Composable Modular Models for Synthetic Biology

Goksel Misirli, Jennifer Hallinan, Anil Wipat
<span title="2014-12-30">2014</span> <i title="Association for Computing Machinery (ACM)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/c2ubcasn2jaunmzahfcdaeyvry" style="color: black;">ACM Journal on Emerging Technologies in Computing Systems</a> </i> &nbsp;
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
more &raquo; ... 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. Abstract 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. 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.
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