genome-atlas 0.0.1

Unified knowledge graph and embedding space for programmable genome-writing enzymes

genome-atlas

A unified knowledge graph and embedding space for programmable genome-writing enzymes — CRISPR, CAST, bridge recombinases, Fanzor, and more — with cross-system selection decision support.

Part of the PEN-STACK infrastructure for non-destructive genome engineering.

Install

pip install genome-atlas

Quickstart

from genome_atlas import Atlas

atlas = Atlas.load()
recs = atlas.select_editor(
    cell_type="HEK293T",
    edit_type="insertion",
    cargo_size_bp=1500,
    delivery="AAV",
    top_k=5,
)
for r in recs:
    print(r.system, r.pen_score, r.aav_fit)

Citation

See CITATION.cff or cite the preprint:

Ahmed, A. (2026). GENOME-ATLAS: A unified knowledge graph for programmable genome-writing enzymes. bioRxiv.

License

MIT — see LICENSE.