2015, DOI: 10.1111/pce.12673
Plants in silico: why, why now and what? — An integrative platform for plant systems biology research
Xin‐Guang Zhu, Jonathan P. Lynch, David S. LeBauer, Andrew J. Millar, Mark Stitt, and Stephen P. Long
A paradigm shift is needed and timely in moving plant modeling from largely isolated efforts to a connected community endeavor 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 toward testing and consensus on quantitative theoretical frameworks. Importantly Psi provides a quantitative knowledge framework where the implications of a discovery at one level, e.g. single gene function or development response, can be examined at the whole plant or even crop and natural ecosystem levels.