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Proceedings Paper

Web-based hydrodynamics computing
Author(s): Alan Shimoide; Luping Lin; Tracie-Lynne Hong; Ilmi Yoon; Sergio Ramiro Aragon
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Paper Abstract

Proteins are long chains of amino acids that have a definite 3-d conformation and the shape of each protein is vital to its function. Since proteins are normally in solution, hydrodynamics (describes the movement of solvent around a protein as a function of shape and size of the molecule) can be used to probe the size and shape of proteins compared to those derived from X-ray crystallography. The computation chain needed for these hydrodynamics calculations consists of several separate programs by different authors on various platforms and often requires 3D visualizations of intermediate results. Due to the complexity, tools developed by a particular research group are not readily available for use by other groups, nor even by the non-experts within the same research group. To alleviate this situation, and to foment the easy and wide distribution of computational tools worldwide, we developed a web based interactive computational environment (WICE) including interactive 3D visualization that can be used with any web browser. Java based technologies were used to provide a platform neutral, user-friendly solution. Java Server Pages (JSP), Java Servlets, Java Beans, JOGL (Java bindings for OpenGL), and Java Web Start were used to create a solution that simplifies the computing chain for the user allowing the user to focus on their scientific research. WICE hides complexity from the user and provides robust and sophisticated visualization through a web browser.

Paper Details

Date Published: 17 January 2005
PDF: 8 pages
Proc. SPIE 5670, Internet Imaging VI, (17 January 2005); doi: 10.1117/12.586208
Show Author Affiliations
Alan Shimoide, San Francisco State Univ. (United States)
Luping Lin, San Francisco State Univ. (United States)
Tracie-Lynne Hong, San Francisco State Univ. (United States)
Ilmi Yoon, San Francisco State Univ. (United States)
Sergio Ramiro Aragon, San Francisco State Univ. (United States)

Published in SPIE Proceedings Vol. 5670:
Internet Imaging VI
Simone Santini; Raimondo Schettini; Theo Gevers, Editor(s)

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