Scientific Inference Systems Laboratory
The Computable Plant
Home | Publications | Research | Gallery | People | Outreach | Software | Models | Links | Tutorials
Project Description | Educational Outreach | Sponsors and Partners
Visit the alpha version of our new website in progress.
The Challenge

How do the genetic makeup and environment interact to shape intricate developmental processes that lead to functional tissues, organs and organisms from undifferentiated cells? This has been a challenging question ever since biologists started wondering about development of multicellular organisms. The researchers have traditionally used microscopy, mutants and other methods to understand molecular and cellular bases for development. Recently, genomics is yet another tool added to the developmental biologists' arsenal. With the advances in biological knowledge, imaging instrumentation, applied biomathematics, and computing, it is now becoming possible create and apply computational modeling to integrate multidisciplinary approaches and different types of biological data in studying development.

The Project

Eric Mjolsness, a computer scientist at University of California, Irvine and Elliot Meyerowitz, a plant developmental biologist at California Institute of Technology will work together to provide a quantitative and cellular description of plant development. They will study meristem development in Arabidopsis thaliana, the model plant that has been used extensively in contemporary plant biology research. Meristems are the inner plant tissues, where regulated cell division, pattern formation and differentiation give rise to plant parts like leaves and flowers. The investigators at Caltech will use green fluorescent proteins to mark specific cell types in the apical meristem and image their lineages through meristem development and differentiation leading to specific arrangement of leaves and reproductive growth. Automation of image acquisition and analysis will help them generate and visualize a vast amount of data, which will be used by the UCI investigators to model cells and their patterns in the developing meristem and simulate developmental processes under different conditions. These simulations will result in predictions that will be tested experimentally using mutants, altered hormone gradients, and other manipulations.

Biological experimentation in this project uses cleverly designed transgenic plants with marker proteins and modification of known developmental genes. The bioinformatics component will manage a vast amount of image and knowledge data. The mathematical component will automatically generate specialized, efficient simulation code from models and link it to suitable bioinformatic datasets through pattern recognition, machine learning, and regulatory circuit inference algorithms. Extensive visualization, image processing, and optimization software will fit these predictive models to image data. Scientific objectives of this effort include the development and use of such mathematical modeling software for plant development, as well as its use to explore alternative hypotheses in silico and to guide in vivo experiments. Thus the project will involve a working loop from experiments, through bioinformatics and mathematical modeling, and back to experiments.

Go to top of Page
Educational Outreach

The researchers also plan to develop, evaluate, and introduce a new set of techniques for high school and pre-service science teachers as well as to undergraduate students. Outreach activities will culminate in a summer institute in which 30 high school students will develop a public kiosk to display the "silicon plant" model for exhibit at the Huntington Botanical Gardens, which hosts 500,000 visitors per year. This program holds remarkable promise for linking cutting-edge knowledge and techniques with K-12 teachers' and students' understanding of plant development and integrative biology.

Go to top of Page
Sponsors and Partners

Sponsored by the National Science Foundation Frontiers in Integrative Biological Research (FIBR) Program

 The sun never sets on The Computable Plant! 

WebCounter Courtesy of