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论文题目: Plants in silico: why, why now and what?an integrative platform for plant systems biology research
英文论文题目: Plants in silico: why, why now and what?an integrative platform for plant systems biology research
第一作者: Zhu, XG; Lynch, JP; LeBauer, DS; Millar, AJ; Stitt, M; Long, SP
英文第一作者: Zhu, XG; Lynch, JP; LeBauer, DS; Millar, AJ; Stitt, M; Long, SP
联系作者: Long, SP (reprint author), Univ Illinois, Inst Genom Biol, Dept Plant Biol, Urbana, IL 61801 USA.
英文联系作者: Long, SP (reprint author), Univ Illinois, Inst Genom Biol, Dept Plant Biol, Urbana, IL 61801 USA.
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发表年度: 2016
卷: 39
期: 5
页码: 1049-1057
摘要: 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.
英文摘要: 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.
刊物名称: PLANT CELL AND ENVIRONMENT
英文刊物名称: PLANT CELL AND ENVIRONMENT
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学科: Plant Sciences
英文学科: Plant Sciences
影响因子: 6.173
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论文类别: Article
英文论文类别: Article
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