Projects per year
Abstract / Description of output
A recent initiative named 'Crops in silico' proposes that multi-scale models “have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts” in plant science, particularly directed to crop species. To that end, the group called for “a paradigm shift in plant modelling, from largely isolated efforts to a connected community” (Marshall-Colon et al., 2017). ‘Wet’ (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community. Parts of this community invested in ‘dry’ (theoretical) research, under the rubric of Systems Biology. Our past research combined concepts from systems biology and crop modelling (Chew et al., 2017; Chew et al., 2014b). Here we outline the approaches that seem most relevant to connected, ‘digital organism’ initiatives. We illustrate the scale of experimental research required, by collecting the kinetic parameter values that are required for a quantitative, dynamic model of a gene regulatory network. By comparison to the SBML community, we note computational resources and community structures that will help to realise the potential for plant systems biology to connect with a broader crop science community.
Original language | English |
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Article number | JEXBOT/2018/235879 |
Pages (from-to) | 2403–2418 |
Number of pages | 16 |
Journal | Journal of Experimental Botany |
Volume | 70 |
Issue number | 9 |
Early online date | 5 Jan 2019 |
DOIs | |
Publication status | Published - 15 Apr 2019 |
Keywords / Materials (for Non-textual outputs)
- Arabidopsis thaliana
- biochemical kinetics
- community standards
- computational modelling
- data science
- whole cell modelling
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Dive into the research topics of 'Practical steps to digital organism models, from laboratory model species to ‘Crops in silico’'. Together they form a unique fingerprint.Projects
- 7 Finished
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Bridging systems biology and advanced computing, to realise multi-scale biological modelling
1/06/15 → 31/05/17
Project: Research
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SynthSys-Mammalian: Edinburgh Mammalian Synthetic Biology Research Centre
14/11/14 → 31/03/22
Project: Research
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Research output
- 3 Article
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Testing the inferred transcription rates of a dynamic, gene network model in absolute units
Urquiza-García, U. & Millar, A. J., 5 Aug 2021, In: In Silico Plants. diab022.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
A multi-model Framework for the Arabidopsis life cycle
Zardilis, A., Hume, A. & Millar, A., 19 Feb 2019, In: Journal of Experimental Botany. 70, 9, p. 2463–2477 16 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform
Marshall-colon, A., Long, S. P., Allen, D. K., Allen, G., Beard, D. A., Benes, B., Von Caemmerer, S., Christensen, A. J., Cox, D. J., Hart, J. C., Hirst, P. M., Kannan, K., Katz, D. S., Lynch, J. P., Millar, A. J., Panneerselvam, B., Price, N. D., Prusinkiewicz, P., Raila, D., Shekar, R. G., & 9 others , 15 May 2017, In: Frontiers in plant science. 8, 786.Research output: Contribution to journal › Article › peer-review
Open Access
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Steering Group for the joint NERC:BBSRC Molecules to Landscapes programme (External organisation)
Andrew Millar (Member)
2021 → 2025Activity: Membership types › Membership of board
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Institute seminar: "Open Research approaches for genome-driven, multi-scale biology"
Andrew Millar (Invited speaker)
12 Nov 2019Activity: Academic talk or presentation types › Invited talk
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Hutton seminar: "Watching plant clock genes run the organism, to understand growth and selection in crops"
Andrew Millar (Invited speaker)
6 Jun 2018Activity: Academic talk or presentation types › Invited talk