@wentorai/research-plugins 1.0.0 → 1.2.0

package/skills/tools/diagram/mermaid-architect-guide/SKILL.md

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+---
+name: mermaid-architect-guide
+description: "Design complex multi-diagram architectures using advanced Mermaid syntax"
+metadata:
+  openclaw:
+    emoji: "blueprint"
+    category: "tools"
+    subcategory: "diagram"
+    keywords: ["Mermaid", "architecture", "system design", "C4 model", "diagram", "hand-drawn"]
+    source: "https://github.com/mermaid-js/mermaid"
+---
+
+# Mermaid Architect Guide
+
+Design complex, multi-view system architectures and research infrastructure diagrams using advanced Mermaid features including C4 diagrams, hand-drawn rendering mode, subgraph nesting, and theme customization.
+
+## Overview
+
+While basic Mermaid flowcharts are widely known, Mermaid's advanced capabilities enable sophisticated architectural documentation that rivals dedicated tools like Structurizr or Draw.io. This skill focuses on the architectural use cases that matter most to research teams: depicting multi-layer systems, data pipelines, deployment topologies, and complex experimental workflows.
+
+Mermaid v11+ introduced a hand-drawn rendering mode (via the `handDrawn` look) that produces a sketch-like aesthetic similar to Excalidraw but with the convenience of text-based Markdown embedding. This makes it ideal for research proposals and informal documentation where a polished diagram would feel premature.
+
+Research software systems often involve intricate interactions between data sources, processing pipelines, ML models, and visualization layers. The C4 model support in Mermaid allows teams to document these systems at multiple levels of abstraction -- from high-level context diagrams down to detailed component views -- all in version-controlled Markdown files.
+
+## Hand-Drawn Mode
+
+Enable the sketchy, informal rendering style:
+
+```mermaid
+---
+config:
+  look: handDrawn
+  theme: neutral
+---
+flowchart LR
+    A[Raw Data] --> B[Preprocessing]
+    B --> C[Feature Engineering]
+    C --> D[Model Training]
+    D --> E[Evaluation]
+    E -->|Poor| C
+    E -->|Good| F[Deployment]
+```
+
+The `handDrawn` look applies rough.js-style rendering to all elements, giving them a natural sketched appearance. This is particularly useful for early-stage architecture discussions and research proposals.
+
+## C4 Architecture Diagrams
+
+### Context Diagram (Level 1)
+
+```mermaid
+C4Context
+    title Research Platform - System Context
+
+    Person(researcher, "Researcher", "Academic user conducting studies")
+    Person(admin, "Platform Admin", "Manages skills and users")
+
+    System(platform, "Wentor Platform", "AI-powered research assistant ecosystem")
+
+    System_Ext(scholar, "Semantic Scholar", "Academic paper database")
+    System_Ext(crossref, "CrossRef", "DOI resolution and metadata")
+    System_Ext(github, "GitHub", "Code and skill repositories")
+
+    Rel(researcher, platform, "Uses", "HTTPS")
+    Rel(admin, platform, "Manages", "HTTPS")
+    Rel(platform, scholar, "Queries papers", "REST API")
+    Rel(platform, crossref, "Resolves DOIs", "REST API")
+    Rel(platform, github, "Fetches skills", "REST API")
+```
+
+### Container Diagram (Level 2)
+
+```mermaid
+C4Container
+    title Research Platform - Container View
+
+    Person(researcher, "Researcher")
+
+    Container_Boundary(platform, "Wentor Platform") {
+        Container(web, "Web App", "React + UmiJS", "Browser-based UI")
+        Container(api, "API Server", "FastAPI", "REST endpoints")
+        Container(claw, "Research-Claw", "Node.js", "Local AI agent")
+        ContainerDb(db, "Database", "PostgreSQL", "User data, skills, tokens")
+        ContainerDb(cache, "Cache", "Redis", "Session and rate limit data")
+    }
+
+    System_Ext(llm, "LLM Provider", "Claude / GPT")
+
+    Rel(researcher, web, "Browses", "HTTPS")
+    Rel(researcher, claw, "Runs locally", "WS localhost")
+    Rel(web, api, "Calls", "REST/JSON")
+    Rel(api, db, "Reads/Writes", "SQL")
+    Rel(api, cache, "Caches", "Redis protocol")
+    Rel(claw, llm, "Sends prompts", "HTTPS")
+```
+
+## Advanced Subgraph Patterns
+
+### Nested Research Pipeline
+
+```mermaid
+flowchart TB
+    subgraph ingestion ["Data Ingestion Layer"]
+        direction LR
+        A1[PubMed API] --> B1[Raw Store]
+        A2[arXiv API] --> B1
+        A3[CrossRef API] --> B1
+    end
+
+    subgraph processing ["Processing Pipeline"]
+        direction LR
+        C1[Text Extraction] --> C2[NER & Entity Linking]
+        C2 --> C3[Citation Graph Construction]
+        C3 --> C4[Embedding Generation]
+    end
+
+    subgraph serving ["Serving Layer"]
+        direction LR
+        D1[Search Index] --> D2[Recommendation Engine]
+        D2 --> D3[REST API]
+    end
+
+    ingestion --> processing --> serving
+```
+
+### Experiment Workflow with Decision Gates
+
+```mermaid
+flowchart TD
+    Start([Begin Experiment]) --> Design[Study Design]
+    Design --> IRB{IRB Approval?}
+    IRB -->|Approved| Pilot[Pilot Study n=30]
+    IRB -->|Revision needed| Design
+    Pilot --> PilotCheck{Pilot Successful?}
+    PilotCheck -->|Yes| FullStudy[Full Study n=300]
+    PilotCheck -->|No| Redesign[Revise Protocol]
+    Redesign --> Pilot
+    FullStudy --> Analysis[Statistical Analysis]
+    Analysis --> Results{Significant?}
+    Results -->|p < 0.05| Write[Write Manuscript]
+    Results -->|p >= 0.05| Explore[Exploratory Analysis]
+    Explore --> Write
+    Write --> Submit([Submit to Journal])
+```
+
+## State Diagrams for Research Processes
+
+```mermaid
+stateDiagram-v2
+    [*] --> Ideation
+    Ideation --> ProposalDrafting : Concept validated
+
+    state ProposalDrafting {
+        [*] --> Writing
+        Writing --> InternalReview
+        InternalReview --> Writing : Revisions needed
+        InternalReview --> Ready : Approved
+    }
+
+    ProposalDrafting --> Submitted : Submit to funder
+    Submitted --> UnderReview : Acknowledged
+    UnderReview --> Funded : Award
+    UnderReview --> Rejected : Decline
+    Rejected --> Ideation : Revise concept
+    Funded --> Active : Project kickoff
+    Active --> Reporting : Milestone due
+    Reporting --> Active : Report accepted
+    Active --> Completed : All deliverables met
+    Completed --> [*]
+```
+
+## Theme Customization
+
+```mermaid
+%%{init: {
+  'theme': 'base',
+  'themeVariables': {
+    'primaryColor': '#1971c2',
+    'primaryTextColor': '#ffffff',
+    'primaryBorderColor': '#1864ab',
+    'lineColor': '#495057',
+    'secondaryColor': '#e03131',
+    'tertiaryColor': '#f8f9fa',
+    'fontFamily': 'Inter, sans-serif'
+  }
+}}%%
+flowchart LR
+    A[Input] --> B[Process] --> C[Output]
+```
+
+## Rendering and Integration
+
+| Platform | Support | Notes |
+|----------|---------|-------|
+| GitHub Markdown | Native | Renders in README, issues, PRs |
+| GitLab | Native | Full Mermaid support |
+| Obsidian | Native | Real-time preview |
+| Notion | Via embed | Use mermaid.ink URL encoding |
+| LaTeX | Pre-render | Use `mmdc` CLI to export SVG/PDF |
+| Jupyter | Via plugin | `mermaid-py` or iframe rendering |
+
+### CLI Rendering
+
+```bash
+# Install Mermaid CLI
+npm install -g @mermaid-js/mermaid-cli
+
+# Render to SVG
+mmdc -i architecture.mmd -o architecture.svg -t neutral
+
+# Render with hand-drawn look
+mmdc -i architecture.mmd -o sketch.svg --configFile mermaid-config.json
+```
+
+## References
+
+- Mermaid official documentation: https://mermaid.js.org
+- C4 model specification: https://c4model.com
+- Mermaid CLI (mmdc): https://github.com/mermaid-js/mermaid-cli
+- Mermaid Live Editor: https://mermaid.live

package/skills/tools/diagram/scientific-graphical-abstract/SKILL.md

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+---
+name: scientific-graphical-abstract
+description: "Design effective graphical abstracts and scientific figures for papers"
+metadata:
+  openclaw:
+    emoji: "🎨"
+    category: "tools"
+    subcategory: "diagram"
+    keywords: ["graphical abstract", "scientific illustration", "figure design", "paper figures", "visual abstract", "publication graphics"]
+    source: "https://clawhub.ai/scientific-graphical-abstract"
+---
+
+# Scientific Graphical Abstract and Figure Design
+
+## Overview
+
+A graphical abstract is a single-panel visual summary of a paper's key finding or methodology. Increasingly required by journals (Cell, Elsevier, ACS, Wiley), a good graphical abstract increases paper visibility, social media engagement, and citation rates. This guide covers design principles, tools, and workflows for creating effective graphical abstracts and publication-quality scientific figures.
+
+## Graphical Abstract Design Principles
+
+### The 10-Second Rule
+
+A graphical abstract must communicate the core message in under 10 seconds:
+
+```
+Layout formula:
+  [Input/Problem] → [Method/Process] → [Output/Result]
+
+Visual flow: left-to-right or top-to-bottom
+Maximum elements: 5-7 distinct visual components
+Text: minimal labels only (no sentences)
+```
+
+### Composition Templates
+
+```
+Template 1: Linear Pipeline
+┌──────┐    ┌──────┐    ┌──────┐    ┌──────┐
+│Input │ → │Step 1│ → │Step 2│ → │Result│
+└──────┘    └──────┘    └──────┘    └──────┘
+
+Template 2: Comparison
+┌──────────────┐  ┌──────────────┐
+│  Before/      │  │  After/       │
+│  Baseline     │  │  Proposed     │
+│  [visual]     │  │  [visual]     │
+└──────────────┘  └──────────────┘
+
+Template 3: Central Method
+            ┌────────┐
+  ┌────┐    │        │    ┌────────┐
+  │Data├───→│ Method ├───→│Results │
+  └────┘    │        │    └────────┘
+            └────────┘
+  ┌────────────────────────────────┐
+  │      Key Finding Statement      │
+  └────────────────────────────────┘
+
+Template 4: Multi-panel
+  ┌─────────────────────────────┐
+  │ (a) Problem │ (b) Solution  │
+  ├─────────────┼───────────────┤
+  │ (c) Results │ (d) Impact    │
+  └─────────────┴───────────────┘
+```
+
+### Color and Typography
+
+```
+Color rules:
+  - Maximum 4-5 colors per figure
+  - Use colorblind-friendly palette (avoid red-green only)
+  - Suggested palettes:
+    * IBM Design: #648FFF, #785EF0, #DC267F, #FE6100, #FFB000
+    * Tol Bright: #EE6677, #228833, #4477AA, #CCBB44, #66CCEE
+    * Okabe-Ito: #E69F00, #56B4E9, #009E73, #F0E442, #0072B2
+
+Typography:
+  - Sans-serif for labels (Arial, Helvetica, Calibri)
+  - Minimum 8pt font in final printed size
+  - Consistent font size hierarchy (title > labels > annotations)
+  - Bold for emphasis, not underlining or italics
+```
+
+## Tools and Software
+
+| Tool | Type | Best For | Price |
+|------|------|----------|-------|
+| **BioRender** | Web app | Biological/medical illustrations | $0-39/mo |
+| **Adobe Illustrator** | Desktop | Professional vector graphics | $23/mo |
+| **Inkscape** | Desktop (free) | Vector graphics (Illustrator alternative) | Free |
+| **Figma** | Web app | Collaborative design, templates | Free tier |
+| **PowerPoint/Keynote** | Desktop | Quick diagrams, accessible | Bundled |
+| **draw.io (diagrams.net)** | Web/Desktop | Flowcharts, architecture diagrams | Free |
+| **Matplotlib/Seaborn** | Python | Data-driven figures | Free |
+| **Mermaid** | Text-based | Simple flowcharts in Markdown | Free |
+| **TikZ/PGF** | LaTeX | Publication-quality technical diagrams | Free |
+
+## Publication Figure Standards
+
+### Journal Requirements
+
+| Aspect | Standard |
+|--------|---------|
+| **Resolution** | 300 DPI (print), 150 DPI (screen) |
+| **Format** | TIFF/EPS for print; PDF for vector; PNG for web |
+| **Size** | Single column: 85 mm; Double column: 170 mm; Full page: 170 × 225 mm |
+| **Color mode** | RGB for digital, CMYK for print |
+| **Font** | Arial, Helvetica, or Times; 7-10 pt at final size |
+| **Line width** | Minimum 0.5 pt at final size |
+| **Panel labels** | (a), (b), (c) — bold, top-left corner |
+
+### Multi-Panel Figure Construction
+
+```python
+import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
+
+fig = plt.figure(figsize=(7, 4))  # inches (double column ≈ 7")
+gs = gridspec.GridSpec(1, 3, width_ratios=[1, 1.5, 1],
+                       wspace=0.3)
+
+ax1 = fig.add_subplot(gs[0])
+ax2 = fig.add_subplot(gs[1])
+ax3 = fig.add_subplot(gs[2])
+
+# Panel labels
+for ax, label in zip([ax1, ax2, ax3], ['a', 'b', 'c']):
+    ax.text(-0.1, 1.05, f'({label})', transform=ax.transAxes,
+            fontsize=12, fontweight='bold', va='top')
+
+# Your plots here...
+ax1.set_title("Input Data")
+ax2.set_title("Method Overview")
+ax3.set_title("Results")
+
+plt.savefig("figure1.pdf", dpi=300, bbox_inches='tight')
+plt.savefig("figure1.tiff", dpi=300, bbox_inches='tight')
+```
+
+### Colorblind-Accessible Design
+
+```python
+# Okabe-Ito colorblind-safe palette
+COLORS = {
+    'orange':   '#E69F00',
+    'sky_blue': '#56B4E9',
+    'green':    '#009E73',
+    'yellow':   '#F0E442',
+    'blue':     '#0072B2',
+    'vermilion':'#D55E00',
+    'purple':   '#CC79A7',
+    'black':    '#000000'
+}
+
+# Use shapes AND colors to encode categories
+markers = ['o', 's', '^', 'D', 'v']  # circle, square, triangle, diamond, inverted triangle
+
+# Test: convert to grayscale to verify distinguishability
+from PIL import Image
+img = Image.open("figure1.png").convert("L")
+img.save("figure1_grayscale.png")
+```
+
+## Workflow: From Concept to Final Figure
+
+```markdown
+1. Sketch on paper (5 min)
+   - Layout, flow direction, key elements
+   - Don't start in software without a plan
+
+2. Identify visual metaphors
+   - Data table → heatmap or bar chart
+   - Process → arrows and boxes
+   - Comparison → side-by-side panels
+   - Network → node-edge graph
+
+3. Create in vector software (30-60 min)
+   - Build at the final print size (not zoomed in)
+   - Use layers: background, main elements, labels, annotations
+   - Align elements to grid
+
+4. Apply consistent styling
+   - Same font throughout all figures in the paper
+   - Same color scheme throughout
+   - Same line widths, marker sizes, label formats
+
+5. Export and verify
+   - Export at 300 DPI
+   - Check at actual print size (100% zoom)
+   - Verify readability of smallest text
+   - Verify in grayscale for colorblind accessibility
+```
+
+## References
+
+- Rougier, N. P., et al. (2014). "Ten Simple Rules for Better Figures." *PLOS Computational Biology*, 10(9), e1003833.
+- Tufte, E. R. (2001). *The Visual Display of Quantitative Information*. Graphics Press.
+- [BioRender Templates](https://biorender.com/)
+- [Inkscape Documentation](https://inkscape.org/doc/)
+- [Colorbrewer 2.0](https://colorbrewer2.org/)