pen-compare 0.1.0

Hierarchical Certification Framework for Non-Destructive Genome Editors

PEN-COMPARE

Hierarchical Certification Framework for Non-Destructive Genome Editors

Part of PEN-STACK — the first unified computational infrastructure for programmable genome integration design.

Status: Alpha (v0.1.0a1) — under active development.

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What is PEN-COMPARE?

PEN-COMPARE is the capstone integrative paper of PEN-STACK. It answers:

Given the four PEN-STACK datasets, how do we operationally certify an editor as a "Molecular Pen" rather than a "Molecular Scissor"?

The deliverable is a framework (5-gate hierarchical TrueWriterScore certification), an analysis (cross-source triangulation across all 4 PEN-STACK packages), a public tool (Streamlit webserver + local LLM RAG Q&A), and a paper (Bioinformatics Application Note).

Quick start

pip install pen-compare
pen-compare compare ISCro4 IS621

5-Gate Framework

Gate	Type	Axis	Threshold
G1 — DSB Avoidance	Necessary	S_DSB	≥ 0.95
G2 — Programmability	Qualifying	S_Prog	≥ 0.95
G3 — Native Cargo	Qualifying	S_Cargo + intrinsic	≥ 0.90
G4 — Deliverability	Qualifying	length_aa	≤ 900 aa
G5 — Evidence	Qualifying	multi-source	≥ 2 sources

Tier	Requirement
TRUE_WRITER	G1 + all 4 qualifying + cell-based evidence
PROBABLE_WRITER	G1 + 3–4 qualifying (no cell-based OR 3/4 with cell-based)
EMERGING_WRITER	G1 + 1–2 qualifying
NOT_WRITER	G1 fails OR 0 qualifying

Upstream packages (pinned versions)

Package	Version	Role
genome-atlas	≥ 0.7.2	Knowledge graph, PFAM evidence, triangulation
mech-class	≥ 0.5.4	DSB classification, Tier-A gate decisions
pen-score	≥ 0.1.3	8-axis PenScores, get_editor_metadata() API
pen-assemble	≥ 0.5.2	1,029-design catalog with cargo/cell-based fields

Documentation

https://ahmedanees-m.github.io/pen-compare

Citation

@software{pen_compare_2026,
  author = {Mahaboob Ali, Anees Ahmed},
  title  = {PEN-COMPARE: Hierarchical Certification Framework for Non-Destructive Genome Editors},
  year   = {2026},
  url    = {https://github.com/ahmedanees-m/pen-compare},
}

License

MIT — see LICENSE.