Plant Systems Biology: Methods and Protocols

Dedication...Preface...Table of Contents...Contributing Authors...
1.Plant Systems Biology: Lessons from TeachingMikaël Lucas 
2.How to Use the TDCor Algorithm to Infer Gene Regulatory Networks from Time Series Transcriptomic DataJulien Lavenus and Mikaël Lucas
3.Gene Regulatory Network Investigation Using Ordinary Differential EquationsEtienne Farcot and Nathan Mellor
4.Gene Regulatory Network Dynamical Logical Models for Plant DevelopmentJose Davila-Velderrain, Jose Luis Caldu-Primo, Juan Carlos Martinez-Garcia, Elena R. Alvarez-Buylla
5.Post-Embryonic Organogenesis in Plants: Experimental Induction of New Shoot and Root OrgansSoazig Guyomarc'h, Mikaël Lucas, and Laurent Laplaze
6.NanoIndentation, an ImageJ Plugin for the Quantification of Cell MechanicsVincent Mirabet, Nelly Dubrulle, Léa Rambaud, Léna Beauzamy, Mathilde Dumond, Yuchen Long, Pascale Milani, and Arezki Boudaoud
7.Introduction to Computational Modeling of Multicellular Tissues Jean-Louis Dinh, Christophe Godin, and Eugenio Azpeitia
8.The Virtual Root: Mathematical Modelling of Auxin Transport in the Arabidopsis Root Tip using the Open Source Software SimuPlantHeather Collis, Leah Band, John Fozard, Teodor Ghetiu, Michael Wilson, Nathan Mellor, Malcolm Bennett, and Markus Owen
9.Modeling Plant Tissue Development using VirtualLeafClaudiu-Cristi Antonovici, Guacimo Y. Peerdeman, Harold B. Wolff, and Roeland M.H. Merks
10. Identifying Developmental Patterns in Structured Plant Phenotyping DataYann Guédon, Yves Caraglio, Christine Granier, Pierre-Éric Lauri, and Bertrand Muller
11. Putting Plant Roots at Light: Temporal Imaging of Plant Roots and Soil Water with a Light Transmission Technique for Linking Water and Root Observations to Soil-Plant ModelsClaude Doussan
12. RACINE2.2: A Software Application for Processing and Mapping Spatial Distribution of Root Length Density and Potential Root Extraction Ratio from Root Counts on Trench ProfilesAwa Faye, Laurent Laplaze, Bassirou Sine, and Jean-Louis Chopart
13. Investigating Soil-Root Interactions with the Numerical Model R-SWMSFélicien Meunier, Valentin Couvreur, Xavier Draye, Guillaume Lobet, Katrin Huber, Nathalie Schroerder, Helena Jorda, Axelle Koch, Magdalena Landl, Andrea Schnepf, Jan Vanderborght, Harry Vereecken, and Mathieu Javaux
14. How to Define the Appropriate Spatial Resolution of Root Segments When Solving Water Flow in Root System Hydraulic Architectures?Félicien Meunier, Valentin Couvreur, Jan Vanderborght, and Mathieu Javaux
15. Simulating Crop Root Systems using OpenSimRootErnst D. Schäfer, Markus R. Owen, Johannes Postma, Christian Kuppe, Christopher K. Black, Jonathan P. Lynch
16. Future Challenges in Plant Systems BiologyMikaël Lucas
17. Plant Systems Biology: Further Reading and ResourcesMikaël Lucas
Subject Index List...