Toward Building Grid Applications in Bioinformatics

Gong, X., Nakamura, K., Yura, K. and Go, N.

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.

Cite as: Gong, X., Nakamura, K., Yura, K. and Go, N. (2006). Toward Building Grid Applications in Bioinformatics. In Proc. Fourth Australasian Symposium on Grid Computing and e-Research (AusGrid 2006), Hobart, Australia. CRPIT, 54. Buyya, R. and Ma, T., Eds. ACS. 17-23.

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