Plants in silico: why, why now and what?--an integrative platform for plant systems biology research.
Plants in silico: why, why now and what?--an integrative platform for plant systems biology research.
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DOI：
10.1111/pce.12673
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发表时间：
2016-05
期刊：
影响因子：
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通讯作者：
Xinguang Zhu;J. Lynch;David LeBauer;A. Millar;M. Stitt;S. Long
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文献类型：
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作者：
Xinguang Zhu;J. Lynch;David LeBauer;A. Millar;M. Stitt;S. Long
在将植物建模从很大程度上孤立的努力转移到可以充分利用计算机科学进步和对植物过程的机械理解的联系社区努力方面，需要及时的范式转变。硅中植物（Psi）设想了分层动态模块的数字表示，从基因网络和代谢途径连接到细胞组织、组织、器官和整个植物的发育，以及动态竞争环境中的资源捕获和利用效率，最终允许对硅中植物或植物群落进行机械丰富的模拟。这个概念是将来自不同组织层的模型或模块整合在一个模块化框架中，从基因组到现象组再到生态系统，允许使用代表相同生物过程的不同机制细节的模块。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。开源将加强协作，并朝着量化理论框架的测试和共识迈进。重要的是，Psi提供了一个定量的知识框架，在这个框架中，单个基因功能或发育反应等一个层面上的发现，可以在整个植物甚至作物和自然生态系统层面上进行检验。
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.