Research Project Scaffold

Research Project Scaffold Skill

Scaffolding new academic research projects and refactoring existing ones for Alex-assisted workflows.

Purpose

Provide standardized structures and refactoring procedures for academic research projects that maximize Alex's ability to assist throughout the research lifecycle.

Scaffolding New Projects

Recommended Folder Structure

project-root/
├── .github/
│   ├── copilot-instructions.md    # Research-specific Alex context
│   └── prompts/
│       └── literature-synthesis.prompt.md
├── docs/
│   ├── RESEARCH-PLAN.md           # Objectives, timeline, milestones
│   ├── METHODOLOGY.md             # Research design decisions
│   └── DECISION-LOG.md            # Key decisions with rationale
├── data/
│   ├── raw/                       # Untouched source data
│   ├── processed/                 # Cleaned/transformed data
│   └── DATA-DICTIONARY.md         # Variable definitions
├── analysis/
│   ├── scripts/                   # Analysis code
│   ├── outputs/                   # Generated figures, tables
│   └── notebooks/                 # Exploratory analysis
├── writing/
│   ├── drafts/                    # Work in progress
│   ├── figures/                   # Publication-ready figures
│   └── submissions/               # Submitted versions
├── references/
│   ├── LITERATURE-MATRIX.md       # Systematic literature tracking
│   ├── pdfs/                      # Source papers (if permitted)
│   └── notes/                     # Reading notes
└── README.md                      # Project overview

Essential Files

RESEARCH-PLAN.md Template

# Research Plan: [Title]

## Research Questions
1. Primary: [Main question]
2. Secondary: [Supporting questions]

## Methodology
- Type: [Qualitative/Quantitative/Mixed/Case Study]
- Design: [Experimental/Survey/Longitudinal/etc.]
- Participants: [Sample description]

## Timeline
| Phase | Duration | Deliverable |
|-------|----------|-------------|
| Literature Review | Weeks 1-4 | LITERATURE-MATRIX.md complete |
| Data Collection | Weeks 5-12 | Raw data in data/raw/ |
| Analysis | Weeks 13-16 | Results in analysis/outputs/ |
| Writing | Weeks 17-20 | Draft in writing/drafts/ |
| Revision | Weeks 21-24 | Submission-ready manuscript |

## Success Criteria
- [ ] [Specific measurable outcome]
- [ ] [Publication target]
- [ ] [Other goals]

## Risks & Mitigations
| Risk | Likelihood | Mitigation |
|------|------------|------------|
| [Risk 1] | Medium | [Plan] |

LITERATURE-MATRIX.md Template

# Literature Matrix

## Search Strategy
- Databases: [List sources]
- Keywords: [Search terms]
- Inclusion criteria: [What qualifies]
- Exclusion criteria: [What's out]

## Matrix

| Citation | Year | Methodology | Key Findings | Gaps | Relevance | Notes |
|----------|------|-------------|--------------|------|-----------|-------|
| Author1 et al. | 2024 | Controlled study | Finding X | Gap Y | ⭐⭐⭐ | Foundational |
| Author2 | 2023 | Survey (n=500) | Finding Z | — | ⭐⭐ | Supports H2 |

## Synthesis Notes
- Theme 1: [Pattern across sources]
- Theme 2: [Another pattern]
- Gap: [What's missing that your research addresses]

METHODOLOGY.md Template

# Methodology

## Research Design
**Approach**: [Paradigm - positivist, interpretivist, pragmatic]
**Strategy**: [Case study, experiment, survey, ethnography, etc.]

## Data Collection
**Sources**: [What data, from where]
**Instruments**: [Surveys, interviews, logs, artifacts]
**Procedure**: [Step-by-step process]

## Analysis Method
**Technique**: [Thematic analysis, statistical tests, content analysis]
**Tools**: [Software, frameworks]
**Validation**: [Member checking, triangulation, statistical power]

## Ethical Considerations
- IRB Status: [Approved/Exempt/N/A]
- Consent: [Process]
- Data protection: [How handled]

## Limitations
1. [Known limitation and why acceptable]
2. [Another limitation]

copilot-instructions.md Template (Research Projects)

# [Project Title] - Research Context

## Project Overview
[2-3 sentence summary of research focus and goals]

## Current Phase
- [x] Literature Review
- [ ] Data Collection  
- [ ] Analysis
- [ ] Writing

## Key Files
- Research plan: docs/RESEARCH-PLAN.md
- Literature: references/LITERATURE-MATRIX.md
- Methodology: docs/METHODOLOGY.md

## Alex Guidance
- When reviewing literature: Add entries to LITERATURE-MATRIX.md
- When analyzing data: Document steps in DECISION-LOG.md
- When writing: Check references against LITERATURE-MATRIX.md
- Citation style: [APA 7 / Chicago / IEEE / etc.]

## Domain Context
[Key concepts, terminology, or background Alex needs]

## Quality Standards
- All claims require citations or data references
- Methodology decisions logged with rationale
- Raw data never modified (work from processed/)

Refactoring Existing Projects

Assessment Checklist

Run this audit on any existing research project:

## Research Project Audit

### Structure Assessment
- [ ] Has dedicated .github/ folder with copilot-instructions.md
- [ ] Data separated: raw vs processed
- [ ] Clear separation: analysis code vs writing
- [ ] References organized and tracked

### Documentation Assessment  
- [ ] Research questions documented
- [ ] Methodology decisions recorded
- [ ] Literature systematically tracked (not scattered notes)
- [ ] Decision rationale captured

### Alex-Readiness Assessment
- [ ] Context file exists (copilot-instructions.md or equivalent)
- [ ] Current phase clearly marked
- [ ] Key terminology defined
- [ ] Citation style specified

### Data Management Assessment
- [ ] Raw data preserved unchanged
- [ ] Data dictionary exists
- [ ] Analysis reproducible
- [ ] Sensitive data protected

Refactoring Procedure

Phase 1: Inventory (Non-Destructive)

1. Create inventory file:

   # Refactoring Inventory - [Project Name]
   
   ## Current Structure
   [Tree output of existing folders]
   
   ## Identified Files by Type
   ### Writing/Drafts
   - file1.docx - [description]
   
   ### Data
   - dataset.csv - [raw/processed?]
   
   ### Analysis
   - script.py - [purpose]
   
   ### References
   - [scattered papers, notes]
   
   ### Unknown/Misc
   - [files needing classification]
   

2. Identify gaps:

   • Missing: RESEARCH-PLAN? METHODOLOGY? LITERATURE-MATRIX?
   • Undocumented: Key decisions made but not recorded?
   • Scattered: References in multiple locations?

Phase 2: Scaffold Creation

1. Create target structure (empty folders):

   mkdir .github docs data data/raw data/processed analysis writing references
   

2. Create missing essential files:

   • RESEARCH-PLAN.md (even if retrospective)
   • METHODOLOGY.md
   • LITERATURE-MATRIX.md
   • copilot-instructions.md

3. Populate retrospectively:

   • Extract research questions from drafts
   • Document methodology from what was done
   • Build literature matrix from existing citations

Phase 3: File Migration

Principle: Move, don't copy (avoid duplicates). Use git.

# Example migration commands
git mv old-data.csv data/raw/
git mv cleaned-data.csv data/processed/
git mv draft-v3.docx writing/drafts/
git mv analysis.py analysis/scripts/

Migration mapping template:

Phase 4: Retroactive Documentation

Fill in documentation from what exists:

1. RESEARCH-PLAN.md: Extract from proposal, drafts, or reconstruct
2. DECISION-LOG.md: Interview yourself about choices made
3. LITERATURE-MATRIX.md: Build from reference list in drafts
4. DATA-DICTIONARY.md: Document variables from analysis code

Retroactive documentation prompts:

• "What was I trying to answer?"
• "Why did I choose this method over alternatives?"
• "What did Author X contribute to my thinking?"
• "What does this variable actually represent?"

Phase 5: Link Updates

1. Update any internal links in documents
2. Update file paths in analysis scripts
3. Update .gitignore for new structure
4. Update any build/compile scripts

Phase 6: Validation

• All files accounted for (nothing lost)
• Analysis scripts run from new locations
• Links in documents work
• Git history preserved (used mv, not delete+create)
• README.md updated with new structure

Best Practices

By Research Phase

Common Refactoring Patterns

File Naming Conventions

# Data files
data/raw/survey-responses-2024-01-15.csv     # Source + date
data/processed/survey-clean-v2.csv           # Description + version

# Writing
writing/drafts/paper-draft-01.md             # Numbered versions
writing/submissions/journal-name-2024-03.pdf # Venue + date

# Analysis
analysis/scripts/01-data-cleaning.py         # Numbered sequence
analysis/scripts/02-descriptive-stats.py
analysis/outputs/figure-1-demographics.png   # Matches paper reference

Version Control Practices

• Commit at logical checkpoints (completed section, working analysis)
• Use meaningful commit messages: "Add literature synthesis for RQ1"
• Tag important versions: git tag submission-v1
• Never commit sensitive data (use .gitignore)

Integration with Other Skills

• academic-research: Use for methodology guidance, committee navigation
• practitioner-research: Use for publication workflows (Ship→Document→Promote)
• project-scaffolding: Base patterns for folder structure
• bootstrap-learning: For learning new research methods
• writing-publication: For manuscript preparation

Clinical Research Extension

Patterns from Lithium Alzheimer's prevention research project (Feb 2026)

Clinical Research Folder Structure

project-root/
├── .github/
│   └── copilot-instructions.md
├── clinical/
│   ├── IRB-PROTOCOL.md           # Full IRB submission document
│   ├── IRB-SELECTION-GUIDE.md    # IRB comparison if no internal IRB
│   ├── INFORMED-CONSENT.md       # English consent form
│   ├── INFORMED-CONSENT-ES.md    # Spanish translation
│   ├── INFORMED-CONSENT-PT.md    # Portuguese translation
│   ├── CASE-REPORT-FORMS.md      # Data collection instruments
│   ├── SCREENING-CHECKLIST.md    # Eligibility criteria forms
│   ├── FUNDING-STRATEGY.md       # Grant/funding applications
│   └── MASTER-CHECKLIST.md       # Project-wide task tracker
├── literature/
│   ├── LITERATURE-MATRIX.md      # Systematic evidence tracking
│   ├── PRIMARY-SOURCES.md        # Key papers with PMIDs
│   ├── CLINICAL-TRIALS.md        # Existing trial summaries
│   └── EPIDEMIOLOGICAL-STUDIES.md # Population-level evidence
├── research/
│   └── RESEARCH-PROTOCOL.md      # Scientific methodology
├── analysis/
│   ├── EVIDENCE-SYNTHESIS.md     # Meta-analysis results
│   └── HYPOTHESIS-EVALUATION.md  # Systematic claim validation
├── docs/
│   ├── EXECUTIVE-SUMMARY.md      # Leadership/stakeholder brief
│   ├── CLINICAL-IMPLICATIONS.md  # Provider guidance
│   ├── STUDY-GOALS.md            # Research objectives
│   └── FUTURE-RESEARCH.md        # Next steps, Phase 2+
└── README.md                     # 3-minute pitch + overview

IRB Protocol Template Sections

1. Protocol Information — Title, version, sponsor, IND status
2. Principal Investigators — Names, credentials, roles, contacts
3. Study Synopsis — Background, rationale, objectives, design
4. Study Population — Inclusion/exclusion criteria with rationale
5. Study Intervention — What is being tested, dosing, duration
6. Study Procedures — Visit schedule, assessments, data collection
7. Safety Monitoring — Adverse event definitions, reporting, stopping rules
8. Data Management — Collection, storage, HIPAA compliance
9. Statistical Analysis — Power calculation, analysis plan
10. Ethical Considerations — Risk/benefit, consent process, vulnerable populations

Inclusion/Exclusion Criteria Pattern

### Inclusion Criteria
1. Age ≥ [minimum] years
2. [Clinical condition or symptom]
3. [Baseline test values] (e.g., eGFR > 60)
4. Ability to provide informed consent
5. Willing to comply with study procedures

### Exclusion Criteria
1. **Organ impairment**: [specific threshold]
2. **Current medication use**: [contraindicated drugs]
3. **Comorbid conditions**: [list with rationale]
4. **Concurrent medications** due to interaction risk:
   - [Drug class 1] (rationale)
   - [Drug class 2] (rationale)
5. **Pregnancy or planning pregnancy**
6. **Life expectancy < [study duration]**

External IRB Selection (Non-Academic Settings)

Budget: Add $2,000-3,000 for IRB fees + 4-6 weeks to timeline.

Evidence Confidence Levels

Stakeholder Materials

• README.md — 3-minute pitch for decision-makers
• EXECUTIVE-SUMMARY.md — 1-page BLUF for busy executives
• CLINICAL-IMPLICATIONS.md — Provider-focused guidance

Clinical Research Localization

For multi-language studies, maintain parallel informed consent documents. Use standard suffixes:

Quick Commands

# New project setup
mkdir -p .github/prompts docs data/{raw,processed} analysis/{scripts,outputs} writing/{drafts,figures} references/notes
touch docs/RESEARCH-PLAN.md docs/METHODOLOGY.md docs/DECISION-LOG.md references/LITERATURE-MATRIX.md .github/copilot-instructions.md README.md

# Audit existing project
find . -type f -name "*.md" -o -name "*.csv" -o -name "*.py" | head -50

# Migration with git tracking
git mv source destination

Troubleshooting

This skill makes research projects Alex-ready from day one, or gets them there through systematic refactoring.