Institute of Systems and Synthetic Biology, Université d'Évry Val d'Essonne - CNRS UPS3201 - Genopole, 91034 Évry, France.
FEBS Lett. 2012 Jul 16;586(15):2037-42. doi: 10.1016/j.febslet.2012.02.031. Epub 2012 Feb 27.
Automatic design is based on computational modeling and optimization methods to provide prototype designs to targeted problems in an unsupervised manner. For biological circuits, we need to produce quantitative predictions of cell behavior for a given genotype as consequence of the different molecular interactions. Automatic design techniques aim at solving the inverse problem of finding the sequences of nucleotides that better fit a targeted behavior. In the post-genomic era, our molecular knowledge and modeling capabilities have allowed to start using such methodologies with success. Herein, we describe how the emergence of this new type of tools could enable novel synthetic biology applications. We highlight the essential elements to develop automatic design procedures for synthetic biology pointing out their advantages and bottlenecks. We discuss in detail the experimental difficulties to overcome in the in vivo implementation of designed networks. The use of automatic design to engineer biological networks is starting to emerge as a new technique to perform synthetic biology, which should not be neglected in the future.
自动设计基于计算建模和优化方法，以非监督的方式为目标问题提供原型设计。对于生物电路，我们需要根据不同的分子相互作用，对给定基因型的细胞行为产生定量预测。自动设计技术旨在解决寻找更符合目标行为的核苷酸序列的逆问题。在后基因组时代，我们的分子知识和建模能力使得这些方法能够成功地被应用。在此，我们描述了这种新型工具的出现如何能够为新型合成生物学应用提供可能。我们强调了为合成生物学开发自动设计程序的基本要素，指出了它们的优势和瓶颈。我们详细讨论了在体内实现设计网络时需要克服的实验困难。使用自动设计来工程生物网络作为执行合成生物学的新技术开始出现，在未来不应被忽视。
