Zhu Xin-Guang, Lynch Jonathan P, LeBauer David S, Millar Andrew J, Stitt Mark, Long Stephen P
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
Department of Plant Science, Penn State University, University Park, PA, 16802, USA.
Plant Cell Environ. 2016 May;39(5):1049-57. doi: 10.1111/pce.12673. Epub 2015 Dec 21.
A paradigm shift is needed and timely in moving plant modelling from largely isolated efforts to a connected community endeavour that can take full advantage of advances in computer science and in mechanistic understanding of plant processes. Plants in silico (Psi) envisions a digital representation of layered dynamic modules, linking from gene networks and metabolic pathways through to cellular organization, tissue, organ and whole plant development, together with resource capture and use efficiency in dynamic competitive environments, ultimately allowing a mechanistically rich simulation of the plant or of a community of plants in silico. The concept is to integrate models or modules from different layers of organization spanning from genome to phenome to ecosystem in a modular framework allowing the use of modules of varying mechanistic detail representing the same biological process. Developments in high-performance computing, functional knowledge of plants, the internet and open-source version controlled software make achieving the concept realistic. Open source will enhance collaboration and move towards testing and consensus on quantitative theoretical frameworks. Importantly, Psi provides a quantitative knowledge framework where the implications of a discovery at one level, for example, single gene function or developmental response, can be examined at the whole plant or even crop and natural ecosystem levels.
现在需要且时机已到进行一场范式转变，将植物建模从大量孤立的工作转变为一个相互关联的群体努力，从而能够充分利用计算机科学的进步以及对植物过程的机械理解。植物计算机模拟（Psi）设想了一个分层动态模块的数字表示，从基因网络和代谢途径一直连接到细胞组织、组织、器官和整个植物的发育，以及在动态竞争环境中的资源获取和利用效率，最终实现对植物或植物群落进行计算机模拟的丰富机械模拟。其概念是在一个模块化框架中整合来自从基因组到表型组再到生态系统的不同组织层次的模型或模块，允许使用代表相同生物过程但具有不同机械细节的模块。高性能计算、植物功能知识、互联网和开源版本控制软件的发展使实现这一概念成为现实。开源将加强合作，并朝着对定量理论框架进行测试和达成共识的方向发展。重要的是，Psi提供了一个定量知识框架，在这个框架中，例如在单个基因功能或发育反应等一个层面上的发现所产生的影响，可以在整个植物甚至作物和自然生态系统层面上进行研究。
