Java for Bioinformatics and Biomedical Applications describes the work
of the U.S. National Cancer Institute (NCI, National Institutes of
Health, U.S. Department of Health and Human Services) and a large number
of cancer centers across the U.S. under the caBIG™ (cancer Biomedical
Informatics Grid) program, as well as standard bioinformatics
applications. The goal of NCI caBIG™ is to create a standards based,
interoperable network of individuals, applications and data to enhance
the pace of cancer research. CaBIG™ uses J2EE and open source standards
for all software development work.
This book examines the tools and
technologies being developed under caBIG™ to meet the goal of
eliminating suffering and death from cancer by 2015 as formulated by the
former NCI Director, Dr. Andrew von Eschenbach.In doing so, it provides
a vignette into the efforts of thousands of people – molecular
biologists, medical practitioners, software developers, to name a few -
across the country to bring the promise of translational research to
individuals with cancer.
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 and any
software libraries that have been used (for example, BioJava, Apache,
etc.) are taught not in isolation but in the context of discrete
definable research problems that enable the user to relate how the
different parts of the language fit together in the big picture. All
examples are derived from practical problems faced in
biomedical/clinical data retrieval and analysis during routine
bioinformatics and cancer research. Further, the book illustrates how
individual bioinformatics applications (such as BLAST and Genscan) can
be stitched together into a pipeline so that users can direct the output
of one tool (for example, gene predictions using Genscan) to perform
further analysis (say, homology searching using BLAST)
