research-toolkit

name	research-toolkit
description	Use this skill to find the right tool for a research task across the TZD Labs ecosystem. Maps research needs (visualization, manuscript writing, data extraction, systematic review, analysis) to specific tools, packages, and agents. Triggers on "what tool should I use", "how do I do X", "research workflow", "which agent", "find the right tool", "project index".

Research Toolkit

Unified index of all research tools, libraries, and capabilities available across the TZD Labs ecosystem. Use this skill to find the right tool for a research task.

Tool Index

Data Visualization

Tool	What It Does	Install / Location
flowmpl	Matplotlib design system — charts, flow diagrams, concept frames, AI illustrations	uv pip install flowmpl[all]
prs-dataviz	Journal-compliant medical figures (300+ DPI, CMYK, TIFF)	uv pip install prs-dataviz
dubois-style	W.E.B. Du Bois-inspired matplotlib palettes (7 color schemes)	uv pip install dubois-style
infographic-generator	Modular infographic generation (Typst rendering, AI images)	/Users/shakes/DevProjects/infographic-generator

Manuscript Pipeline

Tool	What It Does	Install / Location
quartopress	Quarto manuscript scaffolding, PRS table builder, build pipeline	uv pip install quartopress
plastic-surgery-research	PRS manuscript writing guidance + dataviz best practices	Claude plugin at /Users/shakes/DevProjects/plastic-surgery-research

Data Extraction & Processing

Tool	What It Does	Install / Location
ai-structured-data-extractor	Systematic literature review — PRISMA screening, citation extraction	/Users/shakes/DevProjects/ai-structured-data-extractor
markdown-table-extractor	Extract and transform tables from markdown documents	/Users/shakes/DevProjects/markdown_table_extractor
pdf-extractor (agent)	Mistral OCR for PDFs — regulatory filings, financial reports, utility orders	Built-in tzd-labs agent
paperquizr	Interactive paper reader with gated quiz stages and concept mapping	/Users/shakes/DevProjects/paperquizr

Interactive Notebooks

Tool	What It Does	Install / Location
marimo	Reactive Python notebooks — charts, data analysis, interactive UI	uv pip install marimo
Observable Framework	D3.js-based web publication — scroll-driven charts, responsive design	Integrated via observable-converter agent

Analysis & Research

Tool	What It Does	Install / Location
causal-compass	Causal inference methodology and analysis	/Users/shakes/DevProjects/causal-compass
SystemDynamics	System dynamics modeling and simulation	/Users/shakes/DevProjects/SystemDynamics
van-research	Parameterized financial analysis with Quarto reports	/Users/shakes/DevProjects/van_research

Document Collaboration

Tool	What It Does	Install / Location
docucolab	Document collaboration platform	/Users/shakes/DevProjects/docucolab
docucolab-parallel-docx	Parallel DOCX document processing	/Users/shakes/DevProjects/docucolab-parallel-docx
docucolab-parallel-pptx	Parallel PPTX presentation processing	/Users/shakes/DevProjects/docucolab-parallel-pptx

Education

Tool	What It Does	Install / Location
survival-guide	USMLE Step 1 study material with OCR extraction	/Users/shakes/DevProjects/survival_guide
NotebookLM prompts	Generate Audio Overview prompts for educational chapters	Built-in tzd-labs agent + command

Task-to-Tool Routing

"I need to create a publication figure"

1. Use flowmpl for the chart (annotated_series, stacked_bar, waterfall_chart, flow_diagram)
2. Apply prs-dataviz for journal-compliant export (TIFF, 300 DPI, CMYK)
3. Use dubois-style if you want historically-inspired aesthetics

"I need to write a manuscript"

1. Scaffold with quartopress (quartopress-init)
2. Configure journal with /set-journal
3. Build tables with table-builder agent
4. Create figures with flowmpl + prs-dataviz
5. Fix AI tells with /fix-ai-tells
6. Check compliance with journal-compliance skill
7. Build upload package with /build-manuscript

"I need to do a systematic review"

1. Set up screening database with ai-structured-data-extractor
2. Extract data from PDFs with pdf-extractor agent
3. Extract tables with markdown-table-extractor
4. Analyze with marimo notebooks
5. Visualize with flowmpl (PRISMA flowchart via flow_diagram)
6. Write up with quartopress

"I need to analyze infrastructure data"

1. Research with researcher agent (finds primary data sources)
2. Extract from PDFs with pdf-extractor agent
3. Analyze in marimo notebooks
4. Visualize with flowmpl design system
5. Write with accountability-cascade prose style
6. Review with critic + fact-checker agents
7. Publish via Observable Framework (observable-converter agent)

"I need to review my writing"

1. prose-reviewer agent — structural narration quality (show vs tell)
2. ai-tell-fixer agent — detect and fix AI writing markers
3. critic agent — intellectual rigor, logic, evidence quality
4. writer agent — transform into accessible publication-ready narrative
5. swd-reviewer agent — chart/visualization quality (Storytelling with Data)
6. fact-checker agent — verify every claim, number, citation

"I need to create a presentation or infographic"

1. Use infographic-generator for standalone infographics
2. Use flowmpl concept frames for whiteboard-style explainers
3. Use docucolab-parallel-pptx for PowerPoint processing