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

Tópicos

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Resumo

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 mechanistic terms. In turn, such mechanistic explanations can assist in designing synthetic biological systems. We also discuss, giving practical guidance to users, how Designer interfaces with the Registry of Standard Biological Parts, the de facto compendium of parts used in synthetic biology applications.

Resumo Limpo

model tool can play import role synthet biolog way model help engin disciplin simul can quick probe mechan provid clear pictur differ compon influenc behavior whole present brief review avail tool present synbioss design synthet biolog softwar suit synbioss use generat store retriev quantit simul synthet biolog network synbioss consist three distinct compon desktop simul wiki design synbioss design take input molecular part involv gene express regul eg promot transcript factor ribosom bind site etc automat generat complet network reaction repres transcript translat regul induct degrad part effect design use dna sequenc input generat network biomolecular reaction output paper describ design use univers principl molecular biolog generat model arbitrari synthet biolog system model use explain biolog phenotyp complex mechanist term turn mechanist explan can assist design synthet biolog system also discuss give practic guidanc user design interfac registri standard biolog part de facto compendium part use synthet biolog applic

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