Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform.
Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform.
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DOI：
10.3389/fpls.2017.00786
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发表时间：
2017
影响因子：
5.6
通讯作者：
Zhu XG
中科院分区：
文献类型：
--
作者：
Marshall-Colon A;Long SP;Allen DK;Allen G;Beard DA;Benes B;von Caemmerer S;Christensen AJ;Cox DJ;Hart JC;Hirst PM;Kannan K;Katz DS;Lynch JP;Millar AJ;Panneerselvam B;Price ND;Prusinkiewicz P;Raila D;Shekar RG;Shrivastava S;Shukla D;Srinivasan V;Stitt M;Turk MJ;Voit EO;Wang Y;Yin X;Zhu XG
通过将基因网络、蛋白质合成、代谢途径、生理和生长联系起来，多尺度模型可以促进整个植物的模拟。整个植物模型可以进一步与生态系统、天气和气候模型相结合，以预测各种相互作用如何响应环境扰动。这些模型有可能填补缺失的机械细节，并产生新的假设，以确定定向工程工作的优先顺序。这些成果可能会加快作物产量、可持续性的提高，并增加未来的粮食安全。现在是工厂建模模式转变的时候了，从很大程度上孤立的努力转变为一个相互联系的社区，利用高性能计算的进步和对工厂过程的机械理解。迫切需要指导未来作物育种和工程的工具，了解分子水平上的发现对整个植物行为的影响，以及改进对植物和生态系统对环境反应的预测。这一观点的目的是将作物引入Silico(cropsinsilo.org)，这是一个综合的多尺度建模平台，作为一个解决方案，将孤立的建模工作结合到虚拟作物的生成中，该虚拟作物对整个植物生物学社区是开放的和可访问的。本招股说明书总结了开发和部署共享的多尺度建模平台所涉及的主要挑战，最近在Silico研讨会和研讨会的第一批作物中确定了这些挑战。
Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.