This book examines the tools being developed to meet the goal of eliminating suffering and death from cancer by 2015. It focuses on creating and integrating practical, useful tools for the scientific community in the context of real-life, real-value biomedical problems. From a software perspective, a functional approach is used to teach the Java platform and its features for enterprise-level application development. Under this approach, the various syntactical and operative elements of the language are taught in the context of definable research problems that enable the user to relate how the different parts of the language fit together. The book illustrates how individual bioinformatics applications can be stitched together into a pipeline so that users can direct the output of one tool to perform further analysis. All examples are derived from practical problems faced in biomedical/clinical data retrieval and analysis during routine bioinformatics and cancer research.