PNNL

Abstract

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 bio-informatics. The architecture integrates a J2EE 3-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.