Designing and encoding models for synthetic biology

作者：Endler Lukas^*; Rodriguez Nicolas; Juty Nick; Chelliah Vijayalakshmi; Laibe Camille; Li Chen; Le Novere Nicolas

来源：Journal of the Royal Society Interface, 2009, 6(suppl_4).

DOI：10.1098/rsif.2009.0035.focus

• synthetic biology
• systems biology markup language
• computational biology

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 reuse. 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'.

• 出版日期2009-8-6