iPlants – A Brief Look at Virtual Plants (From Avatar To Systems Biology)

Ava_Scenery.jpgiPlants: An Introduction

From movies and video games to landscape design to education to scientific research, we are increasingly encountering plants in silico (that is, computer-simulated plants).

Virtual plants fall into three categories: (1) computer-generated images, (2) outputs from computer algorithms, and (3) computer-searchable plant gene and protein databases.

What follows is a summary of my experiences with virtual plants, mainly online. (However, I don’t claim this is a comprehensive review – please let me know via comments what I’ve missed.)

The Botany of Pandora

The alien planet Pandora in the movie Avatar (and also the video game based on the movie) is swathed in a bioluminescent tropical landscape, populated with truly “out of this world” plants and fungi. As a consultant, plant physiologist Professor Jodie S. Holt helped create this computer-generated imaginary world as well-described here.

Virtual Landscaping

Landscape designers have been using cad programs for years. But thanks to web-based apps such as Second Life® and Google Sketchup anyone so-inclined can landscape in silico.

For example, some fantastic examples of such landscapes in Second Life® are presented here. And Google Sketchup has a 3D warehouse full of virtual plants for your virtual landscape.

Virtual Plants For Education

For years I’ve referred students to Virtual Plant Cell to help visualize plants at the cellular level.

At a more macro scale, one can learn some plant anatomy, for example, at The Virtual Plant.

Botany for Computer Geeks

Way back in the day, when I first taught a class in plant development, I introduced the class to the computer modeling of plant growth.

The example I chose was the so-called L-system or Lindenmayer system of the computer modeling of plants. An example of such modeling can be found at Algorithmic Botany, the website of the Biological Modeling and Visualization research group in the Department of Computer Science at the University of Calgary.

As head of this program, Professor Przemyslaw Prusinkiewicz has greatly refined and expanded this system. An illustrated list of their publications can be found here.

Is Plant Research Going To Be Like Shopping On Amazon.com?

One aspect of iPlant-related research involves functional genomics (putting the genetic puzzle pieces together), exemplified by MetNet at Iowa State University.

The VirtualPlant is another web-based software platform to support systems biology research. According to a recent report: “VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology,..”

As shown in this figure, “VirtualPlant follows the e-commerce site logic…users browse and query the database and add products of interest to their shopping cart”, analogous to Amazon.com. (Thanks, by the way, to the journal Plant Physiology for public access to this paper.)

“Big-Ass Science”

The ultimate “iPlant”, however, may be The iPlant Collaborative Project or, in other words, a $50,000,000 US-taxpayer-funded project to do plant research by committee. An excellent summary of this giant project can be found here.

Years ago a colleague referred to such endeavors as “big-ass science”. Personally, I feel that giving 200 young (under 40) plant scientists (profs or post-docs, by the way) $250,000 each to pursue her/his personal research interests would yield much more creative and innovative outcomes. But that’s a discussion for another day….

HowPlantsWork © 2008-2011 All Rights Reserved.

Post-Script:
Inorganic Flora
A couple of weeks after editing the original post, I discovered some amazingly beautiful images of flowers by botanical CG artist Macoto Murayama.

More about Murayama can be found here and here.

One Comment

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