Plant genome-scale modeling and implementation

Dal'Molin, Cristiana G. O., Quek, Lake-Ee, Palfreyman, Robin W. and Nielsen, Lars K. (2014). Plant genome-scale modeling and implementation. In Plant metabolic flux analysis: methods and protocols (pp. 317-332) New York, NY, United States: Humana Press. doi:10.1007/978-1-62703-688-7_19


Author Dal'Molin, Cristiana G. O.
Quek, Lake-Ee
Palfreyman, Robin W.
Nielsen, Lars K.
Title of chapter Plant genome-scale modeling and implementation
Title of book Plant metabolic flux analysis: methods and protocols
Place of Publication New York, NY, United States
Publisher Humana Press
Publication Year 2014
Sub-type Research book chapter (original research)
DOI 10.1007/978-1-62703-688-7_19
Series Methods in Molecular Biology
ISBN 9781627036887
9781627036870
ISSN 1064-3745
Volume number 1090
Chapter number 19
Start page 317
End page 332
Total pages 16
Total chapters 21
Collection year 2015
Language eng
Abstract/Summary Considerable progress has been made in plant genome-scale metabolic reconstruction and modeling in recent years. Such reconstructions made it possible to explore metabolic phenotypes through appropriate model formulation and optimization methods. As a result, plant genome-scale modeling has increasingly attracted interest from the plant research community. In this chapter, the first generation of plant genome-scale metabolic reconstructions is presented, along with the important concepts behind model and constraint formulation. A brief protocol describing the use of constraint-based reconstruction and analysis (COBRA) Toolbox in flux simulation and model modification is provided. This is followed by a presentation of metabolic constraints required to generate fluxes in AraGEM using COBRA that describe photosynthesis, photorespiration, and respiration, respectively. Overall, plant genome-scale modeling is a powerful approach that is accessible and readily adopted.
Keyword Plant metabolic reconstruction
Genome-scale modeling
AraGEM
Constraint-based reconstruction
COBRA Toolbox
Flux simulation
Q-Index Code BX
Q-Index Status Confirmed Code
Institutional Status UQ

 
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