Title |
ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web
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Published in |
PLOS ONE, January 2011
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DOI | 10.1371/journal.pone.0015237 |
Pubmed ID | |
Authors |
Geoffrey Fucile, David Di Biase, Hardeep Nahal, Garon La, Shokoufeh Khodabandeh, Yani Chen, Kante Easley, Dinesh Christendat, Lawrence Kelley, Nicholas J. Provart |
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). |
X Demographics
Geographical breakdown
Country | Count | As % |
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Unknown | 6 | 100% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 3 | 50% |
Scientists | 3 | 50% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Germany | 3 | 3% |
United Kingdom | 3 | 3% |
United States | 2 | 2% |
Chile | 1 | 1% |
Australia | 1 | 1% |
Canada | 1 | 1% |
Netherlands | 1 | 1% |
Slovenia | 1 | 1% |
Luxembourg | 1 | 1% |
Other | 0 | 0% |
Unknown | 86 | 86% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 21 | 21% |
Student > Ph. D. Student | 16 | 16% |
Student > Master | 16 | 16% |
Student > Bachelor | 14 | 14% |
Other | 10 | 10% |
Other | 15 | 15% |
Unknown | 8 | 8% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 56 | 56% |
Biochemistry, Genetics and Molecular Biology | 19 | 19% |
Computer Science | 6 | 6% |
Chemistry | 3 | 3% |
Engineering | 2 | 2% |
Other | 5 | 5% |
Unknown | 9 | 9% |