Genetic Design Automation

Title:

Genetic circuit design automation

Author(s):

A. A. K. Nielsen B. S. Der J. Shin P. Vaidyanathan V. Paralanov E. A. Strychalski D. Ross D. Densmore C. A. Voigt

Publication:

Published in: Science
Volume: 352, Issue: 6281, Pages: aac7341-aac7341
Published: 03/31/2016
DOI: 10.1126/science.aac7341
Website: http://www.sciencemag.org/cgi/doi/10.1126/science.aac7341

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Our Discussion:

Genetic Design Automation: Proof of Concept

This is an impressive paper that gives the impression that genetic design automation is within reach. The paper builds on a number of previous results spanning a range of disciplines. They take advantage of previously characterized genetic parts and software applications that the authors developed over the last 10 years.

I did not find it easy to reach this paper. I lack the background in electronic design automation to fully understand the software aspect. Readers who come to this article with an engineering background will be more comfortable with that aspect of the paper than me. Conversely, readers coming from the life sciences will probably fell more at home reading the biological sections of the article.

It’s hard to tell how automated is the toolchain. It seems that some steps are still manual.

At a more fundamental level, it is important to keep in mind that the authors focused on the design of digital genetic circuits. This simplification greatly helps with the predictions. However, not all artificial gene networks can be analyzed in this framework. For instance, the design of genetic oscillators would require an analog approach.

Genetic Design Automation vs. Biodesign Automation

Our community was divided regarding the best appellation for our new field. Many people referred to it as Biodesign Automation. For instance, IWBDA, the International Workshop for Bio-Design Automation has been an annual gathering of experts in this field for 10 almost 10 years.

I was never comfortable with this term that I find too broad. Biodesign has many facets that are not really within the scope of synthetic biology. I prefer the use of the term “Genetic Design Automation” because “genetic” refers to DNA, which is really what we are dealing with.

So, the title of this paper made me very happy.

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