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Scaffolding academic research projects and refactoring existing ones for Alex-assisted workflows
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npx skills add https://github.com/fabioc-aloha/Alex_Plug_In --skill research-project-scaffoldコマンドは1行のまま表示されます。コピー前に横へスクロールして全体を確認してください。
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SKILL.md を表示中
Create and maintain ASCII visual dashboards for project tracking with parallel lane progress bars
Store and manage voice samples for TTS cloning — portable, version-controlled audio references
Clear documentation through visual excellence
SOC 職業分類に基づく
| name | research-project-scaffold |
| description | Scaffolding academic research projects and refactoring existing ones for Alex-assisted workflows |
| tier | extended |
| applyTo | **/*research*,**/*academic*,**/*scaffold* |
Scaffolding new academic research projects and refactoring existing ones for Alex-assisted workflows.
Provide standardized structures and refactoring procedures for academic research projects that maximize Alex's ability to assist throughout the research lifecycle.
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
# 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
## 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
## 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]
# [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/)
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
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:
Create target structure (empty folders):
mkdir .github docs data data/raw data/processed analysis writing references
Create missing essential files:
Populate retrospectively:
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 |
Fill in documentation from what exists:
Retroactive documentation prompts:
| 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/ |
| 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 |
# 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
git tag submission-v1Patterns from Lithium Alzheimer's prevention research project (Feb 2026)
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
### 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]**
| 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.
| 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 |
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 |
# 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
| 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.