9. Research Workflow and Tools
9. Research Workflow and Tools
The decision
Choose tools by the research job they perform. Every job needs one source of truth.
| Job | Minimum capability | Source of truth |
|---|---|---|
| find | export stable metadata and links | search log |
| store | keep reference, PDF, and identifier together | reference library |
| understand | preserve source location and your analysis separately | source card |
| compare | sort studies by design, finding, and limit | evidence matrix |
| produce | control draft, citations, analysis, and versions | project folder |
Adding a second tool for the same job is justified only when it solves a named problem.
1. Use a minimal stack
For most projects:
one reference manager
+ one matrix or structured note table
+ one writing environment
+ one backed-up project folder
Examples include a reference manager such as Zotero, a spreadsheet for comparison, and Word/Google Docs or LaTeX for drafting. The brands may change; the functions do not.
2. Keep a stable project structure
project-name/
├── README.md
├── 01-protocol/
│ ├── question-scope.md
│ └── search-log.csv
├── 02-sources/
│ └── evidence-matrix.csv
├── 03-data-or-material/
├── 04-analysis/
├── 05-draft/
├── 06-output/
└── 07-decisions/
├── decision-log.md
└── ai-use-log.md
Keep sensitive data only in approved storage. A tidy folder is not a substitute for access control, consent, and retention rules.
3. Name versions by state
Avoid final-final-v7-really-final.docx.
2026-10-12-outline.md
2026-10-18-draft-for-peer-review.docx
2026-10-24-revised-after-method-check.docx
2026-10-30-submitted.pdf
Use version control when plain files cannot show who changed what or when analysis code and text must evolve together.
4. Connect notes to evidence
A highlight without a source location is fragile. A useful note contains:
reference → exact location → source meaning → my analysis → planned use → boundary
Tag by function, not only topic:
definition pattern counterevidence mechanism context method limitation
This makes it possible to retrieve all counterevidence or all method sources when revising a claim.
5. Run one repeatable loop
At each loop:
- save metadata and the stable link immediately;
- make a source card before highlighting more;
- update the matrix after three to five sources;
- write one synthesis sentence;
- search again only for a named uncertainty.
This prevents endless collection without argument.
6. Add tools only after a failure
| Failure | Add or change |
|---|---|
| references are mistyped | use citation insertion from the reference manager |
| sources cannot be compared | use a sortable matrix |
| long-term concepts are disconnected | use linked notes |
| equations/templates dominate formatting | consider LaTeX |
| analysis cannot be reproduced | use scripts/notebooks and version control |
| collaborators overwrite drafts | use tracked changes or collaborative version history |
Do not migrate during the final week unless the current system is unusable.
7. Keep a decision log
Date:
Decision:
Alternatives considered:
Evidence/reason:
Consequence for question, method, or claim:
Revisit when:
Examples: exclude a population, change an outcome, merge codes, handle missing data, reject a peer comment, or retain an AI suggestion.
The log turns “I remember deciding” into an auditable research history.
8. Apply the three-copy rule
For important non-sensitive files, keep:
- the working copy;
- an automatically synchronised or versioned copy;
- a separate recovery copy.
Test recovery once. A backup that has never been restored is only a hope.
Practice: a 20-minute workflow audit
- List every location containing sources, notes, data, code, or drafts.
- Assign one source of truth to each research job.
- Remove or archive one duplicate path.
- Create the project folders and README.
- Add three sources with location, use, and boundary.
- Record one real decision in the log.
Quality check
- every research job has one clear source of truth;
- source metadata, notes, and citations remain connected;
- filenames reveal date and purpose;
- sensitive material uses approved storage and permissions;
- analysis and important decisions can be reconstructed;
- backups are automatic and recoverable.