ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web

Geoffrey Fucile, David Di Biase, Hardeep Nahal, Garon La, Shokoufeh Khodabandeh, Yani Chen, Kante Easley, Dinesh Christendat, Lawrence Kelley and Nicholas J Provart

PLOS ONE, 2011, vol. 6, issue 1, 1-10

Abstract: Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed “ePlant” (http://bar.utoronto.ca/eplant) – a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the “3D Data Display Initiative” (http://3ddi.org).

Date: 2011
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0015237

DOI: 10.1371/journal.pone.0015237

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