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.

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

Upstream packages (pinned versions)

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.