Grid computing and bioinformatics development. A case study
on the Oryza sativa (rice) genome*
Wasinee Rungsarityotin, Noppadon Khiripet, Chularat Tanpraset, and
Royol Chitradon**
National Electronics and Computer Technology Center,
National Science and Technology Development Agency, 112 Paholyothin
Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
Abstract: The bioinformatics research area is now
faced with a mountain of ever-increasing and distributed information.
For example, finding a single gene of the Oryza sativa (rice) genome
one must spend weeks, if not months, wandering through approximately
40 million base pairs. These data are scattered in many data repositories.
Thus, not only do we need an efficient tool to visualize and analyze
DNA data, but the integration and exchange of information on a particular
gene or coding regions from different international collaborative databases
needs to be done in a careful, but robust manner as well. This research
suggests a feasible means to overcome these problems by employing two
main technologies. To support the exchange and communication between
several sources of data, the grid database technology will be employed
on the fast Internet2 backbone. Then, XML-based DNA data will be transported
between collaborative sources for further analysis and representation.
A preliminary version of our Web-based viewer for the XML data of the
Oryza sativa genome is presented to illustrate the idea.
* Plenary lecture presented at the International Conference
on Bioinformatics 2002: North-South Networking, Bangkok, Thailand, 6-8
February 2002. Other presentations are presented in this issue, pp.
881-914.
** Corresponding author.
Page last modified 18 July 2002.
Copyright © 2002 International Union of Pure and Applied Chemistry.
Questions or comments about IUPAC, please contact, the Secretariat.
Questions regarding the website, please contact web
manager.
