paper-writing

brycewang-stanford/Auto-Empirical-Research-Skills Science & research Office & PDF

paper-writing is a skill in brycewang-stanford/Auto-Empirical-Research-Skills, last changed 29 Oct 2026. It can install more skills, run shell commands and pre-approve tools — read the findings before installing.

From the author

Workflow 3: Full paper writing pipeline that goes from a narrative report to a polished, submission-ready PDF. Use when user says "写论文全流程", "write paper pipeline", "从报告到PDF", "paper writing", or wants the complete paper generation workflow.

How much a skill can do, not whether it is risky.

Pattern check

1 item to review

Broad tools pre-approved in allowed-tools

R34 · High · SKILL.md:5

Commit bfa0a6e · 3 Nov 2026

How the check works

Pattern check:1 item to reviewSee it

Install

Each tab says whether it installs commit bfa0a6e, the one we checked, or the latest version.

OpenCode also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.

Goose also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.

Windsurf (Devin Desktop) also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.

Zed also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.

Roo Code also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.

Factory Droid also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.

Junie also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.

Amp also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.

No install command here reaches Kiro. Copy the skill's folder into .kiro/skills/ in your project, or ~/.kiro/skills/ for all your projects. brycewang-stanford/Auto-Empirical-Research-Skills/skills/42-wanshuiyin-ARIS/skills/paper-writing (opens in a new tab)

Antigravity also looks in .agents/skills/, so the Any agent steps reach it with This project. For All projects, see where Antigravity looks.

Cline also looks in .claude/skills/, so the Claude Code steps reach it with This project. For All projects, see where Cline looks.

No tab for your agent? Use Any agent for OpenCode, Goose, Windsurf (Devin Desktop), Zed, Roo Code, Factory Droid, Junie and Amp. With This project, Any agent also reaches Antigravity and Claude Code reaches Cline. Kiro needs the folder copied by hand.

Read this before installing: Broad tools pre-approved in allowed-tools — SKILL.md:5

Pinned to commit bfa0a6e, the one we checked.

From your project's root folder:

tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&git -C "$tmp" sparse-checkout set -- skills/42-wanshuiyin-ARIS/skills/paper-writing &&git -C "$tmp" checkout -q bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&mkdir -p .claude/skills &&mkdir .claude/skills/paper-writing &&cp -R "$tmp"/skills/42-wanshuiyin-ARIS/skills/paper-writing/. .claude/skills/paper-writing/ &&rm -rf "$tmp"

If Claude Code was already running and this created the skills folder, run /reload-skills.

Claude Code docs

Pinned to commit bfa0a6e, the one we checked.

Skills in the Claude apps belong to your account rather than to a project.

Make paper-writing.zip, with the skill folder at the top level:

tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&git -C "$tmp" sparse-checkout set -- skills/42-wanshuiyin-ARIS/skills/paper-writing &&git -C "$tmp" checkout -q bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&out="$(mktemp -d)" &&cp -R "$tmp"/skills/42-wanshuiyin-ARIS/skills/paper-writing "$out"/paper-writing &&(cd "$out" && zip -qr - paper-writing) > paper-writing.zip &&rm -rf "$tmp" "$out"

In Claude, open Customize > Skills, select +, then + Create skill > Upload a skill, and choose paper-writing.zip.

On Free, Pro and Max plans, turn on Code execution and file creation (Create and edit files in newer settings) under Settings > Capabilities.

Claude apps docs

Pinned to commit bfa0a6e, the one we checked.

From your project's root folder:

tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&git -C "$tmp" sparse-checkout set -- skills/42-wanshuiyin-ARIS/skills/paper-writing &&git -C "$tmp" checkout -q bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&mkdir -p .agents/skills &&mkdir .agents/skills/paper-writing &&cp -R "$tmp"/skills/42-wanshuiyin-ARIS/skills/paper-writing/. .agents/skills/paper-writing/ &&rm -rf "$tmp"

Codex picks up new skills on its own; restart it if this one does not appear.

Codex docs

Pinned to commit bfa0a6e, the one we checked.

From your project's root folder:

tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&git -C "$tmp" sparse-checkout set -- skills/42-wanshuiyin-ARIS/skills/paper-writing &&git -C "$tmp" checkout -q bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&mkdir -p .cursor/skills &&mkdir .cursor/skills/paper-writing &&cp -R "$tmp"/skills/42-wanshuiyin-ARIS/skills/paper-writing/. .cursor/skills/paper-writing/ &&rm -rf "$tmp"

Cursor docs

Pinned to commit bfa0a6e, the one we checked.

From your project's root folder:

tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&git -C "$tmp" sparse-checkout set -- skills/42-wanshuiyin-ARIS/skills/paper-writing &&git -C "$tmp" checkout -q bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&mkdir -p .github/skills &&mkdir .github/skills/paper-writing &&cp -R "$tmp"/skills/42-wanshuiyin-ARIS/skills/paper-writing/. .github/skills/paper-writing/ &&rm -rf "$tmp"

In a running Copilot CLI session, run /skills reload.

Or install it with gh skill, which also installs the commit we checked. Needs GitHub CLI 2.90 or later.

gh skill install brycewang-stanford/Auto-Empirical-Research-Skills skills/42-wanshuiyin-ARIS/skills/paper-writing/SKILL.md@bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba --agent github-copilot --scope project

Copilot & VS Code docs

Pinned to commit bfa0a6e, the one we checked.

From your project's root folder:

tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&git -C "$tmp" sparse-checkout set -- skills/42-wanshuiyin-ARIS/skills/paper-writing &&git -C "$tmp" checkout -q bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&mkdir -p .gemini/skills &&mkdir .gemini/skills/paper-writing &&cp -R "$tmp"/skills/42-wanshuiyin-ARIS/skills/paper-writing/. .gemini/skills/paper-writing/ &&rm -rf "$tmp"

In a running session, run /skills reload.

Or use Gemini CLI’s own installer. Installs the latest version, not the one we checked.

gemini skills install https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git --path skills/42-wanshuiyin-ARIS/skills/paper-writing --scope workspace

Gemini CLI docs

Pinned to commit bfa0a6e, the one we checked.

OpenCode, Goose, Windsurf (Devin Desktop), Zed, Roo Code, Factory Droid, Junie, Amp and Antigravity read .agents/skills in a project.

From your project's root folder:

tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&git -C "$tmp" sparse-checkout set -- skills/42-wanshuiyin-ARIS/skills/paper-writing &&git -C "$tmp" checkout -q bfa0a6e5a843babbf45a1ef1663fd5dc4f07c0ba &&mkdir -p .agents/skills &&mkdir .agents/skills/paper-writing &&cp -R "$tmp"/skills/42-wanshuiyin-ARIS/skills/paper-writing/. .agents/skills/paper-writing/ &&rm -rf "$tmp"

Or use the skills CLI from skills.sh. Installs the latest version, not the one we checked. The skills CLI reports installs to skills.sh unless you set DISABLE_TELEMETRY=1.

npx skills@1.7.4 add brycewang-stanford/Auto-Empirical-Research-Skills --skill paper-writing

Agent Skills docs

Read SKILL.md first

Licence not identified

Licence

4.9k

Repo stars

Folder last changed

Publisher

Files

Checked

3 Nov 2026

What it can touch

From the files and frontmatter at commit bfa0a6e. This is how much a skill can do, not whether it is risky.

Installs more skills
It tells the agent to install other skills, plugins or tool servers.
SKILL.md:348 (opens in a new tab)
Runs shell commands
Its instructions or files give the agent commands to run on your computer.
SKILL.md:348 (opens in a new tab)
Pre-approves tools
Its allowed-tools field lists tools the agent may use without asking you first, in agents that honour it.
SKILL.md:5 (opens in a new tab)

Pattern check

Pattern check: 1 item to review · commit bfa0a6e · 3 Nov 2026

R34 · HighBroad tools pre-approved in allowed-tools

SKILL.md:5

allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, Skill, mcp__codex__codex, mcp__codex__codex-reply, mcp__antigravity__antigravity, mcp__antigravity__antigravity-reply, mcp__grok__grok, mcp__gro…

We checked every text file in this skill, at commit bfa0a6e on 3 Nov 2026, against 45 published patterns such as download-and-run commands, hidden text and credential access. We don't run the skill, we don't read the web pages it points to, and we can't judge everything its instructions might lead an agent to do. In published tests, pattern checks like this one missed most malicious skills. Read the skill before you install it — especially anything it asks you to download or run.

How the check works Report an incorrect finding

Format check

Each agent reads SKILL.md a little differently. We check the file against each one's published rules; we don't run the skill in any agent.

Agent Skills specPasses with warnings
The open format from agentskills.io, held to the strictest version of each rule among the agents we check.
- Warning
  Fields outside the spec: argument-hint (read by Claude Code and VS Code). Uploads to the Claude apps and API, and the spec's validator, reject the file; most agents ignore these fields. O1
  Fix: Delete them for a portable skill, or keep them if you only target the agents that read them.
- Warning
  The body is 935 lines; the spec suggests under 500. B1
  Fix: Move detailed sections into reference files and link to them from SKILL.md.
- Warning
  The body is about 12,658 tokens (approx.); the spec suggests under 5,000. B2
  Fix: Move detail into reference files that the agent reads only when needed.
- Warning
  Paths that may not work once the skill is installed: line 10: ../shared-references/reviewer-backends.md (outside the skill folder), line 139: ../shared-references/integration-contract.md (outside the skill folder), line 347: ../shared-references/integration-contract.md#2-canonical-helper--one-implementation-not-copy-pasted (outside the skill folder), line 611: ../integrity-forensics/SKILL.md (outside the skill folder), line 777: ../shared-references/integration-contract.md (outside the skill folder) and 3 more. B6
  Fix: Use forward-slash paths relative to SKILL.md, and copy shared files into the skill.
- Note
  There is no license field, so readers can't tell whether they may reuse the skill. O2
  Fix: Add license: with an SPDX name such as MIT or Apache-2.0, or the name of a bundled licence file.
- Note
  Line 644 has dated wording ("Since 2026"), which goes stale. B8
  Fix: Describe the current way, and move old patterns into their own clearly marked section.
Claude CodePasses with warnings
Claude Code reads its own extra fields, ignores unknown ones, and still loads a skill whose frontmatter is broken, without its fields.
- Warning
  Paths that may not work once the skill is installed: line 10: ../shared-references/reviewer-backends.md (outside the skill folder), line 139: ../shared-references/integration-contract.md (outside the skill folder), line 347: ../shared-references/integration-contract.md#2-canonical-helper--one-implementation-not-copy-pasted (outside the skill folder), line 611: ../integrity-forensics/SKILL.md (outside the skill folder), line 777: ../shared-references/integration-contract.md (outside the skill folder) and 3 more. B6
  Fix: Use forward-slash paths relative to SKILL.md, and copy shared files into the skill.
- Note
  The body is 935 lines; the spec suggests under 500. Claude Code's docs say the same. B1
  Fix: Move detailed sections into reference files and link to them from SKILL.md.
- Note
  The body is about 12,658 tokens (approx.); the spec suggests under 5,000. After compaction Claude Code keeps only the first 5,000 tokens of a skill. B2
  Fix: Move detail into reference files that the agent reads only when needed.
- Note
  Line 644 has dated wording ("Since 2026"), which goes stale. B8
  Fix: Describe the current way, and move old patterns into their own clearly marked section.
Claude apps & API uploadFails
Uploading to claude.ai or the Claude API, or packaging with Anthropic's script, accepts only the six spec fields and stops on anything else.
- Error
  Upload and packaging fail on fields outside the spec: argument-hint. O1
  Fix: Delete them, and keep your own data under metadata as text values.
- Warning
  Paths that may not work once the skill is installed: line 10: ../shared-references/reviewer-backends.md (outside the skill folder), line 139: ../shared-references/integration-contract.md (outside the skill folder), line 347: ../shared-references/integration-contract.md#2-canonical-helper--one-implementation-not-copy-pasted (outside the skill folder), line 611: ../integrity-forensics/SKILL.md (outside the skill folder), line 777: ../shared-references/integration-contract.md (outside the skill folder) and 3 more. B6
  Fix: Use forward-slash paths relative to SKILL.md, and copy shared files into the skill.
- Note
  The description is 240 characters. The claude.ai Help Center says 200 at most, though Anthropic's API docs and validator allow 1,024. D4
  Fix: If the claude.ai upload refuses it, trim the description to 200 characters.
- Note
  The body is 935 lines; the spec suggests under 500. Anthropic's guidance says the same. B1
  Fix: Move detailed sections into reference files and link to them from SKILL.md.
- Note
  The body is about 12,658 tokens (approx.); the spec suggests under 5,000. Anthropic's guidance says the same. B2
  Fix: Move detail into reference files that the agent reads only when needed.
- Note
  Line 213 names an MCP tool as mcp__codex__codex. For the Claude apps and API, Anthropic's guidance is Server:tool, such as GitHub:create_issue. B7
  Fix: Write it as codex:codex, using the server's own name.
- Note
  Line 644 has dated wording ("Since 2026"), which goes stale. B8
  Fix: Describe the current way, and move old patterns into their own clearly marked section.
OpenAI (Codex & API)Passes with warnings
Codex finds SKILL.md by its exact name and needs a description; OpenAI's Skills API checks the frontmatter against the spec and caps uploads.
- Warning
  Fields outside the spec: argument-hint. Codex ignores them; OpenAI doesn't say whether its upload accepts them. O1
  Fix: Delete them, or move your own data under metadata as text values.
- Warning
  Paths that may not work once the skill is installed: line 10: ../shared-references/reviewer-backends.md (outside the skill folder), line 139: ../shared-references/integration-contract.md (outside the skill folder), line 347: ../shared-references/integration-contract.md#2-canonical-helper--one-implementation-not-copy-pasted (outside the skill folder), line 611: ../integrity-forensics/SKILL.md (outside the skill folder), line 777: ../shared-references/integration-contract.md (outside the skill folder) and 3 more. B6
  Fix: Use forward-slash paths relative to SKILL.md, and copy shared files into the skill.
VS Code & CopilotPasses with warnings
VS Code reads skills one folder below .github/skills, .claude/skills or .agents/skills and falls back to the folder name when the name is missing or differs; GitHub's Copilot docs require the exact name SKILL.md.
- Warning
  Paths that may not work once the skill is installed: line 10: ../shared-references/reviewer-backends.md (outside the skill folder), line 139: ../shared-references/integration-contract.md (outside the skill folder), line 347: ../shared-references/integration-contract.md#2-canonical-helper--one-implementation-not-copy-pasted (outside the skill folder), line 611: ../integrity-forensics/SKILL.md (outside the skill folder), line 777: ../shared-references/integration-contract.md (outside the skill folder) and 3 more. B6
  Fix: Use forward-slash paths relative to SKILL.md, and copy shared files into the skill.

SKILL.md

We only show SKILL.md text here when its licence clearly allows it.

Read SKILL.md on GitHub

Files

1 file

Path	Size
SKILL.md (opens in a new tab)	50.7 KB

Copies

These share its SKILL.md or its name and description but not all its files, so we list them separately.

More from brycewang-stanford/Auto-Empirical-Research-Skills

Skill	What it can touch	Pattern check	Licence	Updated
a1VS-Enhanced Research Question Refiner - Prevents Mode Collapse and derives differentiated research questions Enhanced VS 3-Phase process: Modal question avoidance, alternatives presentation, differentiated RQ recommendation Use when: refining research ideas, formulating research questions, clarifying scope Triggers: research question, 연구 질문, PICO, SPIDER, research idea Instructions only Pattern check: Nothing flaggedNo licenceUpdated 2 Apr 2026	Instructions only	Pattern check: Nothing flagged	No licence	2 Apr 2026
a2VS-Enhanced Theoretical Framework Architect with Critique & Visualization Full VS 5-Phase process: Modal theory avoidance, Long-tail exploration, differentiated framework presentation Absorbed A3 (Devil's Advocate) critique and A6 (Conceptual Framework Visualizer) capabilities Use when: building theoretical foundations, designing conceptual models, deriving hypotheses, critiquing frameworks, visualizing models Triggers: theoretical framework, 이론적 프레임워크, conceptual model, 개념적 모형, hypothesis derivation, critique, devil's advocate, 반론, visualization, diagram Instructions only Pattern check: Nothing flaggedNo licenceUpdated 2 Apr 2026	Instructions only	Pattern check: Nothing flagged	No licence	2 Apr 2026
a5Agent A5 - Paradigm & Worldview Advisor - Philosophical foundations for research design. Covers ontology, epistemology, axiology, and methodology alignment. Use when: establishing philosophical foundations, justifying methodological choices, writing positionality statements Triggers: paradigm, 패러다임, ontology, epistemology, worldview, 세계관, philosophical foundations, 철학적 기초 Instructions only Pattern check: Nothing flaggedNo licenceUpdated 2 Apr 2026	Instructions only	Pattern check: Nothing flagged	No licence	2 Apr 2026
abstractReads the manuscript and notebooks to generate a structured abstract. Use when writing or updating the abstract. Runs shell commands +1 more Pattern check: 1 item to reviewNo licenceUpdated 2 Apr 2026	Runs shell commands Pre-approves tools	Pattern check: 1 item to review	No licence	2 Apr 2026
abstract-writing-guideCraft structured research abstracts that maximize clarity and journal acceptance Instructions only Pattern check: Nothing flaggedNo licenceUpdated 2 Apr 2026	Instructions only	Pattern check: Nothing flagged	No licence	2 Apr 2026
academic-baselineUse when working on any empirical academic research context — paper writing, data analysis, literature review, or any task involving citations, results, or publication artifacts. Establishes non-negotiable principles that govern all other superpapers skills. Instructions only Pattern check: Nothing flaggedNo licenceUpdated 3 Jun 2026	Instructions only	Pattern check: Nothing flagged	No licence	3 Jun 2026

All skills in brycewang-stanford/Auto-Empirical-Research-Skills

Other Science & research skills

Same category, most repo stars first.

Skill	What it can touch	Pattern check	Licence	Updated
deep-researchProduce cited research reports from multiple web sources using firecrawl and exa MCP tools — plan sub-questions, search and deep-read sources, then synthesize findings with inline citations and confidence levels. Use when the user asks to research a topic in depth, run a deep dive or investigation, or do competitive analysis, technology evaluation, market sizing, or due diligence on a company. affaan-m/ECC Instructions only Pattern check: Nothing flaggedMITUpdated 27 Sept 2026	Instructions only	Pattern check: Nothing flagged	MIT	27 Sept 2026
healthcare-cdss-patternsClinical Decision Support System (CDSS) development patterns. Drug interaction checking, dose validation, clinical scoring (NEWS2, qSOFA), alert severity classification, and integration into EMR workflows. Use when building clinical decision support — drug interaction checks, dose validation, clinical scoring, or alert severity. affaan-m/ECC Instructions only Pattern check: Nothing flaggedMITUpdated 11 Aug 2026	Instructions only	Pattern check: Nothing flagged	MIT	11 Aug 2026
clinical-case-reportStructured medical case presentation for clinical rounds, conferences, and documentation. Generates SOAP-format or narrative case reports with physiologically accurate vitals, labs, and evidence-based plans. Use when the brief mentions "case report", "case presentation", "SOAP note", "clinical case", "ward rounds", "case summary", or "patient presentation". nexu-io/open-design Instructions only Pattern check: Nothing flaggedApache 2.0Updated 18 Aug 2026	Instructions only	Pattern check: Nothing flagged	Apache 2.0	18 Aug 2026
clinical-case-reportStructured medical case presentation for clinical rounds, conferences, and documentation. Generates SOAP-format or narrative case reports with physiologically accurate vitals, labs, and evidence-based plans. Use when the brief mentions "case report", "case presentation", "SOAP note", "clinical case", "ward rounds", "case summary", or "patient presentation". nexu-io/open-design Names web addresses Pattern check: Nothing flaggedApache 2.0Updated 18 Aug 2026	Names web addresses	Pattern check: Nothing flagged	Apache 2.0	18 Aug 2026
style-samplingMake a new episode in a proven video style - Collage Explainer, Finance Explainer, Animated Science Explainer, 3D Brand Explainer, 3D True Crime - on the person's topic. Use for "an episode of", "in the style of", "sample this style", 「用这个风格做一集」. One video to copy is reverse-any-video. heygen-com/hyperframes Runs shell commands Pattern check: Nothing flaggedApache 2.0Updated 3 Nov 2026	Runs shell commands	Pattern check: Nothing flagged	Apache 2.0	3 Nov 2026
security-research code-yeongyu/oh-my-openagent Names web addresses Pattern check: Nothing flaggedNo licenceUpdated 31 Aug 2026	Names web addresses	Pattern check: Nothing flagged	No licence	31 Aug 2026

At a glance

What it can touch

Pattern check

Install

Claude Code

Claude apps

Codex

Cursor

Copilot & VS Code

Gemini CLI

Any agent

What it can touch

Pattern check

Format check

SKILL.md

Files

Copies

More from brycewang-stanford/Auto-Empirical-Research-Skills

Other Science & research skills