Paper Writing Skills Index

Writing Community

Repo stars 428
Author repo PantheonOS

Interpretation is structured for decision-making; original keeps the upstream SKILL.md unchanged.

Decide Fit First

Core job: | Two modes control which files and gates are loaded. Set mode in triage.md during Phase 0. If any submission trigger word appea…
Best fit: Use it when the task has reusable inputs, steps, and validation criteria rather than a one-off answer.
Avoid forcing it: If the source lacks commands, platform support, or external-service evidence, keep those fields unknown instead of guessing.

Design Intent

Structure: The skill is organized around “Mode”, “Routing + Sequential Pipeline”, “Scenario Routing”, “Family Index”, showing how the author expects the agent to judge fit, collect context, and produce verifiable output.
Trigger evidence: Prioritize the author’s wording around when to use it, what context to collect, and what output shape to produce.
Evidence boundary: Author text states facts, repository files prove commands and paths, and Fluxly only adds fit, limits, and usage judgment.

How To Use It

Inputs: Provide target material, scope, expected result, forbidden changes, and validation method.
Invocation: Name Paper Writing Skills Index directly; if the source includes slash commands, start with the command and then add task context.
Validation: Start small and check whether the result follows “Mode / Routing + Sequential Pipeline / Scenario Routing” before expanding.

Boundaries And Review

Dependencies: It usually needs no extra API key, so start with a small validation task.
Permissions: Declared permissions include read / write; ask the agent to state file, command, and rollback boundaries before acting.
Quality bar: A useful result names the deliverable, evidence, and next action. Generic prose means the task needs tighter context.

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

Audit categories (each must be present and concrete): software & tools (names, versions, OS, libraries); parameters & settings (hyperparameters, seeds, hardware); data (source, version, splits, availability); code (repo URL, license, dependencies, reproducibility script).

Output: ## Reproducibility Check Report with compliance %, sufficient detail list, missing/vague list (current text + fix), availability statement templates, recommendation. Gate: ≥90% excellent / 80-89% good / 70-79% fair / <70% major revision.

Editable HTML Contract

All HTML outputs must be standalone working files, not app-only previews.

<section class="editable-block" contenteditable="true"
  data-block-id="abstract-001" data-section="abstract"
  data-source="draft/paper.md" data-format-role="summary">
  <h2>Abstract</h2><p>…</p>
</section>

Required: single file with embedded CSS; semantic tags (section, figure, figcaption, table, caption); @page or @media print; no frontend runtime required; no absolute positioning for body layout.

Attribute	Meaning
`data-block-id`	stable local block identifier
`data-section`	manuscript/report section
`data-source`	source file, usually `draft/paper.md`
`data-format-role`	`summary`, `claim`, `evidence`, `method`, `response`

Validation (run after every HTML generation): file opens standalone; CSS embedded; main text is semantic HTML not an image; major blocks have contenteditable="true" and all four data-* attributes; print CSS present; figures/tables use semantic tags. If any criterion fails, fix the renderer or source Markdown — do not relax the contract.

Non-Negotiable Rules

Do not write unsupported claims. Mark missing evidence and downgrade or remove the claim.
Do not invent citations, DOIs, accession IDs, page numbers, data repositories, reviewer changes, or experimental results.
Do not let a search result become evidence until it is summarized, attributed, and bound to a specific claim in the Evidence Registry above.
Do not use Sci-Hub or any access-control bypass. Open PDF fetching may use only legal OA routes in paper_fetch.md.
Do not output screenshot-like reports. Main text must remain semantic and editable HTML per the Editable HTML Contract above.
Keep each SKILL.md below 500 lines.

Sources

Anthropic skill design — https://github.com/anthropics/skills/blob/main/skills/skill-creator/SKILL.md
Anthropic doc coauthoring — https://github.com/anthropics/skills/blob/main/skills/doc-coauthoring/SKILL.md
Trail of Bits workflow skill design — https://github.com/trailofbits/skills/blob/main/plugins/workflow-skill-design/skills/designing-workflow-skills/SKILL.md
PaperQA evidence RAG — https://github.com/Future-House/paper-qa
OpenScholar attribution — https://github.com/akariasai/openscholar
Nature-style response/figure/citation/data skills — https://github.com/Yuan1z0825/nature-skills
DeepScientist outline/review/rebuttal/writer skills — https://github.com/ResearAI/DeepScientist
Research-Paper-Writing-Skills (Master-cai, MIT) — abstract / introduction / method / results / discussion section guides
AI-Scientist (SakanaAI, MIT) — NeurIPS-style reviewer rubric
EQUATOR Network — reporting guideline checklists
tw93/Kami (MIT) — academic theme

Fluxly profile Author and license come from source; runtime, permissions, and network are Fluxly detections or estimates

Fluxly category: Writing
Author-declared agents: No explicit declaration found; this is not inferred or tested compatibility
Static check: 88 / 100 · heuristic scan, not runtime safety proof
Author / version / license: @aristoteleo · no license declared
Fluxly token estimate: Lean
Fluxly setup estimate: Guided setup
External API key: No requirement detected
Detected OS requirements: Unspecified
Runtime requirements: Unspecified
Detected file/system behavior: Read-only
Write / modify
Detected network behavior: External requests
Install commands: None (reference only)

Profile is derived at build time from SKILL.md and install vectors. Subject to drift from author intent.

Heads up: 未限定 allowed-tools，默认拥有全部工具权限。

Output preview paper-writing-skills-index.preview

# 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

SKILL.md SKILL.md

# 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](./paper_fetch.md) during Phase 1 |
| Load [writing/claim_evidence_check.md](./writing/claim_evidence_check.md) during Phase 4 |
| Load [writing/reviewer_rubric.md](./writing/reviewer_rubric.md) during Phase 4 |
| Load [reporting_guideline_check.md](./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](./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](./paper_fetch.md), build evidence registry (see Evidence Layer below). | `{workdir}/materials/inventory.md`; `submission`: also `claim_evidence_map.md` |

…

Evidence boundary and execution chain

Author text anchors workflow facts; Fluxly only indexes current sections, terms, files, and commands.

sections -> Mode → Routing + Sequential Pipeline → Scenario Routing → Family Index → Scenario Format Index → Required Outputs
terms    -> Default pipeline · Run order · Validation · Two modes control which files and gates are loaded. · If any submission trigger word appears in the user request, set mode: submission regardless of scenario. · | Phase | Entry criteria | Actions | Exit criteria | |---|---|---|---| | 0. · HTML output for any format must satisfy the Editable HTML Contract below. · 1. Read [reportstandard.md](./reportstandard.md) for the HTML+CSS template.
files/cmd -> mode · triage.md · report · submission · mode: submission · scenarioid · formatid · themeid
body sha256 -> 68e6bcb734e3