DESIGN.md@src/Stage3_Interpretation/C_Annotation/4.Hypothesis/perturbseq-hypothesesA
DESIGN.md@src/Stage3_Interpretation/C_Annotation/4.Hypothesis/perturbseq-hypotheses from engreitzlab/perturbnmf is a DESIGN.md file: the design rules coding agents follow in that repo.
mdr add engreitzlab/perturbnmf/src/Stage3_Interpretation/C_Annotation/4.Hypothesis/perturbseq-hypotheses/DESIGN.md@git:20261019.294698dPins git:20261019.294698d in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 14 of 14 checks passed
- Kind
- DESIGN.md file
- Repository
- engreitzlab/perturbnmf
- Path
src/Stage3_Interpretation/C_Annotation/4.Hypothesis/perturbseq-hypotheses/DESIGN.md- Versions recorded
- 1
- Latest version
- git:20261019.294698d, committed Oct 19, 2026
- Size
- 5,407 bytes
- Repository stars
- 10
- License
- MIT
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
# Design record — `perturbseq-hypotheses` v2
v2 replaced the linear v1 pipeline on 2026-09-23. The v1 design record is in git history
(`git log -- .claude/skills/perturbseq-hypotheses/DESIGN.md`).
## 1. What v1 got wrong
Reviewed on the first blind run, on an endothelial genome-wide screen (Jesse, 2026-09-23):
- **Literature was a label, not a filter.** Hypotheses were generated, one literature pass ran,
and each hypothesis got a verdict (`keep / reframe / downgrade / already published`). Nothing
was revised or killed. The report printed the original claim beside a verdict saying to reframe
it. The final list was hand-typed into a selector script.
- **The report was about the process.** The template required Summary, Goals, Procedure, Datasets
and a gate funnel before the ranked list, which started on line 363 of 770. The title was a
blind-scoring result. The blindness-disclosure machinery pushed "leaked", "uncontaminated" and
"predecessor" into headings.
- **No per-hypothesis figures.** The skill said reports could be figure-free.
- **Hypotheses were observations** ("loss of <core complex> moves sixteen programs"), used
…Read the whole file at its exact version.
How to install
mdr add engreitzlab/perturbnmf/src/Stage3_Interpretation/C_Annotation/4.Hypothesis/perturbseq-hypotheses/DESIGN.md@sha256:b57937a2e559a7e2The line at the top of this page pins the label git:20261019.294698d, 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_52qhu6gsfwdqkh5i)
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Versions
The registry has recorded 1 version of this file, committed on Oct 19, 2026.
Audit of the latest version
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- pass: No link to an exfiltration or paste host
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- 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
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- pass: No script tag
Source
engreitzlab/perturbnmf · 10 stars · license MIT · pushed 2026-10-20 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_52qhu6gsfwdqkh5i GET https://markdownregistry.com/api/v1/resolve?ref=engreitzlab/perturbnmf/src/Stage3_Interpretation/C_Annotation/4.Hypothesis/perturbseq-hypotheses/DESIGN.md GET https://markdownregistry.com/api/v1/blob/b57937a2e559a7e2750dd133757c83f5ffe7e0052d774dda1282abd900d4cfb6
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: what DESIGN.md is and how agents use it · which agent file does what.