| name | paper-writing-workflow |
| description | End-to-end research paper workflow: plan the narrative, draft IMRaD sections, produce figure assets, compile LaTeX to PDF, and debug layout by visually inspecting output (VLM). Use when starting, editing, or submitting a manuscript. |
Paper writing workflow
Deliverable: a reproducible manuscript PDF whose message, figures, and
text agree. Figures are project-generated PDF assets, not chat screenshots.
References (optional): Chamba, Knapen & Black (2022), Papers I–II —
arXiv:2207.12959. Skills work without the PDFs;
fetch from arXiv or keep local copies anywhere convenient. No fixed folder required.
Principles
- Think before you write — define message, gap, and story before opening the
Introduction (Paper I, Sect. 2.1). Methodology alone is not the story.
- Audience — professionals in the field, not necessarily experts in your
sub-field. Explain methods and tools you use; avoid jargon and stating the
obvious (Paper I, Sect. 2.5).
- Reproducibility — enough detail that results can be judged and reproduced.
Never "we reduced the data in the standard way"; cite the procedure or spell
out steps (Paper I, Sect. 2.5; Paper II, Sect. 2.6).
- Figures early — place figures/tables in the outline; draft captions before
polishing body text (Paper I step 4; Paper II, Sect. 2.3).
- IMRaD + hourglass — broad intro → narrow methods/results → broad discussion
(Paper II, Sect. 2.4).
- Compile + debug by looking — paper-layout-review, vlm-figure-audit
(plotting category); fix sources and recompile; do not paste LaTeX in chat.
- Prose → manuscript-writing-style; figures → plotting/ skills
(export, plot-check, physics-check, manifest).
Literature review (before drafting)
For each paper you skim, ask (Paper I, Sect. 2.1):
- Why am I reading this? What question does it answer for my project?
- Why did the authors write it? (title + abstract first)
- What story do the figures and captions tell?
- Are the conclusions supported by the evidence?
- What use is this paper to me — deep read or citation only?
Take notes in your own words; do not copy-paste into the draft (plagiarism risk,
Paper I, Sect. 2.4).
Planning sequence (ten steps, Paper I Sect. 2.3)
- Define message and story (critical thinking + literature).
- Draft title and abstract (~150 words, whole paper in miniature).
- Outline — words, bullets, or flow chart (match your thinking style; Paper I
Sect. 2.2: visual vs verbal planners both valid).
- Place figures/tables; draft captions.
- Paragraph-level notes per section.
- First draft — often data/methods first, Discussion last.
- Track citations as you draft; verify each citation supports your claim.
- Edit ruthlessly — cut what does not serve the message (appendix ok).
- Polish — co-author feedback; share early drafts; fresh-eyes pass after a break.
- Submit when good enough or deadline-bound.
If a fact or figure is missing, note it and keep writing; fill later (Paper I).
Data, code, and ethics (Paper I Sect. 2.3.2)
- Publish data and code with the paper when possible (CDS, Zenodo, Dryad, Figshare).
- Do not rely on personal or institute URLs alone.
- License software explicitly if you release it.
- Acknowledge archives, pipelines, and funding in Acknowledgements (Paper II, Sect. 2.10).
Build loop (after drafting exists)
- Update plot scripts or
.tex in the repo.
- Regenerate figure PDFs; plot-check → physics-check (or results-check).
- vlm-figure-audit each asset; update research-figure-manifest rows.
- Compile; paper-layout-review on affected pages (iterative).
- Record validator status in the project manifest if one exists.
Do not
- Ship without visually inspecting the compiled PDF near final layout.
- Treat "compiles without error" as sufficient.
- Patch unreadable figures only in LaTeX; regenerate the asset.
- Start the Introduction before message + figure plan exist.
- Dump LaTeX or plotting code in chat instead of editing project files.
Integration
| Skill | Role |
|---|
| manuscript-writing-style | IMRaD text, tone, captions, English mechanics |
| scientific-plotting | Vector PDF; colour-blind-safe design (plotting/) |
| plot-check / physics-check | Visual completeness + numeric asserts |
| vlm-figure-audit | Figure/table content QA (plotting/) |
| paper-layout-review | Iterative float/equation clash fix |
| research-figure-manifest | Provenance and validator status (plotting/) |
