Grid computing and bioinformatics development. A case study on the Oryza sativa (rice) genome

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.