Synbioss designer: A web-based tool for the automated generation of kinetic models for synthetic biological constructs

Emma Weeding, Jason Houle, Yiannis Kaznessis

Research output: Contribution to journalArticlepeer-review

35 Scopus citations

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, theWiki, 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.

Original languageEnglish (US)
Article numberbbq002
Pages (from-to)394-402
Number of pages9
JournalBriefings in Bioinformatics
Volume11
Issue number4
DOIs
StatePublished - Feb 24 2010

Keywords

  • Automated design
  • Computational biology
  • Multiscale models
  • Synthetic biology

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