academic-research

name	academic-research
description	Research project scaffolding, thesis/dissertation writing, literature reviews, publication workflows, and Alex-assisted academic workflows
tier	extended
category	documentation
applyTo	**/*paper*,**/*manuscript*,**/*journal*,**/*thesis*,**/*dissertation*,**/*research*,**/*academic*

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

1. Introduction — Problem, significance, research questions
2. Literature Review — Framework, prior work, gaps
3. Methodology — Design, collection, analysis
4. Results — Data without interpretation
5. Discussion — Interpret, connect to literature
6. 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 importance
2. Establish niche — gap in knowledge
3. 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]

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Committee Navigation

Defense Preparation

1. Anticipate likely questions
2. Prepare 20-30 minute presentation
3. Know your limitations
4. Have backup slides
5. 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

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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

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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

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Related Skills

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