EMMA-CAD: Design automation for synthetic mammalian constructs

Yisha Luo, Joshua James, Sally Jones, Patrick Cai

Research output: Contribution to journalArticlepeer-review

Abstract

Computational design tools are the cornerstone of synthetic biology and have underpinned its rapid development over the past two decades. As the field has matured, the scale of biological investigation has expanded dramatically, with computational tools often relied upon by researchers to operate in the high-throughput investigational space. This is especially apparent in the modular design of DNA expression circuits, where complexity is accumulated rapidly. Alongside our automated pipeline for the high-throughput construction of Extensible Modular Mammalian Assembly (EMMA) expression vectors, we recognized the need for an integrated software solution for EMMA vector design. Here, we present EMMA-CAD (https://emma.cailab.org), a powerful, web-based computer-aided design tool for the rapid design of bespoke mammalian expression vectors. EMMA-CAD features a variety of functionalities, including a user-friendly design interface, automated connector selection underpinned by rigorous computer optimization algorithms, customization of part libraries, and personalized design spaces. Capable of translating vector assembly designs into human and machine readable protocols for vector construction, EMMA-CAD integrates seamlessly into our automated EMMA pipeline, hence completing an end-to-end design to production work flow.
Original languageEnglish
JournalACS Synthetic Biology
Publication statusAccepted/In press - 21 Dec 2021

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