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Lookup NU author(s): Dr Goksel Misirli, Dr Jennifer Hallinan, Professor Anil Wipat
Modelling and computational simulation are crucial for the large-scale engineering of biological circuits since they allow the system under design to be simulated prior to implementation in vivo. To support automated, model-driven design it is desirable that in silico models are modular, composable and use standard formats. The synthetic biology design process typically involves the composition of genetic circuits from individual parts. At the most basic level these parts are representations of genetic features such as promoters, ribosome binding sites (RBSs), and coding sequences (CDSs). However, it is also desirable to model the biological molecules and behaviour that arise when these parts are combined in vivo. Modular models of parts can be composed and their associated systems simulated, facilitating the process of model centred design. The availability of databases of modular models is essential to support software tools used in the model-driven design process. In this paper we present an approach to support the development of composable, modular models for synthetic biology, termed Standard Virtual Parts. We then describe a programmatically accessible and publicly available database of these models to allow their use by computational design tools.
Author(s): Misirli G, Hallinan J, Wipat A
Publication type: Report
Publication status: Published
Series Title: School of Computing Science Technical Report Series
Year: 2014
Pages: 20
Print publication date: 01/06/2014
Report Number: 1424
Institution: School of Computing Science, University of Newcastle upon Tyne
Place Published: Newcastle upon Tyne
URL: http://www.cs.ncl.ac.uk/publications/trs/papers/1424.pdf
