ePlant and the 3D data display initiative: integrative systems biology on the world wide web.
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&#...
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2011
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oai:doaj.org-article:9b8e3dc32b5748bc8622706f1939309e2021-11-18T07:00:38ZePlant and the 3D data display initiative: integrative systems biology on the world wide web.1932-620310.1371/journal.pone.0015237https://doaj.org/article/9b8e3dc32b5748bc8622706f1939309e2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21249219/?tool=EBIhttps://doaj.org/toc/1932-6203Visualization 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).Geoffrey FucileDavid Di BiaseHardeep NahalGaron LaShokoufeh KhodabandehYani ChenKante EasleyDinesh ChristendatLawrence KelleyNicholas J ProvartPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 1, p e15237 (2011) |
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Medicine R Science Q Geoffrey Fucile David Di Biase Hardeep Nahal Garon La Shokoufeh Khodabandeh Yani Chen Kante Easley Dinesh Christendat Lawrence Kelley Nicholas J Provart ePlant and the 3D data display initiative: integrative systems biology on the world wide web. |
| description |
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). |
| format |
article |
| author |
Geoffrey Fucile David Di Biase Hardeep Nahal Garon La Shokoufeh Khodabandeh Yani Chen Kante Easley Dinesh Christendat Lawrence Kelley Nicholas J Provart |
| author_facet |
Geoffrey Fucile David Di Biase Hardeep Nahal Garon La Shokoufeh Khodabandeh Yani Chen Kante Easley Dinesh Christendat Lawrence Kelley Nicholas J Provart |
| author_sort |
Geoffrey Fucile |
| title |
ePlant and the 3D data display initiative: integrative systems biology on the world wide web. |
| title_short |
ePlant and the 3D data display initiative: integrative systems biology on the world wide web. |
| title_full |
ePlant and the 3D data display initiative: integrative systems biology on the world wide web. |
| title_fullStr |
ePlant and the 3D data display initiative: integrative systems biology on the world wide web. |
| title_full_unstemmed |
ePlant and the 3D data display initiative: integrative systems biology on the world wide web. |
| title_sort |
eplant and the 3d data display initiative: integrative systems biology on the world wide web. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2011 |
| url |
https://doaj.org/article/9b8e3dc32b5748bc8622706f1939309e |
| work_keys_str_mv |
AT geoffreyfucile eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb AT daviddibiase eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb AT hardeepnahal eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb AT garonla eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb AT shokoufehkhodabandeh eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb AT yanichen eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb AT kanteeasley eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb AT dineshchristendat eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb AT lawrencekelley eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb AT nicholasjprovart eplantandthe3ddatadisplayinitiativeintegrativesystemsbiologyontheworldwideweb |
| _version_ |
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