Designing and encoding models for synthetic biology.

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TitleDesigning and encoding models for synthetic biology.
Publication TypeJournal Article
Year of Publication2009
AuthorsEndler, L, Rodriguez, N, Juty, N, Chelliah, V, Laibe, C, Li, C, Le Novère, N
JournalJ R Soc Interface
Volume6 Suppl 4
PaginationS405-17
Date Published2009 Aug 6
ISSN1742-5662
KeywordsAlgorithms, Biology, Biotechnology, Computational Biology, Computer Simulation, Gene Regulatory Networks, Internet, Models, Biological, Models, Theoretical, Programming Languages, Software, Systems Biology
Abstract

<p>A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology 'loop'.</p>

DOI10.1098/rsif.2009.0035.focus
Alternate JournalJ R Soc Interface
PubMed ID19364720
PubMed Central IDPMC2843962
Grant ListBB/F010516/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
/ / Biotechnology and Biological Sciences Research Council / United Kingdom