Bias: Bioinformatics integrated application software, design and implementation

This thesis introduces a development platform especially tailored to Bioinformatics research and software development. Bias (Bioinformatics Integrated Application Software) provides the tools necessary for carrying out integrative Bioinformatics research. It follows an object-relational strategy for providing persistent objects, allows third-party tools to be easily incorporated within the system, and it supports standards and data-exchange protocols common to Bioinformatics. It is not enough to present the architecture of Bias without showing a working example for which exploits all composites of Bias, thus demonstrating the utility of Bias. We present the architecture of Bias and provide a full example based on the work of Segal et al. for finding transcriptional regulatory relationships. Bias is an OpenSource project and is freely available to all interested users.