHeight + gap },
+        },
+      });
+    }
+  });
+
+  editor.zoomToFit();
+}
+
+// Usage
+generateMethodologyDiagram(editor, [
+  'Data Collection',
+  'Preprocessing',
+  'Feature Extraction',
+  'Model Training',
+  'Evaluation',
+  'Publication',
+]);
+```
+
+## References
+
+- tldraw official site: https://tldraw.com
+- tldraw GitHub repository: https://github.com/tldraw/tldraw
+- tldraw SDK documentation: https://tldraw.dev
+- tldraw examples: https://github.com/tldraw/tldraw/tree/main/apps/examples

package/skills/tools/document/docsgpt-guide/SKILL.md

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+---
+name: docsgpt-guide
+description: "Deploy DocsGPT for private document analysis and research knowledge bases"
+metadata:
+  openclaw:
+    emoji: "📚"
+    category: "tools"
+    subcategory: "document"
+    keywords: ["document-analysis", "knowledge-base", "rag", "private-ai", "enterprise-search", "question-answering"]
+    source: "https://github.com/arc53/DocsGPT"
+---
+
+# DocsGPT Guide
+
+## Overview
+
+DocsGPT is an open-source platform for building private AI-powered document analysis and question-answering systems. It uses Retrieval Augmented Generation (RAG) to enable natural language queries against your own document collections, making it particularly valuable for researchers who need to quickly extract information from large corpora of papers, technical reports, and institutional documentation.
+
+Unlike general-purpose chatbots, DocsGPT operates on your specific documents, providing grounded answers with source citations. This is critical in academic settings where hallucinated information can derail research. The platform supports a wide range of document formats including PDF, DOCX, Markdown, HTML, and plain text, covering the formats most commonly encountered in research workflows.
+
+With over 18,000 GitHub stars and an active development community, DocsGPT offers both self-hosted deployment for data-sensitive research environments and a cloud-hosted option for quick evaluation. The self-hosted approach ensures that proprietary research data, unpublished manuscripts, and confidential institutional documents never leave your infrastructure.
+
+## Installation and Setup
+
+Deploy DocsGPT using Docker Compose for the simplest setup:
+
+```bash
+git clone https://github.com/arc53/DocsGPT.git
+cd DocsGPT
+
+# Copy and configure environment settings
+cp .env_sample .env
+```
+
+Edit the `.env` file to configure your LLM backend:
+
+```bash
+# Set your LLM provider credentials
+LLM_NAME=openai
+API_KEY=$OPENAI_API_KEY
+
+# Or use a local model via Ollama
+LLM_NAME=ollama
+OLLAMA_API_BASE=http://localhost:11434
+MODEL_NAME=llama3
+```
+
+Launch the application:
+
+```bash
+docker compose up -d
+```
+
+The web interface becomes available at `http://localhost:5173`. For production deployments behind a reverse proxy, configure the appropriate `VITE_API_HOST` environment variable.
+
+For development or lightweight usage without Docker:
+
+```bash
+pip install -r requirements.txt
+cd application
+python app.py
+```
+
+## Core Features
+
+**Document Ingestion and Indexing**: Upload documents through the web interface or API. DocsGPT processes them into vector embeddings for efficient semantic search:
+
+```bash
+# Upload documents via the API
+curl -X POST http://localhost:7091/api/upload \
+  -F "file=@research_paper.pdf" \
+  -F "name=my-research-collection"
+```
+
+Supported formats include PDF, DOCX, TXT, MD, HTML, EPUB, and RST files. Large documents are automatically chunked with configurable overlap to maintain context across segment boundaries.
+
+**Conversational Querying**: Ask natural language questions about your documents and receive answers grounded in the source material:
+
+```bash
+# Query your document collection via API
+curl -X POST http://localhost:7091/api/answer \
+  -H "Content-Type: application/json" \
+  -d '{
+    "question": "What statistical methods were used for sample size estimation?",
+    "active_docs": "my-research-collection"
+  }'
+```
+
+Each response includes source references pointing to the specific document sections used to generate the answer, enabling verification.
+
+**Multiple Knowledge Bases**: Create separate document collections for different research projects, courses, or literature review topics. Switch between collections seamlessly during querying.
+
+**API Integration**: The REST API enables programmatic access for building custom research tools, automated analysis pipelines, or integration with existing laboratory information management systems.
+
+## Research Workflow Integration
+
+DocsGPT serves several important functions in academic research:
+
+**Literature Synthesis**: Upload all papers related to a research question and use conversational queries to identify consensus findings, methodological variations, and contradictions across the literature. This accelerates the synthesis phase of literature reviews.
+
+**Thesis and Dissertation Support**: Index your entire reference collection and use DocsGPT to quickly locate specific claims, find supporting evidence for arguments, and verify that your citations accurately represent source material.
+
+**Lab Notebook Analysis**: Upload experimental protocols, lab notebooks, and equipment manuals to create a searchable knowledge base. New lab members can quickly find procedures and troubleshooting information without interrupting senior researchers.
+
+**Grant Proposal Preparation**: Build a collection from relevant prior work, agency guidelines, and successful proposal examples. Query this collection to identify framing strategies, required elements, and alignment between your proposed work and funder priorities.
+
+**Course Material Management**: Instructors can index textbooks, lecture notes, and supplementary readings. Students can then query the collection for study assistance, with all answers grounded in approved course materials.
+
+## Configuration and Customization
+
+Tune retrieval and generation parameters for your use case:
+
+```bash
+# Environment variables for fine-tuning
+CHUNKS_PER_QUERY=5          # Number of document chunks retrieved per query
+CHUNK_SIZE=512              # Size of text chunks during ingestion
+CHUNK_OVERLAP=64            # Overlap between adjacent chunks
+MAX_TOKENS=2048             # Maximum response length
+TEMPERATURE=0.1             # Lower values for more factual responses
+```
+
+For academic use, keep temperature low (0.1-0.3) to prioritize factual accuracy over creative responses. Increase `CHUNKS_PER_QUERY` when questions require synthesizing information from multiple sections of a document.
+
+Custom embeddings models can be configured for domain-specific terminology. If your research involves highly specialized vocabulary (medical terminology, chemical nomenclature), consider using domain-adapted embedding models for improved retrieval accuracy.
+
+## References
+
+- DocsGPT repository: https://github.com/arc53/DocsGPT
+- DocsGPT documentation: https://docs.docsgpt.cloud/
+- REST API reference available in the repository wiki