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e-Science 2008 4th IEEE International Conference on e-Science

Main Conference Sessions

An Extensible, Scalable Architecture for Managing Bioinformatics Data and Analysis


  • Anuj Shah, PNNL
  • Mudita Singhal, Pacific Northwest National Laboratory
  • Tara Gibson, Pacific Northwest National Laboratory
  • Chandrika Sivaramakrishnan, Pacific Northwest National Laboratory
  • Katrina Waters, Pacific Northwest National Laboratory
  • Ian Gorton, Pacific Northwest National Laboratory


Systems biology research demands the availability of tools and technologies that span a comprehensive range of capabilities. These include data generation, transfer, integration, processing for analysis, interpretation, and knowledge extraction. To address these capabilities, we have created the Bioinformatics Resource Manager (BRM), which is a scalable, flexible, and easy-to-use tool for biologists to undertake complex analyses. This paper describes the underlying software architecture of the BRM that integrates multiple commodity platforms to provide a highly extensible and scalable software infrastructure for bioinformatics. The architecture integrates a J2EE three-tier application with an archival data management system Experimental Database Management Systems (EDMS), the GAGGLE framework for desktop tool integration, and the MeDICi Integration Framework (MIF) for high-throughput data analysis workflows. This architecture facilitates a systems biology software solution that enables the entire spectrum of scientific activities, from experimental data access to high-throughput processing and analysis of data for biologists and experimental scientists.

Date and Time

Thursday, December 11, 10:45 a.m. to 11:15 a.m.

Room Number


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