paper-writing-workflow

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

1. Think before you write — define message, gap, and story before opening the Introduction (Paper I, Sect. 2.1). Methodology alone is not the story.
2. 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).
3. 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).
4. Figures early — place figures/tables in the outline; draft captions before polishing body text (Paper I step 4; Paper II, Sect. 2.3).
5. IMRaD + hourglass — broad intro → narrow methods/results → broad discussion (Paper II, Sect. 2.4).
6. Compile + debug by looking — paper-layout-review, vlm-figure-audit (plotting category); fix sources and recompile; do not paste LaTeX in chat.
7. 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)

1. Define message and story (critical thinking + literature).
2. Draft title and abstract (~150 words, whole paper in miniature).
3. Outline — words, bullets, or flow chart (match your thinking style; Paper I Sect. 2.2: visual vs verbal planners both valid).
4. Place figures/tables; draft captions.
5. Paragraph-level notes per section.
6. First draft — often data/methods first, Discussion last.
7. Track citations as you draft; verify each citation supports your claim.
8. Edit ruthlessly — cut what does not serve the message (appendix ok).
9. Polish — co-author feedback; share early drafts; fresh-eyes pass after a break.
10. 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)

1. Update plot scripts or .tex in the repo.
2. Regenerate figure PDFs; plot-check → physics-check (or results-check).
3. vlm-figure-audit each asset; update research-figure-manifest rows.
4. Compile; paper-layout-review on affected pages (iterative).
5. 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/)