XML for Bioinformatics [Hardcover]

Ethan Cerami (Author)

Book Description

ISBN-10: 0387230289 | ISBN-13: 978-0387230283 | Publication Date: March 15, 2005 | Edition: 1

XML for Bioinformatics aims to provide biologists, software engineers, and bioinformatics professionals with a comprehensive introduction to XML and current XML applications in bioinformatics. The book will assume no background in XML, and take readers from basic to intermediate XML concepts. Core topics will include: fundamentals of XML, creating XML grammars, web services via SOAP, and parsing XML documents in Perl and Java.

Editorial Reviews

From the Back Cover

XML, or Extensible Markup Language, is rapidly becoming a critical tool in bioinformatics and biological data exchange. XML is currently used to represent a diverse set of biological data, from nucleotide and protein sequences to protein-protein interactions and signal transduction pathways. XML is also used in a wide array of bioinformatics applications, including stand-alone applications, federated database systems, distributed applications, and web services.

The goal of XML for Bioinformatics is to provide a solid introduction to the emerging use of XML in the field of bioinformatics. It assumes no prior knowledge of XML, and illustrates all core concepts with specific bioinformatics examples and case studies. Core XML concepts include: fundamentals of XML, Document Type Definitions (DTDs), XML Namespaces, XML Schema, XML parsing in Perl and Java, web services and SOAP. Examples and case studies are drawn from a wide range of bioinformatics applications, including the Bioinformatic Sequence Markup Language (BSML), NCBI E-Fetch, the Distributed Annotation System (DAS), and the National Cancer Institute Cancer Bioinformatics Infrastructure Objects (caBIO) project.

A companion web site, available at: http://www.xmlbio.org/, provides complete access to all examples in the book.

About the Author

Ethan Cerami is Senior Software Engineer at the Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY. Since 1997 he has also been a member of the Adjunct Faculty in Computer Science at New York University.

Product Details

• Hardcover: 319 pages
• Publisher: Springer; 1 edition (March 15, 2005)
• Language: English
• ISBN-10: 0387230289
• ISBN-13: 978-0387230283
• Product Dimensions: 9.3 x 6.9 x 0.8 inches
• Shipping Weight: 1.4 pounds (View shipping rates and policies)
• Average Customer Review: 4.0 out of 5 stars  See all reviews (1 customer review)
• Amazon Best Sellers Rank: #1,240,745 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:

4.0 out of 5 stars Nice Brief Overview, June 25, 2006

By 

Elliot Kleiman "technophilic" (San Diego, CA United States) - See all my reviews
(VINE VOICE)    (REAL NAME)   

This review is from: XML for Bioinformatics (Hardcover)

This is a nice brief introductory overview of xml in general and its implementations in biological research. The thing I liked about it was it was not too intensive on any topic, and it provided a lot of useful resources both online and literature-wise for me to look up for more information.

It definitely sparked my interest in certain areas of xml and how I may apply it towards my research. One of the things that I really liked was that the author always spelled out all the mentioned acronyms (thank you, finally someone exists out there that does this!). In addition, I also appreciated that the author did not get too bogged down in anyone topic resulting in a bible-like introductory work - thank you again for that. As a result of this I was literally able to read it in few days and determine the usefulness of this technology called `xml`; and without having to read 1k pages to determine this. In this case 'Less is sometimes definitely more'.

My favorite chapter was the one covering Web Services and now understand the basic concepts behind XML-RPC, REST, and SOAP.
The only reason I give it 4 stars is a.)its pricey for a grad student and b.)I use Perl, and he has a two or so chapters using Java to parse xml. So those chapters were not useful to me. But hey you can't please everyone :)

Overall, it helped me recognize just what xml is, how it may be used, who uses it (esp. in biology) - and how they use it, and a list of references for more info. Definitely a good little book to check out for basic conceptual understanding. I want to say its almost a survey, but its actually a little more than that.