Published online 9 August 2004
Nucleic Acids Research, Vol. 32 No. 14 © Oxford University Press 2004; all rights reserved
BOD: a customizable bioinformatics on demand system accommodating multiple steps and parallel tasks
1 Department of Biological Science and Biotechnology, 2 Institutes of Biomedicine, 3 Department of Computer Science and Technology and 4 Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, People's Republic of China
* To whom correspondence should be addressed. Tel: +86 10 62792997; Fax: +86 10 62792995; Email: frankliu{at}mail.tsinghua.edu.cn
Received March 10, 2004; Revised May 20, 2004; Accepted July 21, 2004
The integration of bioinformatics resources worldwide is one of the major concerns of the biological community. We herein established the BOD (Bioinformatics on demand) system to use Grid computing technology to set up a virtual workbench via a web-based platform, to assist researchers performing customized comprehensive bioinformatics work. Users will be able to submit entire search queries and computation requests, e.g. from DNA assembly to gene prediction and finally protein folding, from their own office using the BOD end-user web interface. The BOD web portal parses the user's job requests into steps, each of which may contain multiple tasks in parallel. The BOD task scheduler takes an entire task, or splits it into multiple subtasks, and dispatches the task or subtasks proportionally to computation node(s) associated with the BOD portal server. A node may further split and distribute an assigned task to its sub-nodes using a similar strategy. In the end, the BOD portal server receives and collates all results and returns them to the user. BOD uses a pipeline model to describe the user's submitted data and stores the job requests/status/results in a relational database. In addition, an XML criterion is established to capture task computation program details.