Research project scaffolding, thesis/dissertation writing, literature reviews, publication workflows, and Alex-assisted academic workflows
Complete research lifecycle: project setup, literature review, writing, publication, and defense.
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
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
| 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 |
| 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? |
| 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 |
| Citation | Year | Method | Findings | Gaps | Relevance |
|----------|------|--------|----------|------|-----------|
| Author1 et al. | 2024 | RCT | X | Y | ⭐⭐⭐ |
| 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 |
| Method | Best For | Sample |
|---|---|---|
| Survey | Breadth, generalization | 100-1000+ |
| Experiment | Causation | Power analysis |
| Quasi-experiment | No randomization | Varies |
| Discipline | Variation |
|---|---|
| Sciences | Methods-heavy |
| Humanities | Multiple thematic chapters |
| Social Sciences | Separate theoretical framework |
| Engineering | Implementation + Evaluation chapters |
| Strong | Hedged |
|---|---|
| "This proves..." | "This suggests..." |
| "Always causes" | "May contribute to" |
| "Definitely shows" | "Evidence indicates" |
| Section | Density |
|---|---|
| Abstract | None |
| Introduction | Medium |
| Related Work | High |
| Methods | Low-Medium |
| Results | Low |
| Discussion | Medium |
| Research Type | Venue |
|---|---|
| User study with metrics | ACM CHI |
| Business implications | Harvard Business Review |
| Cognitive theory | Cognitive Systems Research |
| Philosophical AI argument | Minds & Machines |
| 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 |
## Response to Reviewer 1
### R1.1: "[Concern]"
We appreciate this observation. [How addressed].
Changes: Section X, paragraph Y: [new text]
| 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 |
| Style | Discipline |
|---|---|
| APA 7 | Psychology, social sciences |
| MLA 9 | Humanities |
| Chicago | History |
| IEEE | Engineering, CS |
| Vancouver | Medicine |
git mv old-data.csv data/raw/
git mv cleaned.csv data/processed/
git mv draft.docx writing/drafts/paper-v1.docx
# 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 |
# [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
| Tool | Purpose |
|---|---|
| Zotero | Reference management |
| Overleaf | LaTeX collaboration |
| Connected Papers | Literature discovery |
| Pandoc | Markdown to Word/PDF |