Reproducible Pipelines
brycewang-stanford/Auto-Empirical-Research-Skills
This skill covers reproducible research pipelines and replication packages.
Implement open science practices for a social science study.
Install Scholar Open
$ npx skills add joshzyj/open-scholar-skill --skill scholar-open -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-open --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/scholar-open .claude/skills/scholar-open && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "scholar-open" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-open into .claude/skills/scholar-open/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-open", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-openType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add joshzyj/open-scholar-skill --skill scholar-open -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-open --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/scholar-open .agents/skills/scholar-open && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "scholar-open" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-open into .agents/skills/scholar-open/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-open", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add joshzyj/open-scholar-skill --skill scholar-open -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-open --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/scholar-open .cursor/skills/scholar-open && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "scholar-open" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-open into .cursor/skills/scholar-open/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-open", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/joshzyj/open-scholar-skill.git --path .claude/skills/scholar-open--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add joshzyj/open-scholar-skill --skill scholar-open -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-open --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/scholar-open .gemini/skills/scholar-open && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "scholar-open" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-open into .gemini/skills/scholar-open/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-open", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install joshzyj/open-scholar-skill scholar-openInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add joshzyj/open-scholar-skill --skill scholar-open -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/scholar-open .github/skills/scholar-open && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "scholar-open" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-open into .github/skills/scholar-open/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-open", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add joshzyj/open-scholar-skill --skill scholar-open -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-open --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/scholar-open .opencode/skills/scholar-open && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "scholar-open" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-open into .opencode/skills/scholar-open/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-open", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
scholar-open- GitHub stars
- 168
- Token cost
- ~14k tokens
- SKILL.md length
- 3,111 words
- Files
- 3 (incl. references)
- Skills in repo
- 30
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Implement open science practices for a social science study.
- Works in 7 steps: Argument Parsing & Project State → PREREGISTRATION → DATA SHARING → …
- Tasks that involve Econometrics and empirical research
- SKILL.md covers Dispatch Table, Step 0: Argument Parsing &…, Step 1: PREREGISTRATION and Step 2: DATA SHARING, plus 5 more sections
- Calls conda, bash and git; reaches doi.org and osf.io
What it does
Scholar Open is an agent skill from joshzyj/open-scholar-skill. Implement open science practices for a social science study. Five modes: (1) PREREGISTER — OSF / AsPredicted / EGAP / Registered Reports; secondary-data preregistration; deviation reporting; (2) DATA-SHARE — FAIR principles, de-identification, repository selection (Dataverse / ICPSR / Zenodo / QDR), social media policies, computational data (model weights, embeddings), data availability statements; (3) CODE-SHARE — minimum + gold-standard replication packages, README template, renv / conda / Docker / Makefile…
Its SKILL.md is about 14k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files, including reference files (for example `references/data-sharing.md` and `references/preregistration.md`).
It sits in Research & Science, covering Econometrics and empirical research, Reproducible research and Embeddings. It works with Docker and GitHub. The repository describes itself as: Open scholar skill, a claude code plugin, for academic research.
When your agent uses it
- Tasks that involve Econometrics and empirical research
- Tasks that involve Reproducible research
- Tasks that involve Embeddings
Example prompts
- “/scholar-open”
Requirements
- Docker
Workflow steps
7 steps, taken from the step headings in SKILL.md.
- Argument Parsing & Project State
- PREREGISTRATION
- DATA SHARING
- CODE & REPLICATION PACKAGES
- FULL OPEN SCIENCE PACKAGE
- REPLICATION PACKAGE AUDIT
- Save Output
What it can do on your machine
Read from SKILL.md and the folder at commit 6e5ac8e. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
condabashgitpipdockermake
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
doi.orgosf.iozenodo.orggithub.comorcid.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Scholar Open loads about 14k tokens when it runs, and up to ~23k if it reads all its reference files. Until then it costs about 248 tokens; SKILL.md has 3,111 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 3,111 words (~13,939 tokens).
“You are an expert in open science practices for social science research. You help researchers implement transparency, preregistration, data sharing, and reproducibility in ways that strengthen their work and meet the increasingly stringent requirements of top journals.”
- name
- scholar-open
- tools
- Read, Write, Bash, WebSearch
- argument-hint
- [PREREGISTER|DATA-SHARE|CODE-SHARE|FULL-PACKAGE|REPLICATION-PACKAGE] [study description or journal name]
- user-invocable
- true
Files
SKILL.md and 2 other files (references) in .claude/skills/scholar-open of joshzyj/open-scholar-skill.
- SKILL.md
- references/data-sharing.md
- references/preregistration.md
Open the folder on GitHubat commit 6e5ac8e
Compare with similar skills
Scholar Open next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Scholar Open this skilljoshzyj/open-scholar-skill | 168 | — | ~14k | Automated safety check: Pass | Custom licence | |
| Reproducible Pipelinesbrycewang-stanford/Auto-Empirical-Research-Skills | 4.5k | — | ~3.3k | Automated safety check: Pass | Custom licence | |
| Hugging Face Paper Pageshuggingface/skills | 11k | 3 repos | ~2.3k | Automated safety check: Pass | Apache-2.0 | |
| Phyai Model Arch Researchmingti-org/phyai | 130 | — | ~1.8k | Automated safety check: Pass | MIT | |
| Academic AioAperivue/medsci-skills | 331 | — | ~4.8k | Automated safety check: Pass | MIT | |
| Multimodal Embedding Serving Useropen-edge-platform/edge-ai-libraries | 169 | — | ~1.7k | Automated safety check: Pass | Apache-2.0 |
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Phyai Model Arch Research
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Scholar RAG
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Build and query a local vector database + GraphRAG over your entire reference library (Zotero or a PDF folder) for literature review.
Scholar Causal
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Scholar Data
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Scholar Eda
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Related
Categories
Questions about Scholar Open
What does Scholar Open do?
Implement open science practices for a social science study. Scholar Open is an agent skill from joshzyj/open-scholar-skill. Implement open science practices for a social science study.
When should I use Scholar Open?
Scholar Open fits situations like: tasks that involve Econometrics and empirical research; tasks that involve Reproducible research; tasks that involve Embeddings.
How do I install Scholar Open in Claude Code?
Run `npx skills add joshzyj/open-scholar-skill --skill scholar-open -a claude-code`. Or copy the skill folder (.claude/skills/scholar-open in joshzyj/open-scholar-skill) into .claude/skills/scholar-open in your project. Claude Code loads it when a task matches its description.
How do I install Scholar Open in Codex?
Run `npx skills add joshzyj/open-scholar-skill --skill scholar-open -a codex`. Or copy the skill folder (.claude/skills/scholar-open in joshzyj/open-scholar-skill) into .agents/skills/scholar-open in your project. Codex loads it when a task matches its description.
Can I use Scholar Open in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add joshzyj/open-scholar-skill --skill scholar-open -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/scholar-open, .gemini/skills/scholar-open, .github/skills/scholar-open and .opencode/skills/scholar-open in your project.
What does Scholar Open need to run?
Going by SKILL.md and its folder, Scholar Open needs the command-line tools its instructions call (conda, bash, git, pip, docker and make). Our summary lists: Docker.
Does Scholar Open access the network?
SKILL.md names 5 domains. In commands or code: doi.org, osf.io, zenodo.org, github.com and orcid.org; the agent is likely to contact these when it follows the instructions. This is read from the text; nothing was executed.
Is Scholar Open safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Scholar Open use?
Scholar Open has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Scholar Open use?
About 14k tokens (SKILL.md is roughly 56k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 9.2k tokens, read only when the agent opens those files.
What are the alternatives to Scholar Open?
Skills that share tags, products or a category with Scholar Open: Reproducible Pipelines (brycewang-stanford/Auto-Empirical-Research-Skills, 4.5k stars), Hugging Face Paper Pages (huggingface/skills, 11k stars), Phyai Model Arch Research (mingti-org/phyai, 130 stars) and Academic Aio (Aperivue/medsci-skills, 331 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Scholar Open?
joshzyj (a GitHub user) maintains it in joshzyj/open-scholar-skill, which has 168 GitHub stars. The repository holds 30 skills in this directory. The repository was last updated on September 18, 2026.
Source: joshzyj/open-scholar-skill on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.