title: Consistent design schematics for biological systems: standardization of representation in biological engineering.
abstract: The discovery by design paradigm driving research in synthetic biology entails the engineering of de novo biological constructs with well-characterized input-output behaviours and interfaces. The construction of biological circuits requires iterative phases of design, simulation and assembly, leading to the fabrication of a biological device. In order to represent engineered models in a consistent visual format and further simulating them in silico, standardization of representation and model formalism is imperative. In this article, we review different efforts for standardization, particularly standards for graphical visualization and simulation/annotation schemata adopted in systems biology. We identify the importance of integrating the different standardization efforts and provide insights into potential avenues for developing a common framework for model visualization, simulation and sharing across various tools. We envision that such a synergistic approach would lead to the development of global, standardized schemata in biology, empowering deeper understanding of molecular mechanisms as well as engineering of novel biological systems.
authors.affiliation: The Systems Biology Institute, Tokyo, Japan. myukiko@sbi.jp
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Matsuoka
authors.forename: Samik
authors.initials: S
authors.lastname: Ghosh
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
mesh_terms: D000465:Algorithms; D000818:Animals; D001709:Biotechnology / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D005818:Genetic Engineering / Q000379:methods*; D006801:Humans; D008954:Models, Biological; D008962:Models, Theoretical; D015202:Protein Engineering / Q000379:methods*; D012984:Software; D049490:Systems Biology