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Systems biology research demands the availability of tools and technologies that span a comprehensive range of computational capabilities, including data management, transfer, processing, integration, and interpretation. To address these needs, we have created the Bioinformatics Resource Manager (BRM), 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 3-tier application with an archival Experimental Data Management System, the GAGGLE framework for desktop tool integration, and the MeDICi IntegrationFramework 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.