Python for Bioinformatics (Chapman & Hall/CRC Mathematical and Computational Biology) - Softcover

Bassi, Sebastian

Softcover

ISBN 10: 1584889292 ISBN 13: 9781584889298

Publisher: Chapman and Hall/CRC, 2009

Synopsis

Programming knowledge is often necessary for finding a solution to a biological problem. Based on the author’s experience working for an agricultural biotechnology company, Python for Bioinformatics helps scientists solve their biological problems by helping them understand the basics of programming. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language.

The book begins with a very basic introduction that teaches the principles of programming. It then introduces the Biopython package, which can be useful in solving life science problems. The next section covers sophisticated tools for bioinformatics, including relational database management systems and XML. The last part illustrates applications with source code, such as sequence manipulation, filtering vector contamination, calculating DNA melting temperature, parsing a genbank file, inferring splicing sites, and more. The appendices provide a wealth of supplementary information, including instructions for installing Python and Biopython and a Python language and style guide.

By incorporating examples in biology as well as code fragments throughout, the author places a special emphasis on practice, encouraging readers to experiment with the code. He shows how to use Python and the Biopython package for building web applications, genomic annotation, data manipulation, and countless other applications.

About this title

Review:

The book will be helpful for its intended audience. Numerous code fragments in the book will be beneficial for biologists who are unfamiliar with programming. Readers can try out, test, and modify the code to suit their needs. ... a useful introduction to the topic. The style of presentation is good, and the code samples are worthwhile. ... I strongly recommend this book as a useful reference for computational biologists, programmers, and bioinformatics specialists (students as well as researchers).
―Computing Reviews, November 2011

Synopsis:

Python is a popular computer language used in a wide range of applications, from peer-to-peer software to dynamic generated web pages. "Python for Bioinformatics" provides an accessible introduction to both the Python and BioPython languages. The book addresses advanced topics, from web applications and XML to databases and version control. In addition to useful appendices with reference material on biological file formats, the book presents commented working code and new programming techniques, such as error handling, functions, and modules. It also includes source code as well as a companion CD-ROM that contains a virtual machine with complete installation and a working web server.

About this edition

• Publisher: Chapman and Hall/CRC
• Publication date: 2009
• ISBN 10: 1584889292
• ISBN 13: 9781584889298
• Binding: Paperback
• Edition number: 1
• Number of pages: 587