Composable Modular Models for Synthetic Biology

ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS

Article

Misirli, Goksel¹  Hallinan, Jennifer¹  Wipat, Anil¹ 

[1] Newcastle Univ, Sch Comp Sci, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England.;Newcastle Univ, Ctr Synthet Biol & Bioexploitat, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England.

关键词: Synthetic biology;    model-driven design;    composable models;    modelannotation;    database of models;    standard virtual parts;    RIBOSOME BINDING-SITES;    COMPUTATIONAL DESIGN;    BACILLUS-SUBTILIS;    SYSTEMS;    NETWORK;    EXPRESSION;    STANDARD;    NOISE;    OPTIMIZATION;    RESOURCE;   

DOI  :  10.1145/2631921

来源: SCIE

【 摘 要 】

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 article, 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.

【 授权许可】

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