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 language | English (US) |
|---|---|
| Pages (from-to) | 1049-1057 |
| Number of pages | 9 |
| Journal | Plant Cell and Environment |
| Volume | 39 |
| Issue number | 5 |
| DOIs | |
| State | Published - May 1 2016 |
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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 S.; 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 journal › Review article
}
TY - JOUR
T1 - Plants in silico
T2 - Why, why now and what?-an integrative platform for plant systems biology research
AU - Zhu, Xin Guang
AU - Lynch, Jonathan P.
AU - Lebauer, David S.
AU - Millar, Andrew J.
AU - Stitt, Mark
AU - Long, Stephen P.
PY - 2016/5/1
Y1 - 2016/5/1
N2 - 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.
AB - 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.
KW - Crop models
KW - Earth System models
KW - Ecosystem models
KW - Gene networks
KW - Metabolic networks
KW - Photosynthesis
KW - Plant models
KW - Plant molecular biology
KW - Root architecture
KW - Stomata
KW - System analysis
KW - Virtual organisms
UR - http://www.scopus.com/inward/record.url?scp=84963627720&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84963627720&partnerID=8YFLogxK
U2 - 10.1111/pce.12673
DO - 10.1111/pce.12673
M3 - Review article
C2 - 26523481
AN - SCOPUS:84963627720
VL - 39
SP - 1049
EP - 1057
JO - Plant, Cell and Environment
JF - Plant, Cell and Environment
SN - 0140-7791
IS - 5
ER -