| 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
- 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
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
Tools
| Tool | Purpose |
|---|
| Zotero | Reference management |
| Overleaf | LaTeX collaboration |
| Connected Papers | Literature discovery |
| Pandoc | Markdown to Word/PDF |
Related Skills
