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)

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]

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

Phase 2: Scaffold Creation

Create target structure (empty folders):

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

Create missing essential files:
- RESEARCH-PLAN.md (even if retrospective)
- METHODOLOGY.md
- LITERATURE-MATRIX.md
- copilot-instructions.md
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:

Original Location	New Location	Action
`data.csv`	`data/raw/original-data.csv`	Rename + move
`data_cleaned.csv`	`data/processed/data-cleaned.csv`	Move
`paper.docx`	`writing/drafts/paper-v1.docx`	Version + move
`notes.txt`	`references/notes/reading-notes.md`	Convert + move

Phase 4: Retroactive Documentation

Fill in documentation from what exists:

RESEARCH-PLAN.md: Extract from proposal, drafts, or reconstruct
DECISION-LOG.md: Interview yourself about choices made
LITERATURE-MATRIX.md: Build from reference list in drafts
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

Update any internal links in documents
Update file paths in analysis scripts
Update .gitignore for new structure
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

Phase	Alex Integration	Key Actions
Planning	Research design consultation	Create RESEARCH-PLAN.md, set up structure
Literature	Summarization, gap analysis	Build LITERATURE-MATRIX.md systematically
Data Collection	Instrument review, protocol checking	Document in METHODOLOGY.md
Analysis	Code review, interpretation checking	Log decisions, version scripts
Writing	Drafting, citation checking, editing	Use references/ for fact-checking
Revision	Peer review response, formatting	Track versions in writing/submissions/

Common Refactoring Patterns

Smell	Refactoring
All files in root	Create folder hierarchy
Data mixed with analysis	Separate data/raw, data/processed, analysis/
Multiple draft versions scattered	Consolidate in writing/drafts with clear naming
References in random locations	Centralize in references/
No context for AI assistance	Create copilot-instructions.md
Decisions made but not recorded	Create retrospective DECISION-LOG.md
Literature notes disorganized	Build structured LITERATURE-MATRIX.md

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

Protocol Information — Title, version, sponsor, IND status
Principal Investigators — Names, credentials, roles, contacts
Study Synopsis — Background, rationale, objectives, design
Study Population — Inclusion/exclusion criteria with rationale
Study Intervention — What is being tested, dosing, duration
Study Procedures — Visit schedule, assessments, data collection
Safety Monitoring — Adverse event definitions, reporting, stopping rules
Data Management — Collection, storage, HIPAA compliance
Statistical Analysis — Power calculation, analysis plan
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)

IRB	Cost Range	Timeline	Best For
Sterling IRB	$1,500-3,000	2-3 weeks	Supplement studies
Solutions IRB	$1,000-2,500	2-3 weeks	Budget-conscious
Advarra	$2,000-4,000	2-4 weeks	Academic spinoffs
WCG IRB	$2,500-5,000	2-4 weeks	Large commercial

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

Evidence Confidence Levels

Level	Meaning	Basis
HIGH	Strong consensus	Multiple RCTs, mechanisms confirmed
MODERATE	Promising	Animal studies, small human trials
LOW	Emerging	Case reports, theoretical basis only
INSUFFICIENT	Unknown	No quality evidence available

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:

Language	Suffix	Example
English	(none)	INFORMED-CONSENT.md
Spanish	-ES	INFORMED-CONSENT-ES.md
Portuguese	-PT	INFORMED-CONSENT-PT.md
Chinese	-ZH	INFORMED-CONSENT-ZH.md

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

Issue	Solution
Project too messy to audit	Start with just essential files, refactor incrementally
Lost track of versions	Use git log, create retrospective changelog
Data too sensitive for repo	Use .gitignore, document in DATA-DICTIONARY.md what exists
Analysis scripts break after move	Update relative paths, consider using project root as working directory
Can't remember decisions	Check email, drafts, commit messages for clues

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