Literature DB >> 28246188

Design Automation in Synthetic Biology.

Evan Appleton1, Curtis Madsen2,3, Nicholas Roehner2,3, Douglas Densmore2,3.   

Abstract

Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, and learn-and introduce the existing software tools designed to solve problems in these areas. We then detail the functionality of some of these tools and show how they can be used together to create the desired behavior of two types of modern synthetic genetic regulatory networks.
Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2017        PMID： 28246188      PMCID： PMC5378053          DOI： 10.1101/cshperspect.a023978

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN： 1943-0264            Impact factor:   10.005


  92 in total

1.  Sensitivity analysis of pharmacokinetic and pharmacodynamic systems: I. A structural approach to sensitivity analysis of physiologically based pharmacokinetic models.

Authors:  I A Nestorov
Journal:  J Pharmacokinet Biopharm       Date:  1999-12

Review 2.  It's a noisy business! Genetic regulation at the nanomolar scale.

Authors:  H H McAdams; A Arkin
Journal:  Trends Genet       Date:  1999-02       Impact factor: 11.639

Review 3.  Modeling and simulation of genetic regulatory systems: a literature review.

Authors:  Hidde de Jong
Journal:  J Comput Biol       Date:  2002       Impact factor: 1.479

4.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

5.  Mfold web server for nucleic acid folding and hybridization prediction.

Authors:  Michael Zuker
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

6.  Modelling cellular systems with PySCeS.

Authors:  Brett G Olivier; Johann M Rohwer; Jan-Hendrik S Hofmeyr
Journal:  Bioinformatics       Date:  2004-09-28       Impact factor: 6.937

7.  The slow-scale stochastic simulation algorithm.

Authors:  Yang Cao; Daniel T Gillespie; Linda R Petzold
Journal:  J Chem Phys       Date:  2005-01-01       Impact factor: 3.488

Review 8.  Foundations for engineering biology.

Authors:  Drew Endy
Journal:  Nature       Date:  2005-11-24       Impact factor: 49.962

Review 9.  Estimation of quantitative genetic parameters.

Authors:  Robin Thompson; Sue Brotherstone; Ian M S White
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2005-07-29       Impact factor: 6.237

10.  The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression.

Authors:  Gang Wu; Nabila Bashir-Bello; Stephen J Freeland
Journal:  Protein Expr Purif       Date:  2005-11-15       Impact factor: 1.650
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  14 in total

Review 1.  Building a biofoundry.

Authors:  Maciej B Holowko; Emma K Frow; Janet C Reid; Michelle Rourke; Claudia E Vickers
Journal:  Synth Biol (Oxf)       Date:  2020-12-16

2.  Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots.

Authors:  David I Walsh; Marilene Pavan; Luis Ortiz; Scott Wick; Johanna Bobrow; Nicholas J Guido; Sarah Leinicke; Dany Fu; Shreya Pandit; Lucy Qin; Peter A Carr; Douglas Densmore
Journal:  SLAS Technol       Date:  2019-02-15       Impact factor: 3.047

3.  Cell-machine interfaces for characterizing gene regulatory network dynamics.

Authors:  Jean-Baptiste Lugagne; Mary J Dunlop
Journal:  Curr Opin Syst Biol       Date:  2019-02-01

4.  AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms.

Authors:  Yi Yang; Yufeng Mao; Ruoyu Wang; Haoran Li; Ye Liu; Haijiao Cheng; Zhenkun Shi; Yu Wang; Meng Wang; Ping Zheng; Xiaoping Liao; Hongwu Ma
Journal:  Nucleic Acids Res       Date:  2022-05-26       Impact factor: 19.160

Review 5.  Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms

Authors:  Samuel G V Charlton; Michael A White; Saikat Jana; Lucy E Eland; Pahala Gedara Jayathilake; J Grant Burgess; Jinju Chen; Anil Wipat; Thomas P Curtis
Journal:  J Bacteriol       Date:  2019-08-22       Impact factor: 3.490

6.  Contextual dependencies expand the re-usability of genetic inverters.

Authors:  Huseyin Tas; Lewis Grozinger; Ruud Stoof; Victor de Lorenzo; Ángel Goñi-Moreno
Journal:  Nat Commun       Date:  2021-01-13       Impact factor: 14.919

7.  How To Quantify a Genetic Firewall? A Polarity-Based Metric for Genetic Code Engineering.

Authors:  Markus Schmidt; Vladimir Kubyshkin
Journal:  Chembiochem       Date:  2020-12-30       Impact factor: 3.164

8.  Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway.

Authors:  Kealan Exley; Christopher Robert Reynolds; Lorna Suckling; Soo Mei Chee; Argyro Tsipa; Paul S Freemont; David McClymont; Richard Ian Kitney
Journal:  J Biol Eng       Date:  2019-01-18       Impact factor: 4.355

9.  Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers.

Authors:  Christopher J Robinson; Pablo Carbonell; Adrian J Jervis; Cunyu Yan; Katherine A Hollywood; Mark S Dunstan; Andrew Currin; Neil Swainston; Reynard Spiess; Sandra Taylor; Paul Mulherin; Steven Parker; William Rowe; Nicholas E Matthews; Kirk J Malone; Rosalind Le Feuvre; Philip Shapira; Perdita Barran; Nicholas J Turner; Jason Micklefield; Rainer Breitling; Eriko Takano; Nigel S Scrutton
Journal:  Metab Eng       Date:  2020-04-23       Impact factor: 9.783

Review 10.  Multiplex Genome Engineering Methods for Yeast Cell Factory Development.

Authors:  Koray Malcı; Laura E Walls; Leonardo Rios-Solis
Journal:  Front Bioeng Biotechnol       Date:  2020-10-29
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