title: VirtualPlant: a software platform to support systems biology research.
abstract: Data generation is no longer the limiting factor in advancing biological research. In addition, data integration, analysis, and interpretation have become key bottlenecks and challenges that biologists conducting genomic research face daily. To enable biologists to derive testable hypotheses from the increasing amount of genomic data, we have developed the VirtualPlant software platform. VirtualPlant enables scientists to visualize, integrate, and analyze genomic data from a systems biology perspective. VirtualPlant integrates genome-wide data concerning the known and predicted relationships among genes, proteins, and molecules, as well as genome-scale experimental measurements. VirtualPlant also provides visualization techniques that render multivariate information in visual formats that facilitate the extraction of biological concepts. Importantly, 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, such as: What are the molecular mechanisms by which internal or external perturbations affect processes controlling growth and development? We illustrate the use of VirtualPlant with three case studies, ranging from querying a gene of interest to the identification of gene networks and regulatory hubs that control seed development. Whereas the VirtualPlant software was developed to mine Arabidopsis (Arabidopsis thaliana) genomic data, its data structures, algorithms, and visualization tools are designed in a species-independent way. VirtualPlant is freely available at www.virtualplant.org.
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA.
authors.forename: Manpreet S
authors.initials: MS
authors.lastname: Katari
authors.forename: Steve D
authors.initials: SD
authors.lastname: Nowicki
authors.forename: Felipe F
authors.initials: FF
authors.lastname: Aceituno
authors.forename: Damion
authors.initials: D
authors.lastname: Nero
authors.forename: Jonathan
authors.initials: J
authors.lastname: Kelfer
authors.forename: Lee Parnell
authors.initials: LP
authors.lastname: Thompson
authors.forename: Juan M
authors.initials: JM
authors.lastname: Cabello
authors.forename: Rebecca S
authors.initials: RS
authors.lastname: Davidson
authors.forename: Arthur P
authors.initials: AP
authors.lastname: Goldberg
authors.forename: Dennis E
authors.initials: DE
authors.lastname: Shasha
authors.forename: Gloria M
authors.initials: GM
authors.lastname: Coruzzi
authors.forename: Rodrigo A
authors.initials: RA
authors.lastname: Gutiérrez
mesh_terms: D019295:Computational Biology / Q000379:methods; D003628:Database Management Systems; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics; D020411:Oligonucleotide Array Sequence Analysis; D010944:Plants / Q000235:genetics*; D049490:Systems Biology; D014584:User-Computer Interface