research-workflow

name: research-workflow description: Specialized workflow for theoretical biophysics research. Use when working with research documents, theoretical frameworks, mathematical derivations, or scientific papers. Triggers include creating research documents, converting between formats (Markdown/LaTeX/PDF), managing figures, citing references, or organizing theoretical frameworks. Supports scoliosis research, biomechanics, control theory, General Relativity applications, and mathematical modeling (Cosserat theory, AdS/CFT).

Research Workflow Skill

Structured workflows for theoretical biophysics research, optimized for mathematical frameworks and scientific documentation.

Quick Reference

Research Document Creation

Standard Structure

Use this structure for theoretical frameworks:

1. Abstract - Concise summary (150-250 words)
2. Introduction - Context and motivation
3. Theoretical Framework - Core mathematical derivations
4. Results - Key findings and predictions
5. Discussion - Implications and future work
6. References - Citations in BibTeX format

Mathematical Notation

Follow these conventions:

• Vectors: Bold ($\mathbf{r}$, $\mathbf{v}$)
• Tensors: Sans-serif ($\mathsf{T}$, $\mathsf{g}_{\mu\nu}$)
• Operators: Hat notation ($\hat{H}$, $\hat{L}$)
• Physical quantities: Italics ($E$, $m$, $c$)
• Functions: Roman ($\sin$, $\log$, $\text{erf}$)

Equation Formatting

For inline math: $E = mc^2$

For display equations:
$$
\frac{\partial \mathbf{r}}{\partial t} = \mathbf{v}
$$

For aligned derivations:
$$
\begin{aligned}
F &= ma \\
  &= m\frac{dv}{dt}
\end{aligned}
$$

Figure Management

Organization

Store figures in research/figures/ with descriptive names:

• scoliosis_phase_diagram.png
• cosserat_rod_schematic.svg
• energy_optimization_plot.pdf

Embedding in Markdown

![Figure caption describing the content](../figures/filename.png)

Embedding Script

Use scripts/embed_figures.py to automatically:

• Find referenced figures
• Check file existence
• Validate image formats
• Generate proper markdown syntax

Format Conversion

Markdown to LaTeX

Convert research Markdown to manuscript-ready LaTeX:

python .agent/skills/research-workflow/scripts/md_to_latex.py input.md --output manuscript.tex

Features:

• Preserves mathematical equations
• Converts markdown headings to LaTeX sections
• Handles figure references
• Generates BibTeX citations

See references/latex-templates.md for LaTeX document templates.

PDF Generation

Generate publication-ready PDFs:

python .agent/skills/research-workflow/scripts/generate_pdf.py manuscript.tex

Automatically handles:

• Multiple LaTeX compilation passes
• Bibliography generation (BibTeX)
• Figure resolution optimization

Domain Knowledge

For quick reference on theoretical concepts, see references/domain-knowledge.md which covers:

• Cosserat rod theory basics
• Control theory with delay fundamentals
• AdS/CFT correspondence in biology
• Standard notation conventions

Research Prompts

Creating Effective Prompts

Structure research prompts with:

1. Objective - Clear research question
2. Background - Relevant prior work
3. Methodology - Proposed approach
4. Constraints - Limitations and assumptions
5. Deliverables - Expected outputs

Template

Use .agent/templates/research-prompt.md for consistent prompt structure.

Collaboration Workflows

Creating Word Documents

For sharing with collaborators who use Word:

Ask: "Convert the scoliosis framework to a Word document"

Uses the docx skill to create properly formatted documents with:

• Preserved equations (as images or MathType)
• Embedded figures
• Professional formatting

Creating Presentations

For conferences and talks:

Ask: "Create a presentation from the gravity paradox research"

Uses the pptx skill to generate slides with:

• Title slide
• Key equations
• Figure visualizations
• Conclusion slide

Tracked Changes

For collaborative editing:

Ask: "Add tracked changes suggesting revisions to section 3"

Uses the doc-coauthoring skill for structured document refinement.

Best Practices

Version Control

• Commit research documents to git regularly
• Use meaningful commit messages
• Tag significant versions (e.g., v1.0-preprint)

Citation Management

• Store references in references.bib
• Use consistent citation keys (author_year_keyword)
• Include DOIs when available

Code and Data

• Link to analysis scripts in scripts/
• Reference data files in data/
• Document computational methods

Reproducibility

• Include software versions in methods
• Provide environment specifications
• Document random seeds for simulations

Common Workflows

New Theoretical Framework

1. Use template: .agent/templates/theoretical-framework.md
2. Fill in sections systematically
3. Add mathematical derivations
4. Generate figures with analysis scripts
5. Embed figures using embed_figures.py
6. Convert to LaTeX when ready for submission

Literature Review Integration

1. Collect references in BibTeX format
2. Organize by topic in references.bib
3. Cite using [@author_year] syntax
4. Auto-generate bibliography on PDF creation

Manuscript Preparation

1. Start with research Markdown document
2. Refine content using doc-coauthoring skill
3. Convert to LaTeX using md_to_latex.py
4. Fine-tune LaTeX formatting
5. Generate PDF using generate_pdf.py
6. Review and iterate

Troubleshooting

LaTeX Compilation Errors

• Check equation syntax (missing $ or $$)
• Verify figure paths are correct
• Ensure BibTeX file exists
• Check for special characters needing escaping

Figure Display Issues

• Verify figure file exists in specified path
• Check image format (PNG, PDF, SVG recommended)
• Ensure proper markdown syntax
• Use relative paths from document location

Mathematical Notation

• Test complex equations in isolation first
• Use \text{} for text within math mode
• Split long equations with aligned environment
• Reference equations with \label{} and \ref{}