Designing a Systems Biology Course¶

Advanced / educator resource

This page outlines how the AIR tools and research can be assembled into a university-level systems biology course. The software it mentions is summarised on the Tools & Software page, and the bracketed citations correspond to the Literature & References list.

Creating a Systems Biology Course Using Root Biology Research¶

The sources provide a rich collection of methods, tools, and data focused on root biology research, which can be effectively used to design a comprehensive systems biology course. Here's a potential course structure:

Module 1: Introduction to Systems Biology and Root Biology¶

Begin with an introduction to systems biology, emphasizing the importance of studying biological systems holistically.
Introduce root biology, focusing on root structure, function, and its importance in plant growth and development.
Discuss the concept of the root system as a complex network and the need for computational tools to analyze its properties.

Module 2: Root Image Analysis and Phenotyping¶

This module would cover techniques for acquiring and analyzing root images to extract meaningful data.
Introduce students to both open-source and commercial image analysis tools mentioned in the sources, such as ImageJ for general image analysis [1-5], WebPlotDigitizer for digitizing figures [4], and specialized tools like RootScan, PHIV-RootCell, and RootAnalyzer for automated quantification of root anatomical properties [5-7].
Discuss the advantages and limitations of different tools.
Hands-on exercises using these tools on real root images would provide practical experience.

Module 3: Modeling Root System Architecture¶

Introduce various root system architecture models, including structural models like CRootBox, ArchiSimple, RootTyp, and DigR , as well as functional-structural models like CPlantBox, PiafMunch [8-11], and SmartRoot .
Discuss the principles behind each model and their applications.
Students could work on projects to simulate root growth using these models and analyze the impact of different environmental factors.

Module 4: Root Hydraulics and Water Transport¶

Focus on understanding water movement in the root system.
Introduce tools like MECHA for estimating hydraulic properties of root cross-sections [6, 12-23].
Discuss models for simulating root system water flow like R-SWMS, PlaNet-Maize, and OpenSimRoot .
Integrate the knowledge gained from image analysis and architectural modeling to understand the relationship between root structure and hydraulic function.

Module 5: Data Analysis and Visualization¶

Equip students with essential data analysis and visualization skills.
Teach them how to use R and packages like tidyverse for data manipulation and statistical analysis [24, 25].
Include training on creating informative graphs and figures to present research findings.

Project-Based Learning¶

A significant component of the course could involve project-based learning. Students can choose a specific research question related to root biology and use the tools and techniques learned throughout the course to address it.
Example projects could include:
Investigating the impact of drought stress on root architecture using image analysis and modeling tools.
Comparing the hydraulic properties of different root types.
Developing a model to predict root growth under specific environmental conditions.

Incorporating Data from Sources¶

The specific datasets used in the source papers, if publicly available, could be incorporated into the course for hands-on analysis.
Alternatively, similar datasets could be used to replicate the analyses performed in the source papers, allowing students to gain practical experience with the tools and methods.

By combining theoretical knowledge with practical application of computational tools and data analysis, this course will equip students with a comprehensive understanding of root systems biology and the power of systems-level approaches in biological research.