research-repo SKILL.md skillA
research-repo from scdenney/open-science-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add scdenney/open-science-skills/research-repo@git:20261022.299a868Pins git:20261022.299a868 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- scdenney/open-science-skills
- Path
codex/research-repo/SKILL.md- Versions recorded
- 6
- Latest version
- git:20261022.299a868, committed Oct 22, 2026
- First version recorded
- Jul 2, 2026
- Size
- 21,031 bytes
- Repository stars
- 69
- License
- a license file GitHub does not identify
Scaffold or audit a research-project repository organized around its source library (PDFs, Markdown conversions, bibliography, intake pipeline) plus the analysis, manuscript, and review folders it needs. Use when starting or auditing a research repo. Not for one-PDF intake or publication replication packages.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Research Repository Scaffold & Audit ## Scope and organizing principle This skill sets up a new research repository, or audits an existing one, around a single organizing principle: **the source library is the spine of the project, and everything else grows from it.** `sources/og/` holds the original PDFs and documents — archival, **gitignored** (size + copyright), rarely read directly. `sources/md/` holds their Markdown conversions, **tracked in git**: this is the LLM-readable knowledge base, and *sources are always read from here, not from the PDFs*. `sources/unprocessed/` is the drop zone where new PDFs land until they are named, converted, and filed. `sources/inbox/` sits beside it for notes, links, screenshots and loose files that feed the knowledge base without going through intake: agents read them as context and build on them, but `process-source` never converts or moves them; a file enters the corpus only when the author moves it into `unprocessed/`. `sources/references.bib` keys the corpus to the manuscript — one entry per source, author+year resolvable to its `md/` file, so a `\cite` key maps to a document actually read. A conversion script… …
Read the whole file at its exact version.
How to install
mdr add scdenney/open-science-skills/research-repo@sha256:f4b2e01e6fb3e59eThe line at the top of this page pins the label git:20261022.299a868, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_awywl7fowb3eam3m)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between Jul 2, 2026 and Oct 22, 2026, about one every 22 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261022.299a868 latest | 2026-10-22 | 299a868 | 21,031 B | A | view · diff |
| git:20261022.ac6a052 | 2026-10-22 | ac6a052 | 20,823 B | A | view · diff |
| git:20261008.697c89f | 2026-10-08 | 697c89f | 20,259 B | A | view · diff |
| git:20260808.4ee3386 | 2026-08-08 | 4ee3386 | 20,656 B | A | view · diff |
| git:20260726.ec471db | 2026-07-26 | ec471db | 20,240 B | A | view · diff |
| git:20260702.0d142fe | 2026-07-02 | 0d142fe | 22,633 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (21031 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
scdenney/open-science-skills · 69 stars · license a license file GitHub does not identify · pushed 2026-11-05 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_awywl7fowb3eam3m GET https://markdownregistry.com/api/v1/resolve?ref=scdenney/open-science-skills/research-repo GET https://markdownregistry.com/api/v1/blob/f4b2e01e6fb3e59e366ec06cb527ca193056ccbd3c5701afa9f2ecd87c986673
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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