Paper Writing Skills Index
- Repo stars 428
- Author updated Live
- Author repo PantheonOS
- Domain
- Writing
- Compatible agents
-
- Claude Code
- Cursor
- Cline
- Codex
- Windsurf
- Gemini CLI
- +20
- Trust score
- 88 / 100 · community maintained
- Author / version / license
- @aristoteleo · no license declared
- Token usage
- Lean
- Setup complexity
- Guided setup
- External API key
- Not required
- Operating systems
- Unspecified (assume cross-platform)
- Runtime requirements
- No special requirements
- Permissions
-
- Read-only
- Write / modify
- Network behavior
- External requests
- Install commands
- 26 variants
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。
---
name: Paper Writing Skills Index
description: | Two modes control which files and gates are loaded. Set mode in triage.md during Phase 0. If a…
category: writing
runtime: no special runtime
---
# Paper Writing Skills Index output preview
## PART A: Task fit
- Use case: | Two modes control which files and gates are loaded. Set mode in triage.md during Phase 0. If any submission trigger word appears in the user request, set mode: submission regardless of scenario. Otherwise default to report. makes outbound network calls. Works with Claude Code, Cursor, Cline and 23 more..
- Inputs: target material, constraints, expected output, and acceptance criteria.
- Evidence boundary: follow “Mode / Routing + Sequential Pipeline / Scenario Routing” and do not present inference as author intent.
## PART B: Execution result
- **01** The card summarizes the use case; runtime output centers on “| Two modes control which files and gates are loaded. Set mode in triage.md during Phase 0. If any submission trigger word appears in the user request, set mode: submission regardless of scenario. Otherwise default to report. makes outbound network calls. Works with Claude Code, Cursor, Cline and 23 more.”.
- **02** When the source has headings, the agent prioritizes “Mode / Routing + Sequential Pipeline / Scenario Routing” so the result follows the author’s structure.
- **03** Typical output includes task judgment, concrete steps, required commands or file edits, validation, and follow-up options.
- **04** Risk context follows the fingerprint: read files, write/modify files; may access external network resources; usually needs no extra API key.
## Running Rules
- read files, write/modify files; may access external network resources; usually needs no extra API key.
- Validate with a small sample before expanding scope.
- Return the result, validation criteria, and next iteration options. The source does not require a stable slash command. After installation, invoke the skill by name and describe the task.
Name target files or source material, expected output, forbidden changes, and whether network or shell access is allowed. Permission fingerprint: read files, write/modify files.
Start with a small task and check whether the result follows “Mode / Routing + Sequential Pipeline / Scenario Routing”. Inspect diffs, logs, previews, or tests before expanding scope.
Confirm the final output includes a concrete result, evidence, and next action. If it stays generic, tighten inputs, boundaries, and acceptance criteria.
---
name: Paper Writing Skills Index
description: | Two modes control which files and gates are loaded. Set mode in triage.md during Phase 0. If a…
category: writing
source: aristoteleo/PantheonOS
---
# Paper Writing Skills Index
## When to use
- | Two modes control which files and gates are loaded. Set mode in triage.md during Phase 0. If any submission trigger…
- Use it when the task has clear inputs, repeatable steps, and validation criteria.
## What to provide
- Target material, scope, expected result, and forbidden changes.
- Whether network, commands, file writes, or external services are allowed.
## Execution rules
- Organize steps around “Mode / Routing + Sequential Pipeline / Scenario Routing” and keep inference separate from source facts.
- read files, write/modify files; may access external network resources; usually needs no extra API key.
- Validate with a small sample before expanding the task.
## Output requirements
- Return the deliverable, key evidence, validation method, and next action.
- Mark missing information as unknown; do not invent commands, platforms, or dependencies. The author source anchors workflow facts; repository files anchor sources and commands; Fluxly only adds fit, limitations, and quality judgment.
skill "Paper Writing Skills Index" {
input -> user goal + target files + boundaries + acceptance criteria
context -> Mode / Routing + Sequential Pipeline / Scenario Routing
rules -> SKILL.md triggers / order / output contract
runtime -> no special runtime | read files, write/modify files | may access external network resources
guardrails -> usually needs no extra API key + small-sample validation + diff/log review
output -> copyable result + checklist + next iteration
} 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.mdto 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.mdorlatex_en.mdbased on language). - Convert
draft/paper.mdto 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.mdbelow 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
Decide Fit First
Design Intent
How To Use It
Boundaries And Review