Toward building grid applications in bioinformatics

Xiujun Gong, Kensuke Nakamura, Kei Yura, Nobuhiro Go

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

In silico bioinformatics experiments involve integration of and access to computational tools and biological databases. The emerging grid computing technologies enable bioinformatics scientists to conduct their researches in a virtual laboratory, in which they share public databases, computational tools as well as their analysis workflows. However, the development of grid applications is still a nightmare for general bioinformatics scientists, due to the lack of grid programming environments, standards and high-level services. Here, we present a system, which we named Bioinformatics: Ask Any Questions (BAAQ), to automate this development procedure as much as possible. BAAQ allows scientists to store and manage remote biological data and program resources, to build analysis workflows that integrate these resources seamlessly, and to discover knowledge from available resources. This paper addresses two issues in building grid applications in bioinformatics: how to smoothly compose an analysis workflow using heterogeneous resources and how to efficiently discover and re-use available resources in the grid community. Correspondingly an intelligent grid programming environment and an active solution recommendation service are proposed. Finally, we present a case study applying BAAQ to a bioinformatics problem.

Original languageEnglish
Title of host publicationACSW Frontiers 2006 - Proc. of the Fourth Australasian Symposium on Grid Computing and e-Research, AusGrid 2006 and the Fourth Australasian Information Security Workshop (Network Security), AISW 2006
Pages17-24
Number of pages8
Publication statusPublished - 2006 Dec 1
Externally publishedYes
Event4th Australasian Symposium on Grid Computing and e-Research, AusGrid 2006 and 4th Australasian Information Security Workshop (Network Security), AISW 2006 - Hobart, TAS, Australia
Duration: 2006 Jan 162006 Jan 19

Publication series

NameConferences in Research and Practice in Information Technology Series
Volume54
ISSN (Print)1445-1336

Other

Other4th Australasian Symposium on Grid Computing and e-Research, AusGrid 2006 and 4th Australasian Information Security Workshop (Network Security), AISW 2006
CountryAustralia
CityHobart, TAS
Period06/1/1606/1/19

Keywords

  • Active solution recommendation
  • Bioinformatics
  • Grid application
  • Task mapping editor

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Computer Science Applications
  • Hardware and Architecture
  • Information Systems
  • Software

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  • Cite this

    Gong, X., Nakamura, K., Yura, K., & Go, N. (2006). Toward building grid applications in bioinformatics. In ACSW Frontiers 2006 - Proc. of the Fourth Australasian Symposium on Grid Computing and e-Research, AusGrid 2006 and the Fourth Australasian Information Security Workshop (Network Security), AISW 2006 (pp. 17-24). (Conferences in Research and Practice in Information Technology Series; Vol. 54).