Java for Bioinformatics and Biomedical Applications [Hardcover]

Harshawardhan Bal (Author), Johnny Hujol (Author)

Book Description

ISBN-10: 0387372350 | ISBN-13: 978-0387372358 | Publication Date: October 25, 2006 | Edition: 1

Medical science and practice have undergone fundamental changes in the last 5 years, as large-scale genome projects have resulted in the sequencing of a number of important microbial, plant and animal genomes. This book aims to combine industry standard software engineering and design principles with genomics, bioinformatics and cancer research. Rather than an exercise in learning a programming platform, the text focuses on useful analytical tools for the scientific community.

Editorial Reviews

From the Back Cover

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).

Product Details

• Hardcover: 360 pages
• Publisher: Springer; 1 edition (October 25, 2006)
• Language: English
• ISBN-10: 0387372350
• ISBN-13: 978-0387372358
• Product Dimensions: 9.3 x 6.5 x 0.9 inches
• Shipping Weight: 1.6 pounds (View shipping rates and policies)
• Average Customer Review: 4.0 out of 5 stars  See all reviews (2 customer reviews)
• Amazon Best Sellers Rank: #1,876,629 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews

4 of 4 people found the following review helpful:

3.0 out of 5 stars Good resource but probably overpriced, July 12, 2008

By 

Techie Evan - See all my reviews

This review is from: Java for Bioinformatics and Biomedical Applications (Hardcover)

This book is more about how to write Java applications that connect to existing systems (such as BLAST) that Bioinformatics and Biomedical professionals already use, rather than how to write Java versions of those systems, the algorithms used in those systems, or algorithms generally relevant to the mentioned fields. While teaching someone to write Java applications that could send data, request service, and parse then display the results received from the queried systems is useful, such a book probably does not warrant such a high price tag as a book that teaches one how to write Java versions of algorithms useful for the Bioinformatics and Biomedical fields.

2 of 5 people found the following review helpful:

5.0 out of 5 stars Excellent Book, October 24, 2007

By 

Peirce, Charles "Karmayogi" (Pittsburgh, PA, USA) - See all my reviews

This review is from: Java for Bioinformatics and Biomedical Applications (Hardcover)

Finally, a book that introduces bioinformatics using Java. While Perl is great for pattern matching and basic scripting, it is not at all an ideal choice for complex bioinformatics applications at all levels of complexity. Books like this one help train a new generation of bioinformatics experts with a broad-based training in computing (not just Perl scripting).