Academic Research

Research project scaffolding, thesis/dissertation writing, literature reviews, publication workflows, and Alex-assisted academic workflows

fabioc-aloha Updated Sep 17, 2026

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Academic Research

Complete research lifecycle: project setup, literature review, writing, publication, and defense.

Project Structure

research-project/
├── .github/
│   └── copilot-instructions.md    # Research context for Alex
├── docs/
│   ├── RESEARCH-PLAN.md           # Questions, timeline, milestones
│   ├── METHODOLOGY.md             # Design decisions
│   └── DECISION-LOG.md            # Key decisions with rationale
├── data/
│   ├── raw/                       # Untouched source data
│   ├── processed/                 # Cleaned/transformed
│   └── DATA-DICTIONARY.md         # Variable definitions
├── analysis/
│   ├── scripts/                   # Analysis code
│   └── outputs/                   # Figures, tables
├── writing/
│   ├── drafts/                    # Work in progress
│   └── submissions/               # Submitted versions
├── references/
│   ├── LITERATURE-MATRIX.md       # Systematic tracking
│   └── notes/                     # Reading notes
└── README.md

Quick Setup

mkdir -p .github docs data/{raw,processed} analysis/{scripts,outputs} writing/{drafts,submissions} references/notes
touch docs/RESEARCH-PLAN.md docs/METHODOLOGY.md references/LITERATURE-MATRIX.md .github/copilot-instructions.md

Research Project Types

Type	Duration	Output	Review
Master's Thesis	1-2 years	80-150 pages	Committee defense
PhD Dissertation	3-7 years	150-300+ pages	Committee + external
Journal Article	3-12 months	5,000-10,000 words	Peer review
Conference Paper	2-6 months	4,000-8,000 words	Peer review

Research Question Development

PICO Framework

Population — Who is being studied?
Intervention — What is being tested?
Comparison — Against what?
Outcome — What is measured?

FINER Criteria

Criterion	Question
Feasible	Can it be done with available resources?
Interesting	Does anyone care?
Novel	Does it add new knowledge?
Ethical	Can it be done ethically?
Relevant	Does it matter to the field?

Literature Review

Synthesis Approaches

Approach	When to Use
Thematic	Organize by concepts across sources
Chronological	Show field evolution
Methodological	Compare research approaches
Concept Matrix	Map concepts to sources in table

Gap Types

Empirical — No studies in specific context
Theoretical — Theory not applied to domain
Methodological — New methods could reveal insights
Population — Understudied demographic

Literature Matrix Template

| Citation | Year | Method | Findings | Gaps | Relevance |
|----------|------|--------|----------|------|-----------|
| Author1 et al. | 2024 | RCT | X | Y | ⭐⭐⭐ |

Methodology

Qualitative Methods

Method	Best For	Sample
Interviews	Deep understanding	10-30
Focus Groups	Group dynamics	4-8/group
Case Study	Detailed exploration	1-10
Grounded Theory	Theory generation	Until saturation

Quantitative Methods

Method	Best For	Sample
Survey	Breadth, generalization	100-1000+
Experiment	Causation	Power analysis
Quasi-experiment	No randomization	Varies

Mixed Methods

Convergent — Qual + quant simultaneously
Explanatory Sequential — Quant → Qual
Exploratory Sequential — Qual → Quant

Thesis/Dissertation Structure

Introduction — Problem, significance, research questions
Literature Review — Framework, prior work, gaps
Methodology — Design, collection, analysis
Results — Data without interpretation
Discussion — Interpret, connect to literature
Conclusion — Summary, contributions, limitations

Discipline Variations

Discipline	Variation
Sciences	Methods-heavy
Humanities	Multiple thematic chapters
Social Sciences	Separate theoretical framework
Engineering	Implementation + Evaluation chapters

Academic Writing

Hedging Language

Strong	Hedged
"This proves..."	"This suggests..."
"Always causes"	"May contribute to"
"Definitely shows"	"Evidence indicates"

CARS Model (Introductions)

Establish territory — topic importance
Establish niche — gap in knowledge
Occupy niche — your contribution

Citation Density

Section	Density
Abstract	None
Introduction	Medium
Related Work	High
Methods	Low-Medium
Results	Low
Discussion	Medium

Publication Workflow

Venue Selection

Research Type	Venue
User study with metrics	ACM CHI
Business implications	Harvard Business Review
Cognitive theory	Cognitive Systems Research
Philosophical AI argument	Minds & Machines

5-Phase Process

Phase	Duration	Focus
Preparation	1-2 weeks	Literature, outline, figures
Rough Draft	1-2 weeks	Write without editing
Revision	1-2 weeks	Structure → Section → Paragraph → Sentence
Feedback	2-4 weeks	Advisor, peers
Polish	1 week	Format, citations, submit

Responding to Reviews

## Response to Reviewer 1

### R1.1: "[Concern]"

We appreciate this observation. [How addressed].

Changes: Section X, paragraph Y: [new text]

Committee Navigation

Defense Preparation

Anticipate likely questions
Prepare 20-30 minute presentation
Know your limitations
Have backup slides
Practice with friendly audience

Common Concerns

Concern	Address With
"Why this topic?"	Strong motivation
"What's your contribution?"	Explicit list
"How is this valid?"	Robust methodology
"What about X?"	Scope, future work

Citation Management

Style	Discipline
APA 7	Psychology, social sciences
MLA 9	Humanities
Chicago	History
IEEE	Engineering, CS
Vancouver	Medicine

Refactoring Existing Projects

Audit Checklist

Has .github/copilot-instructions.md
Data separated: raw vs processed
Research questions documented
Literature systematically tracked
Methodology decisions recorded

Migration Pattern

git mv old-data.csv data/raw/
git mv cleaned.csv data/processed/
git mv draft.docx writing/drafts/paper-v1.docx

File Templates

RESEARCH-PLAN.md

# Research Plan: [Title]

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

## Timeline
| Phase | Duration | Deliverable |
|-------|----------|-------------|
| Literature | Weeks 1-4 | Matrix complete |
| Collection | Weeks 5-12 | Raw data |
| Analysis | Weeks 13-16 | Results |
| Writing | Weeks 17-20 | Draft |

copilot-instructions.md (Research)

# [Project] - Research Context

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

## Alex Guidance
- Add literature to references/LITERATURE-MATRIX.md
- Log decisions in docs/DECISION-LOG.md
- Citation style: APA 7

Pre-Submission Checklist

Abstract stands alone
Contributions stated explicitly
All claims supported
Limitations acknowledged
References complete
Word limit respected
Anonymized if required

Tools

Tool	Purpose
Zotero	Reference management
Overleaf	LaTeX collaboration
Connected Papers	Literature discovery
Pandoc	Markdown to Word/PDF

Related Skills

literature-review — Systematic search
citation-management — APA formatting
md-to-word — Document conversion
dissertation-defense — Defense preparation

---name: academic-researchdescription: Research project scaffolding, thesis/dissertation writing, literature reviews, publication workflows, and Alex-assisted academic workflows---# Academic Research> Complete research lifecycle: project setup, literature review, writing, publication, and defense.---## Project Structure```research-project/├── .github/│ └── copilot-instructions.md # Research context for Alex├── docs/│ ├── RESEARCH-PLAN.md # Questions, timeline, milestones│ ├── METHODOLOGY.md # Design decisions│ └── DECISION-LOG.md # Key decisions with rationale├── data/│ ├── raw/ # Untouched source data│ ├── processed/ # Cleaned/transformed│ └── DATA-DICTIONARY.md # Variable definitions├── analysis/│ ├── scripts/ # Analysis code│ └── outputs/ # Figures, tables├── writing/│ ├── drafts/ # Work in progress│ └── submissions/ # Submitted versions├── references/│ ├── LITERATURE-MATRIX.md # Systematic tracking│ └── notes/ # Reading notes└── README.md```### Quick Setup```bashmkdir -p .github docs data/{raw,processed} analysis/{scripts,outputs} writing/{drafts,submissions} references/notestouch docs/RESEARCH-PLAN.md docs/METHODOLOGY.md references/LITERATURE-MATRIX.md .github/copilot-instructions.md```---## Research Project Types| Type | Duration | Output | Review ||------|----------|--------|--------|| Master's Thesis | 1-2 years | 80-150 pages | Committee defense || PhD Dissertation | 3-7 years | 150-300+ pages | Committee + external || Journal Article | 3-12 months | 5,000-10,000 words | Peer review || Conference Paper | 2-6 months | 4,000-8,000 words | Peer review |---## Research Question Development### PICO Framework- **P**opulation — Who is being studied?- **I**ntervention — What is being tested?- **C**omparison — Against what?- **O**utcome — What is measured?### FINER Criteria| Criterion | Question ||-----------|----------|| **F**easible | Can it be done with available resources? || **I**nteresting | Does anyone care? || **N**ovel | Does it add new knowledge? || **E**thical | Can it be done ethically? || **R**elevant | Does it matter to the field? |---## Literature Review### Synthesis Approaches| Approach | When to Use ||----------|-------------|| **Thematic** | Organize by concepts across sources || **Chronological** | Show field evolution || **Methodological** | Compare research approaches || **Concept Matrix** | Map concepts to sources in table |### Gap Types- **Empirical** — No studies in specific context- **Theoretical** — Theory not applied to domain- **Methodological** — New methods could reveal insights- **Population** — Understudied demographic### Literature Matrix Template```markdown| Citation | Year | Method | Findings | Gaps | Relevance ||----------|------|--------|----------|------|-----------|| Author1 et al. | 2024 | RCT | X | Y | ⭐⭐⭐ |```---## Methodology### Qualitative Methods| Method | Best For | Sample ||--------|----------|--------|| Interviews | Deep understanding | 10-30 || Focus Groups | Group dynamics | 4-8/group || Case Study | Detailed exploration | 1-10 || Grounded Theory | Theory generation | Until saturation |### Quantitative Methods| Method | Best For | Sample ||--------|----------|--------|| Survey | Breadth, generalization | 100-1000+ || Experiment | Causation | Power analysis || Quasi-experiment | No randomization | Varies |### Mixed Methods- **Convergent** — Qual + quant simultaneously- **Explanatory Sequential** — Quant → Qual- **Exploratory Sequential** — Qual → Quant---## Thesis/Dissertation Structure1. **Introduction** — Problem, significance, research questions2. **Literature Review** — Framework, prior work, gaps3. **Methodology** — Design, collection, analysis4. **Results** — Data without interpretation5. **Discussion** — Interpret, connect to literature6. **Conclusion** — Summary, contributions, limitations### Discipline Variations| Discipline | Variation ||------------|-----------|| Sciences | Methods-heavy || Humanities | Multiple thematic chapters || Social Sciences | Separate theoretical framework || Engineering | Implementation + Evaluation chapters |---## Academic Writing### Hedging Language| Strong | Hedged ||--------|--------|| "This proves..." | "This suggests..." || "Always causes" | "May contribute to" || "Definitely shows" | "Evidence indicates" |### CARS Model (Introductions)1. **Establish territory** — topic importance2. **Establish niche** — gap in knowledge3. **Occupy niche** — your contribution### Citation Density| Section | Density ||---------|---------|| Abstract | None || Introduction | Medium || Related Work | High || Methods | Low-Medium || Results | Low || Discussion | Medium |---## Publication Workflow### Venue Selection| Research Type | Venue ||---------------|-------|| User study with metrics | ACM CHI || Business implications | Harvard Business Review || Cognitive theory | Cognitive Systems Research || Philosophical AI argument | Minds & Machines |### 5-Phase Process| Phase | Duration | Focus ||-------|----------|-------|| Preparation | 1-2 weeks | Literature, outline, figures || Rough Draft | 1-2 weeks | Write without editing || Revision | 1-2 weeks | Structure → Section → Paragraph → Sentence || Feedback | 2-4 weeks | Advisor, peers || Polish | 1 week | Format, citations, submit |### Responding to Reviews```markdown## Response to Reviewer 1### R1.1: "[Concern]"We appreciate this observation. [How addressed].Changes: Section X, paragraph Y: [new text]```---## Committee Navigation### Defense Preparation1. Anticipate likely questions2. Prepare 20-30 minute presentation3. Know your limitations4. Have backup slides5. Practice with friendly audience### Common Concerns| Concern | Address With ||---------|--------------|| "Why this topic?" | Strong motivation || "What's your contribution?" | Explicit list || "How is this valid?" | Robust methodology || "What about X?" | Scope, future work |---## Citation Management| Style | Discipline ||-------|------------|| APA 7 | Psychology, social sciences || MLA 9 | Humanities || Chicago | History || IEEE | Engineering, CS || Vancouver | Medicine |---## Refactoring Existing Projects### Audit Checklist- [ ] Has .github/copilot-instructions.md- [ ] Data separated: raw vs processed- [ ] Research questions documented- [ ] Literature systematically tracked- [ ] Methodology decisions recorded### Migration Pattern```bashgit mv old-data.csv data/raw/git mv cleaned.csv data/processed/git mv draft.docx writing/drafts/paper-v1.docx```---## File Templates### RESEARCH-PLAN.md```markdown# Research Plan: [Title]## Research Questions1. Primary: [Main question]2. Secondary: [Supporting questions]## Timeline| Phase | Duration | Deliverable ||-------|----------|-------------|| Literature | Weeks 1-4 | Matrix complete || Collection | Weeks 5-12 | Raw data || Analysis | Weeks 13-16 | Results || Writing | Weeks 17-20 | Draft |```### copilot-instructions.md (Research)```markdown# [Project] - Research Context## Current Phase- [x] Literature Review- [ ] Data Collection## Alex Guidance- Add literature to references/LITERATURE-MATRIX.md- Log decisions in docs/DECISION-LOG.md- Citation style: APA 7```---## Pre-Submission Checklist- [ ] Abstract stands alone- [ ] Contributions stated explicitly- [ ] All claims supported- [ ] Limitations acknowledged- [ ] References complete- [ ] Word limit respected- [ ] Anonymized if required---## Tools| Tool | Purpose ||------|---------|| Zotero | Reference management || Overleaf | LaTeX collaboration || Connected Papers | Literature discovery || Pandoc | Markdown to Word/PDF |---## Related Skills- [literature-review](../literature-review/SKILL.md) — Systematic search- [citation-management](../citation-management/SKILL.md) — APA formatting- [md-to-word](../md-to-word/SKILL.md) — Document conversion- [dissertation-defense](../dissertation-defense/SKILL.md) — Defense preparation

fabioc-aloha/alex-cognitive-architecture/tree/main/.github/skills/academic-research commit 40e90cf14b

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