Fisher Jasmin, Henzinger Thomas A
Microsoft Research, Cambridge CB3 0FB, UK.
Nat Biotechnol. 2007 Nov;25(11):1239-49. doi: 10.1038/nbt1356.
Computational modeling of biological systems is becoming increasingly important in efforts to better understand complex biological behaviors. In this review, we distinguish between two types of biological models--mathematical and computational--which differ in their representations of biological phenomena. We call the approach of constructing computational models of biological systems 'executable biology', as it focuses on the design of executable computer algorithms that mimic biological phenomena. We survey the main modeling efforts in this direction, emphasize the applicability and benefits of executable models in biological research and highlight some of the challenges that executable biology poses for biology and computer science. We claim that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research. This will drive biology toward a more precise engineering discipline.
在努力更好地理解复杂生物行为的过程中，生物系统的计算建模正变得越来越重要。在本综述中，我们区分了两种类型的生物模型——数学模型和计算模型，它们在生物现象的表示方式上有所不同。我们将构建生物系统计算模型的方法称为“可执行生物学”，因为它专注于设计模仿生物现象的可执行计算机算法。我们调查了这一方向上的主要建模工作，强调了可执行模型在生物学研究中的适用性和益处，并突出了可执行生物学给生物学和计算机科学带来的一些挑战。我们认为，为了使可执行生物学充分发挥其作为主流生物学技术的潜力，必须将形式化和算法化方法融入生物学研究。这将推动生物学朝着更精确的工程学科发展。
