VirtualPlant DatabaseWebsite: http://www.virtualplant.org
Our long term goal is to understand how internal and external perturbations affect processes and networks controlling plant growth and development. In this project, we start with data integration of the known relationships among genes, proteins and molecules (extracted from public databases and/or generated with predictive algorithms) as well as experimental measurements under many different treatments. We go beyond data integration to conceptual integration by using novel visualization techniques to render the multivariate information in visual formats that facilitate extraction of biological concepts. We also use mathematical and statistical methods to help summarize the data. We implement and combine these approaches in a system we term "VirtualPlant". Whereas our project relates specifically to Arabidopsis, the data structures, algorithms, and visualization tools are designed in a species-independent way. Thus the informatic, math, statistic and visualization tools that we develop can be used to model the cellular and physiological responses of any organism for which genomic data is available.
We have implemented a proto-type that is already being actively and effectively used (http://www.virtualplant.org). This tool is being used by biologists and computer scientist alike for the purpose it was designed for - to support the analysis of original genomic data generated by the researchers themselves. We have found that working with experimental biologists, even from very early stages of software development, to be the most effective way to generate real solutions to the problems encountered by researchers in the laboratory.