paper-writer

Paper Writer Skill

Full-pipeline academic paper writing assistant. From literature search to submission-ready manuscript.

Overview

This skill manages the entire paper writing workflow:

[Discovery] → Literature Search → Outline → Tables/Figures → Draft → Humanize → References → Quality Review → [Adversarial Review] → Pre-Submission → [Revision] → [Post-Acceptance] → [Rejection → Resubmission]

Each paper is a project directory containing structured Markdown files for every section, a literature matrix, and quality checklists.

AI-for-Science Operating Model

This skill is not only a manuscript factory (write → format → submit). It is a research engine that wraps the writing pipeline in a discovery loop and names the two things only a human can supply. Before doing anything else, read ~/.claude/skills/paper-writer/references/ai-for-science-model.md — it defines:

• The two human-sovereign inputs. 💡 IDEA (what is worth asking, what it means, what is ethical) and 📊 DATA (real, IRB-approved, never machine-originated). AI proposes and executes everything else at full power; the human owns exactly these two gates. AI must never originate a data point, participant, or result.
• The loop. Phase −1 Discovery (hypothesis → novelty → design → pre-registration lock) feeds the existing pipeline; Phase 6.5 Adversarial Review red-teams the central claim before any journal sees it. A red-team KILL sends the project back to Discovery — that is the system working.
• The three integrity guardrails that make AI-accelerated research more rigorous, not less: pre-registration (anti-HARKing), novelty check (anti-reinvention/inflation), adversarial self-review (anti-slop). Each prevents a documented frontier failure mode.
• The autonomy dial (Manual / Co-pilot / Autopilot). Hard rule for clinical work: the 💡 IDEA gate, the 📊 DATA gate, and the pre-registration lock are never autopilot.

The rest of this document is the execution detail. When a phase touches a sovereign gate, stop and get the human; everywhere else, run at full power.