paper-writing-skills-index

id paper_writing_skills_index name Paper Writing Skills Index description Routing and workflow skill family for paper-writing tasks. Covers manuscript drafting, journal and conference papers, grant proposals, lab reports, group-meeting reports, talks, workshop notes, reviewer rebuttals, academic HTML/PDF/LaTeX output with editable-block contracts, citation grounding, evidence checking, and pre-submission quality gates. tags ["paper_writing","manuscript","grant","rebuttal","citation","html","latex"] Paper Writing Skills Mode Two modes control which files and gates are loaded. Set mode in triage.md during Phase 0. Mode Default for Trigger words (override default) report all scenarios (default — no trigger needed) submission journal_article, conference_paper, paper_submission, grant_proposal, revision_response 投稿、submit、journal、conference、SCI、Nature、Cell、NeurIPS、ICLR、grant、基金、申请书、rebuttal、revision、peer review、深度调研、systematic review、meta-analysis If any submission trigger word appears in the user request, set mode: submission regardless of scenario. Otherwise default to report . What changes in submission mode Load paper_fetch.md during Phase 1 Load writing/claim_evidence_check.md during Phase 4 Load writing/reviewer_rubric.md during Phase 4 Load reporting_guideline_check.md during Phase 4 (clinical/observational/systematic review only) Routing + Sequential Pipeline Phase Entry criteria Actions Exit criteria 0. Triage a user request and any UI scenario labels Read workflow/SKILL.md ("Triage" section). Choose scenario_id , format_id , theme_id , mode , language, audience, outputs, constraints. {workdir}/triage.md exists or is updated 1. Materials and evidence triage is known Read the chosen scenario file under scenarios/ . Inventory materials. submission only: fetch/search papers via paper_fetch.md , build evidence registry (see Evidence Layer below). {workdir}/materials/inventory.md ; submission : also claim_evidence_map.md 2. Outline + claim boundary materials are known Read workflow/SKILL.md ("Paper Outline" + "Figure Storyline" sections). submission + novelty claim: also read Knowledge Lineage Audit in scenarios/grant_proposal.md . outline 3. Section drafting outline exists Read writing/SKILL.md . Draft Markdown. {workdir}/draft/paper.md 4. Quality gates draft exists Run gates per mode (see Quality Gates below). quality reports under {workdir}/quality/ 5. Editable output draft + quality notes exist Apply the chosen rendering template + theme per the Editable HTML Contract section below. {workdir}/report/<slug>_preview.html Scenario Routing User intent scenario_id Required scenario file Default mode manuscript, paper submission, write a paper paper_submission scenarios/paper_submission.md submission journal article, SCI, Nature-style paper journal_article scenarios/journal_article.md submission conference paper, workshop paper conference_paper scenarios/conference_paper.md submission grant, proposal, funding application grant_proposal scenarios/grant_proposal.md submission lab report, experiment report lab_report scenarios/lab_report.md report group meeting, weekly report group_report scenarios/group_report.md report conference talk, workshop sharing conference_talk / workshop_share scenarios/conference_talk.md / scenarios/workshop_share.md report reviewer comments, rebuttal, revision response revision_response scenarios/revision_response.md submission Family Index Layer File Contents Workflow phases workflow/SKILL.md 9 phases inlined: triage, material inventory, research question, literature review, paper outline, data analysis summary, figure storyline, reader testing, finalize packet Section writing writing/SKILL.md abstract, introduction, method, results, discussion, claim_evidence_check (citation grounding inlined), reviewer_rubric (+ reviewer_rubric_example), response_letter Evidence layer inlined below paper_fetch, evidence registry, evidence summary, context-bound answering Quality gates inlined below manuscript coverage, format lint, reproducibility; reporting_guideline_check (clinical) at reporting_guideline_check.md Editable HTML contract inlined below block shape, attributes, validation pass criteria Themes themes/kami_academic.md + themes/kami_academic.css warm parchment academic theme Scenario Format Index HTML output for any format must satisfy the Editable HTML Contract below. format_id Scenario file Required structure Special constraints journal_article scenarios/journal_article.md Title, Abstract, Keywords, Introduction, Results, Discussion, Methods, Data Availability, Code Availability, Acknowledgements, References, SI note figure/table numbering, data/code statements, guideline checks when applicable conference_paper scenarios/conference_paper.md Title, Abstract, Introduction, Related Work, Method, Experiments, Results, Discussion, Conclusion, References, Appendix page limit, baseline and ablation completeness, optional LaTeX grant_application scenarios/grant_proposal.md title, abstract, background, gap, aims, research content, key scientific questions, technical route, innovation, feasibility, plan, expected outcomes, team, budget, references form-like blocks, word limits, aim-route consistency lab_report scenarios/lab_report.md experiment name, date, operator, purpose, materials, steps, raw observations, data processing, results, abnormal events, conclusion, next step raw observation separated from interpretation group_report scenarios/group_report.md progress, core question, evidence, current conclusion, blockers, discussion questions, next plan scan-friendly, short sections conference_talk scenarios/conference_talk.md opening, audience context, problem, key idea, evidence sequence, takeaway, Q&A, speaker notes every figure has a spoken takeaway workshop_share scenarios/workshop_share.md prerequisites, materials, steps, checkpoints, expected outputs, troubleshooting, Q&A reproducible from a clean environment revision_response scenarios/revision_response.md Reviewer X Comment Y, Comment, Response, Changes Made, Status preserve every comment Required Outputs {workdir}/triage.md {workdir}/draft/paper.md (Markdown source of truth) {workdir}/report/<slug>_preview.html {workdir}/quality/claim_evidence_report.md {workdir}/quality/reviewer_report.md — submissions, grants, rebuttals, high-risk tasks only Rendering Templates Template File Output report_standard report_standard.md Professional report (Manus-style), HTML+CSS report_academic report_academic.md Formal academic paper, HTML+CSS latex_cn latex_cn.md Chinese academic paper, LaTeX → PDF latex_en latex_en.md English academic paper, LaTeX → PDF Standard rendering flow Read report_standard.md for the HTML+CSS template. Convert draft/paper.md to HTML, wrapping major sections per the Editable HTML Contract below. Apply the selected theme. Write {workdir}/report/<slug>_preview.html . Academic rendering flow (LaTeX → PDF) Read the LaTeX template ( latex_cn.md or latex_en.md based on language). Convert draft/paper.md to LaTeX, fill the template, write <slug>.tex . Read COMPILE.md — probe available engines before compiling. Also produce an HTML preview via report_academic.md . Evidence Layer Evidence skills decide where facts come from. Claims may not be invented or grounded in model memory; they must trace back to a registered piece of evidence. Need Where Search and fetch open-access papers by DOI / arXiv / PMID paper_fetch.md Register claims and supporting evidence Evidence Registry below Ground citations to specific text segments, rerank, attribute sentences writing/claim_evidence_check.md ("Citation Grounding" section) Write data and code availability statements scenarios/journal_article.md ("Data and Code Availability" section) Default pipeline : paper_fetch → evidence_summary → evidence_registry → draft → citation grounding Evidence Registry — claim_evidence_map.md Claim ID Claim Evidence type Source Strength Risk Action C1 … citation/figure/table/data/user_material/missing S001 strong low keep Evidence types: citation , figure , table , experimental_data , statistical_result , user_material , missing . Claims with missing evidence cannot appear as firm conclusions. If support is partial, narrow the wording. Evidence Summary — output table Evidence ID Source Passage/page Query answered Summary Score Claim IDs Preserve locator detail for later attribution. Separate the source's statement from the agent's interpretation. If evidence does not answer the query, say so; do not force fit. Context-Bound Answering Answer only from provided context. Cite context keys, evidence IDs, pages, or material IDs. If context is insufficient, write I cannot answer from the provided context and list what is missing. Do not fall back to model memory. Quality Gates Gates produce reports and risk flags — guardrails, not gatekeepers. Flag issues and suggest fixes; do not silently rewrite a draft to hide problems. Aim for ≥80% compliance; prioritize critical issues (missing data, unsupported claims, fabricated citations) over cosmetic formatting. Gate Where report submission Manuscript coverage inlined below ✅ ✅ Format lint inlined below ✅ ✅ Reproducibility inlined below ✅ ✅ HTML editability Editable HTML Contract below ✅ ✅ Claim / evidence + citation grounding writing/claim_evidence_check.md ❌ ✅ Reviewer simulation (NeurIPS-style) writing/reviewer_rubric.md ❌ ✅ Reporting guideline (CONSORT/STROBE/PRISMA) reporting_guideline_check.md ❌ ✅ clinical only Response consistency scenarios/revision_response.md ❌ ✅ revision_response only Run order : manuscript coverage → format lint → reproducibility → claim/evidence → reporting guideline → reviewer simulation → HTML editability → response consistency. Manuscript Coverage Check Core sections (required): Title, Abstract, Introduction, Methods, Results, Discussion, References. Optional (journal-dependent): Keywords, Conclusion, Acknowledgements, Author Contributions, Competing Interests, Data/Code Availability, Supplementary Materials. Section Must contain Abstract background → gap → method → results → conclusion Introduction background → related work → gap → contribution Methods design, materials, procedure, parameters, analysis Results main findings, figures, tables, statistics, subsections by question Discussion interpretation, comparison, limitations, future, take-home Output: ## Manuscript Coverage Report with completeness %, present/complete list, missing/incomplete list, recommendation. Gate: ≥90% excellent / 80-89% good / <80% major sections missing. Format Lint Check: section structure complete; figure/table numbering sequential with captions; references numbered, no gaps, consistent format; word/page limits met; supplementary files referenced and numbered. Output: ## Format Lint Report with compliance %, correct categories, issues (severity + location + action), word count vs limit, recommendation. Common limits (always verify against journal guidelines): Journal Abstract Main text Figures Refs Nature/Science 150-200 3-4k words 4-6 30-50 Cell 150 5k 7 80 NeurIPS 250 8 pages — — PLOS ONE 300 none none none Gate: ≥90% excellent / 80-89% fix flagged / <80% major problems. Reproducibility Check