@wentorai/research-plugins 1.0.0 → 1.1.0

package/skills/writing/templates/graphical-abstract-guide/SKILL.md

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+---
+name: graphical-abstract-guide
+description: "Create SVG graphical abstracts for journal paper submissions"
+metadata:
+  openclaw:
+    emoji: "🎨"
+    category: "writing"
+    subcategory: "templates"
+    keywords: ["graphical abstract", "SVG", "paper submission", "visual summary", "journal figure", "scientific illustration"]
+    source: "https://github.com/jgraph/drawio"
+---
+
+# Graphical Abstract Guide
+
+## Overview
+
+A graphical abstract is a single visual summary of a research paper, designed to give readers an immediate understanding of the paper's main message at a glance. Many journals now require or strongly encourage graphical abstracts as part of the submission package, and they are increasingly important for visibility on social media and academic platforms.
+
+This skill provides a comprehensive guide to designing effective graphical abstracts for academic papers. It covers design principles specific to scientific communication, layout strategies for common paper types, tools for creating publication-quality SVG graphics, and the specific requirements of major publishers. The emphasis is on creating clear, informative visuals that accurately represent your research without oversimplifying.
+
+A well-designed graphical abstract can significantly increase your paper's readership and citation impact by making it more discoverable and shareable. Conversely, a poor graphical abstract—cluttered, misleading, or low-resolution—can undermine the perception of your work.
+
+## Design Principles
+
+### Visual Hierarchy
+
+Your graphical abstract should guide the viewer's eye through the research story in a logical sequence:
+
+1. **Entry point**: The largest or most visually prominent element should be your main finding or the key concept of the paper. This is what viewers see first.
+2. **Flow direction**: Arrange elements left-to-right or top-to-bottom to suggest a narrative flow (input → method → output/finding).
+3. **Supporting elements**: Smaller elements provide context (data sources, methods, intermediate steps).
+4. **Conclusion emphasis**: The final element in the flow should communicate the main takeaway.
+
+### Color Usage
+
+- **Limit your palette**: Use 3-5 colors maximum. Too many colors create visual noise.
+- **Use color purposefully**: Colors should encode meaning (e.g., different experimental conditions, input vs. output).
+- **Ensure accessibility**: Check that your color choices are distinguishable by readers with color vision deficiency. Use the Coblis color blindness simulator to verify.
+- **Match your paper's figures**: If your paper uses specific colors for specific variables or conditions, use the same colors in the graphical abstract for consistency.
+- **White/light background**: Most journals display graphical abstracts on white backgrounds. Design accordingly.
+
+### Typography
+
+- **Minimal text**: A graphical abstract is primarily visual. Limit text to labels, short annotations, and a one-line conclusion.
+- **Readable font size**: Text should remain legible when the image is displayed at thumbnail size (typically 200-300px wide online). Use a minimum of 10pt at the final output size.
+- **Sans-serif fonts**: Use clean, sans-serif fonts (Helvetica, Arial, Open Sans) for labels. Avoid decorative fonts.
+- **No paragraphs**: If you find yourself writing sentences, the design needs to be more visual.
+
+### Common Layouts
+
+**Linear flow (most common):**
+```
+[Input/Problem] → [Method/Approach] → [Key Finding/Result]
+```
+
+**Comparison layout:**
+```
+[Before/Without]  vs.  [After/With]
+    ↓                     ↓
+[Outcome A]         [Outcome B (better)]
+```
+
+**Central concept layout:**
+```
+        [Aspect 1]
+            ↑
+[Aspect 4] ← [Central Concept] → [Aspect 2]
+            ↓
+        [Aspect 3]
+```
+
+**Process pipeline:**
+```
+[Step 1] → [Step 2] → [Step 3] → [Step 4]
+   ↓          ↓          ↓          ↓
+[Detail]   [Detail]   [Detail]   [Result]
+```
+
+## Creating Graphical Abstracts in SVG
+
+### Why SVG?
+
+SVG (Scalable Vector Graphics) is the ideal format for graphical abstracts because:
+- It scales to any size without loss of quality
+- File sizes are small
+- It can be edited after creation
+- It converts cleanly to any raster format (PNG, TIFF) at any resolution
+
+### Tool Recommendations
+
+**Draw.io (diagrams.net)** — Free, browser-based, excellent for flowcharts and diagrams:
+```
+1. Open https://app.diagrams.net
+2. Select "Create New Diagram"
+3. Use the shape library for arrows, boxes, and connectors
+4. Import your figure images as embedded elements
+5. Export as SVG (File → Export as → SVG)
+```
+
+**Inkscape** — Free, open-source, full vector editor:
+```bash
+# Install
+brew install --cask inkscape  # macOS
+sudo apt install inkscape     # Ubuntu
+
+# Set document size to journal requirements
+# Typical: 530 x 320 pixels (Elsevier) or custom
+```
+
+**Figma** — Collaborative design tool with a free tier:
+- Excellent for teams working on a graphical abstract together
+- Export to SVG, PNG, or PDF
+- Use the "Auto Layout" feature for consistent spacing
+
+**Adobe Illustrator** — Professional vector editor:
+- The industry standard for publication graphics
+- Best compatibility with publisher workflows
+- Available through most university site licenses
+
+### Step-by-Step Workflow
+
+1. **Sketch on paper first**: Draw a rough layout with the flow of your story. Do not open software until you have a clear plan.
+2. **Set canvas size**: Check your target journal's requirements (see Publisher Requirements below).
+3. **Build the framework**: Create the boxes, arrows, and layout structure.
+4. **Add visual elements**: Insert icons, simplified figures from your paper, molecular structures, data visualizations, or photographs.
+5. **Add minimal text**: Labels, short annotations, and a one-line conclusion.
+6. **Review at thumbnail size**: Zoom out to 25% and check if the main message is still clear.
+7. **Export**: Save as SVG for editing, then export PNG/TIFF at the required resolution for submission.
+
+## Publisher Requirements
+
+### Elsevier
+- Size: 531 x 1328 pixels (landscape) or equivalent aspect ratio
+- Format: TIFF, EPS, or high-resolution JPEG/PNG
+- Resolution: 300 DPI minimum
+- Submit via the "Graphical Abstract" file type in Editorial Manager
+
+### Springer Nature
+- No fixed dimensions; recommend landscape orientation
+- Format: TIFF or EPS preferred
+- Resolution: 300 DPI minimum
+- Include as the first figure or as a separate submission file
+
+### Wiley
+- Size: varies by journal; typically 500 x 300 pixels for online display
+- Format: TIFF, EPS, or high-resolution JPEG
+- Many Wiley journals use a "Table of Contents" graphic instead of a graphical abstract
+
+### ACS (American Chemical Society)
+- Size: 3.25 x 1.75 inches at 300 DPI
+- Must be a single-panel image
+- Format: TIFF or high-resolution JPEG
+- Keep text to an absolute minimum
+
+### General Conversion from SVG
+
+```bash
+# Convert SVG to high-resolution PNG
+inkscape input.svg --export-type=png --export-dpi=300 --export-filename=output.png
+
+# Convert SVG to TIFF (for journal submission)
+convert -density 300 input.svg -compress lzw output.tiff
+
+# Resize to specific pixel dimensions
+convert output.png -resize 531x1328 -gravity center -extent 531x1328 output_elsevier.png
+```
+
+## Common Mistakes to Avoid
+
+- **Too much detail**: A graphical abstract is not a reproduction of your paper's figures. It is a new, simplified visual.
+- **Illegible text at thumbnail size**: Test readability at small display sizes.
+- **Low-resolution raster elements**: If you embed photographs or charts, use high-resolution versions.
+- **Missing the main point**: The most common mistake is focusing on the method instead of the finding. Lead with the result.
+- **Copyright issues**: Do not reuse figures from other papers without permission. Create original artwork.
+- **Inconsistent style**: Use a consistent visual language (icon style, line weights, colors) throughout the abstract.
+
+## References
+
+- Draw.io: https://app.diagrams.net
+- Inkscape: https://inkscape.org
+- Elsevier Graphical Abstract Guidelines: https://www.elsevier.com/authors/tools-and-resources/graphical-abstracts
+- ACS Author Guidelines: https://pubs.acs.org/page/4authors/submission/graphics.html
+- Pferschy-Wenzig, E.M. et al. (2016). "Graphical abstracts in scientific publications." Journal of Documentation.

package/skills/writing/templates/novathesis-guide/SKILL.md

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+---
+name: novathesis-guide
+description: "LaTeX thesis template supporting multiple universities and formats"
+version: 1.0.0
+author: wentor-community
+source: https://github.com/joaomlourenco/novathesis
+metadata:
+  openclaw:
+    category: writing
+    subcategory: templates
+    keywords:
+      - thesis-template
+      - latex-thesis
+      - dissertation
+      - university-formatting
+      - academic-typesetting
+---
+
+# NovaThesis Guide
+
+A skill for using and customizing the NovaThesis LaTeX thesis template, which supports formatting requirements from multiple universities worldwide. Based on the novathesis project (955 stars), this skill helps graduate students and researchers produce professionally typeset theses and dissertations that comply with institutional formatting mandates.
+
+## Overview
+
+Writing a thesis is a monumental academic achievement, but formatting it to meet university requirements can be frustratingly time-consuming. NovaThesis eliminates this burden by providing a single LaTeX template that adapts to the formatting requirements of dozens of universities. Students focus on their content while the template handles margins, fonts, title pages, chapter headings, bibliographies, and all the other formatting details that institutions demand.
+
+This skill guides the agent through template selection, customization, content structuring, and troubleshooting, making the thesis writing process smoother for LaTeX beginners and experienced users alike.
+
+## Template Selection and Setup
+
+**Choosing the Right Configuration**
+- NovaThesis supports universities across Portugal, Brazil, and other countries
+- Each university configuration includes the correct title page layout, margin specifications, font requirements, and chapter formatting
+- If your university is not directly supported, the generic configuration provides a solid professional base that can be customized
+- Check the template repository for the most current list of supported institutions
+
+**Initial Setup**
+- Download or clone the novathesis template repository
+- Open the main configuration file (typically `template.tex` or `thesis.tex`)
+- Set the university and department options in the document class declaration
+- Configure the degree type (MSc, PhD, or other as supported)
+- Fill in metadata: title, author, supervisors, date, keywords
+- Set the language (primary and optional secondary for bilingual requirements)
+
+**Directory Structure**
+- `Chapters/` - individual chapter files, one per chapter
+- `Appendices/` - supplementary material files
+- `Figures/` - all figure files organized by chapter
+- `Bibliography/` - BibTeX database files
+- `Config/` - template configuration and customization files
+- Main file ties everything together with `\include` commands
+
+## Content Organization
+
+**Front Matter**
+- Title page: automatically generated from metadata configuration
+- Dedication and acknowledgments: optional pages with appropriate styling
+- Abstract: in the primary language and (if required) in a secondary language
+- Table of contents, list of figures, list of tables: auto-generated
+- List of abbreviations and symbols: manually curated with provided macros
+
+**Main Chapters**
+- Each chapter is a separate .tex file for modular editing
+- Chapter files are included in the main document in order
+- Standard thesis structure: Introduction, Literature Review, Methodology, Results, Discussion, Conclusion
+- The template handles chapter numbering, header formatting, and page styles automatically
+
+**Back Matter**
+- Bibliography: managed via BibTeX or BibLaTeX with university-specified citation style
+- Appendices: formatted with letter-based numbering (Appendix A, B, C)
+- Index: optional, auto-generated from `\index{}` commands throughout the text
+
+## Customization
+
+**Typography**
+- Font selection: the template uses university-specified fonts when available
+- Line spacing: configurable (single, 1.5, double) per university requirements
+- Paragraph indentation and spacing: preset to institutional standards
+- Heading styles: chapter, section, subsection formats are predefined
+
+**Page Layout**
+- Margins: set by university configuration, overridable if needed
+- Header and footer: typically include chapter title and page number
+- Page numbering: roman for front matter, arabic for main content
+- Binding margin: adjustable for print versus digital submission
+
+**Bibliography Styles**
+- The template supports multiple bibliography backends (bibtex, biber)
+- Citation styles are configured per university requirements (APA, IEEE, Chicago, Harvard, numeric)
+- Multiple bibliographies per chapter are supported for some configurations
+- URL and DOI formatting is handled automatically
+
+## Common Tasks
+
+**Adding a New Chapter**
+- Create a new .tex file in the Chapters directory
+- Add the `\include{Chapters/newchapter}` command in the main file
+- The chapter will automatically receive the correct formatting and numbering
+- Cross-references to the new chapter work immediately with `\label` and `\ref`
+
+**Managing Figures**
+- Store figures in the Figures directory, organized by chapter
+- Use `\includegraphics` with relative paths from the main file
+- The template provides figure environments with proper caption placement
+- For subfigures, use the `subcaption` package (included in the template)
+- Ensure figures are referenced in the text before they appear
+
+**Handling References**
+- Add entries to your .bib file using standard BibTeX format
+- Use `\cite{}`, `\citep{}`, or `\citet{}` depending on the required citation style
+- The template configuration determines how citations are formatted in text and in the bibliography
+- Run the full compilation chain (LaTeX, BibTeX/Biber, LaTeX, LaTeX) for correct references
+
+**Bilingual Thesis**
+- Set both primary and secondary languages in the configuration
+- Provide abstracts in both languages using the designated environments
+- Keywords can be provided in both languages
+- Chapter titles can optionally be provided in both languages for the table of contents
+
+## Troubleshooting
+
+**Common Compilation Issues**
+- Missing packages: install from your TeX distribution (TeX Live, MiKTeX)
+- Bibliography not appearing: ensure bibtex/biber is run in the compilation chain
+- Figures not found: check file paths relative to the main .tex file location
+- Encoding issues: ensure all files use UTF-8 encoding
+- Undefined references: run LaTeX twice after adding new labels
+
+**Formatting Overrides**
+- When university requirements conflict with template defaults, use the configuration file to override
+- Document any custom overrides for future maintenance
+- Check with your university's thesis office before making significant formatting changes
+- Some universities provide LaTeX support staff who can help with template customization
+
+## Integration with Research-Claw
+
+This skill supports the Research-Claw thesis writing workflow:
+
+- Generate chapter drafts using composition skills and insert into the template
+- Manage references using citation skills connected to Zotero
+- Create figures using LaTeX drawing skills or export from analysis tools
+- Use paper review skills to debug the thesis before submission
+- Track writing progress with section-level word counts and completion status
+
+## Best Practices
+
+- Start using the template early in the writing process, not at the end
+- Compile frequently to catch formatting issues as they arise
+- Use version control (Git) for the entire thesis directory
+- Keep a backup of the template's original configuration before customizing
+- Write one chapter at a time in separate files for manageable editing
+- Consult your university's thesis formatting guidelines alongside the template documentation

package/skills/writing/templates/scientific-article-pdf/SKILL.md

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+---
+name: scientific-article-pdf
+description: "Generate publication-ready scientific article PDFs from templates"
+metadata:
+  openclaw:
+    emoji: "📑"
+    category: "writing"
+    subcategory: "templates"
+    keywords: ["PDF generation", "article template", "publication-ready", "journal format", "LaTeX template", "manuscript"]
+    source: "https://github.com/elunez/eladmin"
+---
+
+# Scientific Article PDF
+
+## Overview
+
+Producing a publication-ready PDF that meets the exact formatting requirements of a target journal or conference is one of the final and most frustrating steps of the research publication process. Each venue has its own LaTeX class file, formatting rules, margin specifications, font requirements, and reference style. Getting these details wrong can lead to desk rejection before your paper even reaches a reviewer.
+
+This skill provides a systematic approach to generating correctly formatted scientific article PDFs. It covers obtaining and using official LaTeX templates, configuring common elements (title blocks, author affiliations, abstracts, section numbering, bibliography), and troubleshooting formatting issues that arise during compilation. The goal is to produce a PDF that compiles cleanly and passes the publisher's automated format checks on the first try.
+
+The skill focuses on LaTeX-based workflows, as LaTeX remains the standard for most scientific venues, particularly in STEM fields. It includes guidance for major publishers and conference families.
+
+## Obtaining Official Templates
+
+### Major Publisher Templates
+
+Always start from the official template provided by your target venue. Using a custom or outdated template is a common cause of formatting problems.
+
+**IEEE:**
+```bash
+# IEEE conference and journal templates
+# Download from: https://www.ieee.org/conferences/publishing/templates.html
+# Key files: IEEEtran.cls, IEEEtran.bst
+wget https://www.ieee.org/content/dam/ieee-org/ieee/web/org/pubs/conference-latex-template_10-17-19.zip
+```
+
+**ACM (Association for Computing Machinery):**
+```bash
+# ACM Primary Article Template
+# Download from: https://www.acm.org/publications/proceedings-template
+# Key file: acmart.cls (supports all ACM formats)
+# Use: \documentclass[sigconf]{acmart}  % for conference
+#      \documentclass[acmlarge]{acmart}  % for journal
+```
+
+**Springer (LNCS - Lecture Notes in Computer Science):**
+```bash
+# Download from: https://www.springer.com/gp/computer-science/lncs/conference-proceedings-guidelines
+# Key file: llncs.cls
+# Typical usage: \documentclass[runningheads]{llncs}
+```
+
+**Elsevier:**
+```bash
+# Elsevier article template
+# Download from: https://www.elsevier.com/authors/policies-and-guidelines/latex-instructions
+# Key file: elsarticle.cls
+# Usage: \documentclass[preprint,12pt]{elsarticle}  % for submission
+#        \documentclass[final,3p,times]{elsarticle}  % for camera-ready
+```
+
+**NeurIPS / ICML / ICLR:**
+```bash
+# NeurIPS: https://neurips.cc/Conferences/2026/PaperInformation/StyleFiles
+# ICML: https://icml.cc/Conferences/2026/StyleAuthorInstructions
+# ICLR: Uses OpenReview; template available from submission portal
+```
+
+### Template Verification
+
+After downloading a template, verify it compiles correctly before writing:
+
+```bash
+# Compile the sample document
+pdflatex sample.tex
+bibtex sample       # or biber sample
+pdflatex sample.tex
+pdflatex sample.tex  # Two passes to resolve references
+
+# Check for warnings
+grep -i "warning" sample.log | head -20
+```
+
+## Document Structure Template
+
+Here is a general-purpose structure that works across most scientific article templates:
+
+```latex
+\documentclass[options]{template-class}
+
+% ========== Packages ==========
+\usepackage[utf8]{inputenc}     % UTF-8 encoding
+\usepackage{amsmath,amssymb}    % Math symbols
+\usepackage{graphicx}           % Figures
+\usepackage{booktabs}           % Professional tables
+\usepackage{hyperref}           % Clickable links
+\usepackage{algorithm2e}        % Algorithm pseudocode
+\usepackage{microtype}          % Typographic refinement
+
+% ========== Metadata ==========
+\title{Your Paper Title}
+\author{%
+  Author One\thanks{Corresponding author: author@example.edu} \\
+  University of Example \\
+  \and
+  Author Two \\
+  Institute of Research
+}
+\date{}
+
+\begin{document}
+\maketitle
+
+\begin{abstract}
+Your abstract text here (typically 150-300 words).
+\end{abstract}
+
+\section{Introduction}
+\label{sec:intro}
+
+\section{Related Work}
+\label{sec:related}
+
+\section{Method}
+\label{sec:method}
+
+\section{Experiments}
+\label{sec:experiments}
+
+\section{Conclusion}
+\label{sec:conclusion}
+
+\section*{Acknowledgments}
+This work was supported by...
+
+\bibliographystyle{template-bst}
+\bibliography{references}
+
+\appendix
+\section{Additional Results}
+\label{app:results}
+
+\end{document}
+```
+
+## Common Formatting Tasks
+
+### Professional Tables with booktabs
+
+```latex
+\begin{table}[t]
+\centering
+\caption{Comparison of methods on the benchmark dataset.}
+\label{tab:results}
+\begin{tabular}{lccc}
+\toprule
+Method & Accuracy & F1 Score & Params (M) \\
+\midrule
+Baseline A & 82.3 & 79.1 & 110 \\
+Baseline B & 84.7 & 81.4 & 145 \\
+\textbf{Ours} & \textbf{87.6} & \textbf{84.9} & 95 \\
+\bottomrule
+\end{tabular}
+\end{table}
+```
+
+### Figure Placement
+
+```latex
+\begin{figure}[t]  % [t]=top, [b]=bottom, [h]=here, [p]=page of floats
+\centering
+\includegraphics[width=0.9\columnwidth]{figures/architecture.pdf}
+\caption{Overview of the proposed architecture. The encoder (left)
+processes input features while the decoder (right) generates
+predictions autoregressively.}
+\label{fig:architecture}
+\end{figure}
+```
+
+### Algorithm Pseudocode
+
+```latex
+\begin{algorithm}[t]
+\caption{Training Procedure}
+\label{alg:training}
+\KwIn{Dataset $\mathcal{D}$, learning rate $\eta$, epochs $T$}
+\KwOut{Trained model parameters $\theta^*$}
+Initialize $\theta$ randomly\;
+\For{$t = 1$ \KwTo $T$}{
+    \ForEach{batch $(x, y) \in \mathcal{D}$}{
+        $\hat{y} \gets f_\theta(x)$\;
+        $\mathcal{L} \gets \text{Loss}(\hat{y}, y)$\;
+        $\theta \gets \theta - \eta \nabla_\theta \mathcal{L}$\;
+    }
+}
+\Return $\theta$\;
+\end{algorithm}
+```
+
+## Build Pipeline and Automation
+
+### Makefile for Clean Builds
+
+```makefile
+MAIN = paper
+LATEX = pdflatex
+BIB = bibtex
+
+all: $(MAIN).pdf
+
+$(MAIN).pdf: $(MAIN).tex references.bib
+	$(LATEX) $(MAIN)
+	$(BIB) $(MAIN)
+	$(LATEX) $(MAIN)
+	$(LATEX) $(MAIN)
+
+clean:
+	rm -f *.aux *.bbl *.blg *.log *.out *.toc *.fls *.fdb_latexmk
+
+check:
+	@echo "=== Overfull boxes ==="
+	@grep -c "Overfull" $(MAIN).log || echo "None"
+	@echo "=== Undefined references ==="
+	@grep -c "undefined" $(MAIN).log || echo "None"
+	@echo "=== Missing citations ==="
+	@grep -c "Citation.*undefined" $(MAIN).log || echo "None"
+
+.PHONY: all clean check
+```
+
+### Using latexmk for Automatic Rebuilds
+
+```bash
+# latexmk automatically determines how many passes are needed
+latexmk -pdf paper.tex
+
+# Continuous mode: recompiles on file changes
+latexmk -pdf -pvc paper.tex
+
+# Clean up auxiliary files
+latexmk -c paper.tex
+```
+
+## Troubleshooting
+
+| Problem | Solution |
+|---------|----------|
+| "Overfull hbox" warnings | Rephrase text, use `\sloppy` locally, or adjust figure widths |
+| Missing references | Run BibTeX/Biber and re-run LaTeX twice |
+| Figures not found | Use paths relative to the main .tex file; check file extensions |
+| Font not found | Install the required font package: `tlmgr install <font>` |
+| Page limit exceeded | Move content to appendix; tighten prose; reduce figure sizes |
+| "Too many unprocessed floats" | Add `\clearpage` or use the `placeins` package with `\FloatBarrier` |
+
+## References
+
+- IEEE LaTeX templates: https://www.ieee.org/conferences/publishing/templates.html
+- ACM acmart class: https://www.acm.org/publications/proceedings-template
+- Springer LNCS: https://www.springer.com/gp/computer-science/lncs
+- Elsevier elsarticle: https://www.elsevier.com/authors/policies-and-guidelines/latex-instructions
+- LaTeX Wikibook: https://en.wikibooks.org/wiki/LaTeX