SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs.

Briefings in Bioinformatics
Emma M B WeedingYiannis Kaznessis

Abstract

Modeling tools can play an important role in synthetic biology the same way modeling helps in other engineering disciplines: simulations can quickly probe mechanisms and provide a clear picture of how different components influence the behavior of the whole. We present a brief review of available tools and present SynBioSS Designer. The Synthetic Biology Software Suite (SynBioSS) is used for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS consists of three distinct components: the Desktop Simulator, the Wiki, and the Designer. SynBioSS Designer takes as input molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosome binding sites, etc.), and automatically generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. Effectively, Designer uses DNA sequences as input and generates networks of biomolecular reactions as output. In this paper we describe how Designer uses universal principles of molecular biology to generate models of any arbitrary synthetic biological system. These models are useful as they explain biological phenotypic complexity in ...Continue Reading

References

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Citations

Aug 9, 2011·ACS Chemical Biology·Katherine VolzingYiannis N Kaznessis
Jul 27, 2012·Briefings in Bioinformatics·Chang F QuoGil Alterovitz
Jun 15, 2013·Nucleic Acids Research·Robert Sidney CoxTetsuro Toyoda
Jan 21, 2011·BMC Systems Biology·Konstantinos BiliourisYiannis N Kaznessis
Mar 11, 2011·PloS One·Michal GaldzickiJohn H Gennari
Sep 9, 2011·PloS One·Marco ConstanteMark Isalan
Dec 27, 2012·The Journal of Chemical Physics·Patrick Smadbeck, Yiannis Kaznessis
Oct 29, 2013·Annual Review of Pharmacology and Toxicology·Boon Chin HengMartin Fussenegger
Feb 22, 2012·Current Opinion in Biotechnology·Michael G MontagueSanjay Vashee
Oct 14, 2014·Journal of Chemical and Engineering Data·Dan S BolintineanuYiannis N Kaznessis
Apr 8, 2011·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Yiannis N Kaznessis
Sep 13, 2014·Current Opinion in Chemical Engineering·Patrick Smadbeck, Yiannis N Kaznessis
Apr 1, 2015·Trends in Plant Science·Wusheng Liu, C Neal Stewart
May 10, 2013·ACS Synthetic Biology·Jason T Stevens, Chris J Myers
Jan 25, 2011·Integrative Biology : Quantitative Biosciences From Nano to Macro·James T MacDonaldGuy-Bart V Stan
Nov 6, 2015·Scientific Reports·Victor García-GonzálezJaime Mas-Oliva
Jan 24, 2012·Nature Reviews. Microbiology·Marnix H MedemaRainer Breitling
Aug 23, 2021·Molecular Biotechnology·Dipinte GuptaRajiv Ranjan

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