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EPlant and the 3D data display initiative: integrative systems biology on the world wide web.


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).

SUBMITTER: Fucile G 

PROVIDER: S-EPMC3018417 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

Fucile Geoffrey G   Di Biase David D   Nahal Hardeep H   La Garon G   Khodabandeh Shokoufeh S   Chen Yani Y   Easley Kante K   Christendat Dinesh D   Kelley Lawrence L   Provart Nicholas J NJ  

PloS one 20110110 1


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-b  ...[more]

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