Plant systems biology : methods and protocols This second edition volume expands on the previous edition with an update on the latest techniques used to study plant systems biology on three specific scales: the molecular level the tissue level and the whole plant. Chapters cover topics such as gene regulatory network inference and dynamic modeling using ordinary differential equations or Boolean formalisms; protocols for at will induction of plant aerial or root organs or quantification of tissue mechanical properties; mathematical modeling of plant tissue using SimuPlant or VirtualLeaf; and simulating crop root systems using OpenSimRoot or R SWMS. Written in the highly successful Methods in Molecular Biology series format chapters include introductions to their respective topics step by step readily reproducible laboratory protocols or software tutorials and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting edge Plants Systems Biology: Methods and Protocols Second Edition is a valuable resource for plant biologists looking for different approaches to finding solutions to their questions and generating new ideas as well as for students who desire to discover the field of plant systems biology. . Plant Systems Biology: Lessons from Teaching How to Use the TDCor Algorithm to Infer Gene Regulatory Networks from Time Series Transcriptomic Data Gene Regulatory Network Investigation Using Ordinary Differential Equations Gene Regulatory Network Dynamical Logical Models for Plant Development Post Embryonic Organogenesis in Plants: Experimental Induction of New Shoot and Root Organs NanoIndentation an ImageJ Plugin for the Quantification of Cell Mechanics Introduction to Computational Modeling of Multicellular Tissues The Virtual Root: Mathematical Modelling of Auxin Transport in the Arabidopsis Root Tip using the Open Source Software SimuPlant Modeling Plant Tissue Development using VirtualLeaf Identifying Developmental Patterns in Structured Plant Phenotyping Data 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 Models 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 Profiles Investigating Soil Root Interactions with the Numerical Model R SWMS How to Define the Appropriate Spatial Resolution of Root Segments When Solving Water Flow in Root System Hydraulic Architectures Simulating Crop Root Systems using OpenSimRoot Future Challenges in Plant Systems Biology Plant Systems Biology: Further Reading and Resources.