Paper Workflow

Overview

Use this skill as the routing map for paper work. It does not replace the specialized skills. It tells you which one to use next.

Default assumption: unless the user explicitly names a conference venue, the manuscript should follow the journal-oriented, Nature-style workflow.

When writing follows experiments or analysis performed across multiple sessions, freeze a compact handoff first: current paper story, supported findings, unresolved decisions, and the figure list that actually carries those findings.

Routing Map

Use:

• paper-bootstrap when a project is new, messy, or missing a source of truth
• nature-portfolio-playbook when the target is Nature, Nature Methods, Nature Biotechnology, or the venue fit among those journals is still unclear
• scientific-writing when drafting or rewriting sections in prose
• manuscript-optimizer when the paper's claim structure, evidence chain, terminology, or prose need revision
• results-section-revision when the Results section is scientifically stable but the subsection flow, paragraph openings, or argument progression still feel jumpy
• figure-planner when the main bottleneck is figure logic, panel roles, or legend sync
• citation-verifier when bibliography hygiene or source verification is the bottleneck
• data-availability when repository plans, accession numbers, source-data coverage, or Data Availability wording are the bottleneck
• submission-audit when the paper is near submission or resubmission and needs a preflight pass
• rebuttal-response when reviewer comments exist and a response letter plus aligned manuscript edits are needed
• conference-paper-writing only when the user explicitly wants a conference paper for venues such as NeurIPS, ICML, ICLR, ACL, AAAI, or COLM

Default Sequence

For most journal manuscripts, prefer this order:

1. paper-bootstrap
2. nature-portfolio-playbook when venue fit or article type is uncertain
3. Refresh notes/project_truth.md, notes/result_summary.md, and notes/paper_handoff.md after any major experimental or figure update
4. scientific-writing or manuscript-optimizer
5. figure-planner
6. results-section-revision when Results is substantively right but narratively abrupt
7. citation-verifier
8. data-availability
9. submission-audit
10. rebuttal-response after external review

Common Mistakes

• using conference-style writing skills by default for journal manuscripts
• polishing sections before the active manuscript source of truth is clear
• rewriting the manuscript from experiment memory instead of a current result_summary.md or paper_handoff.md
• editing figure legends late without rechecking the Results text
• leaving repository choice, accession IDs, or source-data coverage until the submission portal is already open
• postponing Nature Portfolio article-type or venue-fit decisions until after the paper is mostly rewritten
• treating citation formatting as the same thing as citation verification
• writing a response letter before deciding the underlying manuscript edits