Genetic Engineering Python Packages

streptocad

StreptoCAD is an open-source toolbox that automates the design of genome engineering strategies in Streptomyces. It supports CRISPR-based workflows, generating primers, guide sequences, and plasmid simulations to accelerate genetic engineering and natural product discovery.

dnadesign

A lua package for designing DNA.

crisprzip

A kinetic model of CRISPR-Cas target recognition.

pen-assemble

Automated design and scoring engine for IS110-family bridge recombinase variants, nominating 1,029 candidates via an 8-axis PenScore over pre-registered predictions.

pen-compare

Hierarchical certification framework (5-gate TrueWriterScore) for programmable genome editors, with sensitivity analysis, cross-pipeline triangulation, and a RAG Q&A layer over the PEN-STACK.

pen-stack

A verification and grounding layer for AI-driven genome writing. Foundation models and a grounded co-scientist agent propose edits; PEN-STACK checks each against validated tools, never a language model: where a write is safe and durable, which enzyme makes it, and where it goes off-target. Calibrated, provenance-tracked, pre-registered.

pen-score

Multi-axis scoring framework that ranks programmable genome editors across eight orthogonal axes into a single PenScore to guide experimental design and benchmarking.

mech-class

Two-tier classifier for the catalytic mechanism of programmable genome-writing enzymes, with a biochemical gate that correctly labels IS110-family composite recombinases.

openbioseq

This repo focuses on supervised and self-supervised bio-sequence representation learning