Cross-Species Network Analysis Using VirtualPlant

VirtualPlant (www.virtualplant.org), originally developed for an NSF Arabidopsis 2010 Grant, includes tools for data analysis, integration and visualization such as the Arabidopsis MultiNetwork interaction database, as well as novel data visualization tools including BioMaps and Sungear [1,2]. VirtualPlant enables seamless integration of data and tools into a single software platform by virtue of its unique “Gene Cart”, which enables researchers to store results, enabling iterative cycles of analysis, a highlight of Systems Biology [3]. Additionally, VirtualPlant’s web-based user-friendly GUI enables plant biologists to analyze their own genomic data, enabling them to uncover and infer biological insights.

VirtualPlant has played an integral part in enabling Plant Systems Biology research in Arabidopsis in prominent plant labs around the world. Our recent expansion of VirtualPlant to include important crops such as Maize, Rice, Soy and Cassava, facilitates the comparisons of crop networks to Arabidopsis, hence enabling translational research. For example, VirtualPlant allows researchers to predict how an interacting network of genes/products in crop genomes will react as a system in response to an environmental change or genetic modifications, and predict genes in the crop to target for manipulation.

In our efforts to make VirtualPlant scaleable for next-generation data and also make our tools easily accessible to the community, we have restructured our code base to provide simple interfaces to VirtualPlant and its tools. Details of the API and also how we plan to interact with AIP will be discussed.

[1] Katari, MS, Nowicki, SD, Aceituno, FF, Nero, D, Kelfer, J, Thompson, LP, Cabello, JM, Davidson, RS, Goldberg, AP, Shasha, DE, Coruzzi, GM, and Gutierrez, RA, VirtualPlant: a software platform to support systems biology research. Plant Physiol, 2010. 152(2): p. 500-515.

[2] Poultney, CS, Gutierrez, RA, Katari, MS, Gifford, ML, Paley, WB, Coruzzi, GM, and Shasha, DE, Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics, 2007. 23(2): p. 259-261.

[3] Gutierrez, RA, Shasha, DE, and Coruzzi, GM, Systems biology for the virtual plant. Plant Physiol, 2005. 138(2): p. 550-554.