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Computer Models and Tools

Computational modeling makes use of the powerful abilities of computers to make calculations. Constructing models of real systems allows for testing of conceptual models and related hypotheses before verification is sought in greenhouse and field studies.

This three dimensional simulated root system calculates nutrient and water uptake as the roots grow and receive photosynthate from the shoot in a virtual 3D soil environment.

RootSlice simulation showing a maize root cross section with an intermediate level of aerenchyma

The anatomical structure of roots has been shown to have effects on plant physiological processes but root anatomy has not been explicitly considered in functional-structural root models... until now.

RootScan after anatomical features have been extracted and measured

RootScan is an imaging software designed to codify anatomical features of root cross sections from microscope digital images.

We provide ImageJ and ObjectJ project files to facilitate architectural measurements of maize and bean root crowns

We have developed an dynamic nutrient budget model that models root and shoot growth and resource allocation.

Lab students are encouraged to use R for statistics and graphing. Come here to learn with us.

KineRoot is a MatLab-based program that tracks root movement and growth from a set of sequential photographs.

Simulations aren't all fun and games

Jouke Postma, author of SimRoot, offers advice on how to get started with a scientific model.

The computer has become so central to research that we may need to learn how to organize our experimental proposals, designs, data collection and results in new ways. OneNote may already be installed on your computer and useful for this endeavor.

Solving the problem of sad messes of drives and cables by doing experiment planning, data backup and sharing, and scheduling with an online lab repository.

Good software is necessary for the modern scientist. Here, we review free software supported on multiple platforms. Not only is this all the software one needs for obtaining a graduate degree, but open software leads to open science that benefits everyone.