Plants in silico: Why, why now and what?-an integrative platform for plant systems biology research

Xin Guang Zhu, Jonathan P. Lynch, David Shaner LeBauer, Andrew J. Millar, Mark Stitt, Stephen P Long

Research output: Contribution to journalReview article

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.

Original languageEnglish (US)
Pages (from-to)1049-1057
Number of pages9
JournalPlant Cell and Environment
Volume39
Issue number5
DOIs
StatePublished - May 1 2016

Fingerprint

Systems Biology
Computer Simulation
Biological Sciences
Research
Ecosystem
Plant Organogenesis
Computing Methodologies
Biological Phenomena
computer science
ecosystems
Gene Regulatory Networks
Metabolic Networks and Pathways
Internet
plant development
biochemical pathways
Software
Genome
genome
crops

Keywords

  • Crop models
  • Earth System models
  • Ecosystem models
  • Gene networks
  • Metabolic networks
  • Photosynthesis
  • Plant models
  • Plant molecular biology
  • Root architecture
  • Stomata
  • System analysis
  • Virtual organisms

ASJC Scopus subject areas

  • Physiology
  • Plant Science

Cite this

Plants in silico : Why, why now and what?-an integrative platform for plant systems biology research. / Zhu, Xin Guang; Lynch, Jonathan P.; LeBauer, David Shaner; Millar, Andrew J.; Stitt, Mark; Long, Stephen P.

In: Plant Cell and Environment, Vol. 39, No. 5, 01.05.2016, p. 1049-1057.

Research output: Contribution to journalReview article

Zhu, Xin Guang ; Lynch, Jonathan P. ; LeBauer, David Shaner ; Millar, Andrew J. ; Stitt, Mark ; Long, Stephen P. / Plants in silico : Why, why now and what?-an integrative platform for plant systems biology research. In: Plant Cell and Environment. 2016 ; Vol. 39, No. 5. pp. 1049-1057.
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