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

PLoS One. 2011 Jan 10;6(1):e15237. doi: 10.1371/journal.pone.0015237.


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).

MeSH terms

  • Arabidopsis / chemistry*
  • Computer Graphics
  • Data Display
  • Imaging, Three-Dimensional / methods*
  • Internet*
  • Plants / chemistry
  • Polymorphism, Single Nucleotide
  • Protein Conformation
  • Systems Biology / methods*