Designing and encoding models for synthetic biology

L. Endler, N. Rodriguez, N. Juty, V. Chelliah, C. Laibe, C. Li, N. Le Novere
2009 Journal of the Royal Society Interface  
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
more » ... . 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'. One contribution to a Theme Supplement 'Synthetic biology: history, challenges and prospects'. Electronic supplementary material is available at http://dx.
doi:10.1098/rsif.2009.0035.focus pmid:19364720 pmcid:PMC2843962 fatcat:icdwnd2tcnazjpmfw4y4pomcvq