PEN-COMPARE v0.1.0

PEN-COMPARE v0.1.0 — Hierarchical Certification Framework for Non-Destructive Genome Editors

Capstone of PEN-STACK — the five-paper computational infrastructure for programmable genome integration design.

Key Results

Metric	Value
Universe	1,058 entities (29 natural + 1,029 pen-assemble designs)
TRUE_WRITER	ISCro4 (D2TGM5, C. rodentium ICC168, 326 aa)
ISCro4 robustness	1.000 across 18,000 threshold combinations
PROBABLE_WRITER	4 (IS621, Bxb1, phiC31, eePASSIGE_v2)
Pre-registered predictions	5 / 5 PASS (OSF/4kdvy)
RAG Q&A accuracy	88% (44/50 benchmark questions, llama3.1:8b)
Test coverage	98.8% (155 unit tests, Python 3.10/3.11/3.12)

Upstream PEN-STACK Packages (frozen at pre-registration)

Package	Version	Release Link	Role
GENOME-ATLAS	v0.7.2	v0.7.2	Knowledge graph; PFAM evidence; ISCro4 canonical naming
MECH-CLASS	v0.5.4	v0.5.4	DSB classification; Tier-A gate
PEN-SCORE	v0.1.3	v0.1.3	8-axis scores; get_editor_metadata() API
PEN-ASSEMBLE	v0.5.2	v0.5.2	1,029 computational IS110 designs

Pre-registration locked in SHA256_LOCK_v3.json; deposited at https://osf.io/4kdvy (tag: prereg-v3.2).

Install

pip install pen-compare==0.1.0

See CHANGELOG.md for full details.