title: Plants in silico: why, why now and what?--an integrative platform for plant systems biology research.
abstract: 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.
authors.affiliation: 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.
authors.forename: Xin-Guang
authors.initials: XG
authors.lastname: Zhu
authors.affiliation: Department of Plant Science, Penn State University, University Park, PA, 16802, USA.
authors.forename: Jonathan P
authors.initials: JP
authors.lastname: Lynch
authors.affiliation: Institute for Genomic Biology and National Center for Supercomputer Applications, University of Illinois, 1206 W Gregory Drive, Urbana, IL, 61801, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: LeBauer
authors.affiliation: SynthSys and School of Biological Sciences, University of Edinburgh, Midlothian, Scotland, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Millar
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, D-14476, Potsdam Gölm, Germany.
authors.forename: Mark
authors.initials: M
authors.lastname: Stitt
authors.affiliation: Departments of Crop Sciences and Plant Biology, Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Long
mesh_terms: D003198:Computer Simulation; D008954:Models, Biological; D010944:Plants / Q000378:metabolism*; D012106:Research; D049490:Systems Biology
keywords: Earth System models; crop models; ecosystem models; gene networks; metabolic networks; photosynthesis; plant models; plant molecular biology; root architecture; stomata; system analysis; virtual organisms