Bioinformatics Programming Using Python: Practical Programming for Biological Data

Model, Mitchell

ISBN 10: 059615450X / ISBN 13: 9780596154509

Published by O'Reilly Media, 2010

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Synopsis:

Powerful, flexible, and easy to use, Python is an ideal language for building software tools and applications for life science research and development. This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. In a short time, you'll be using sophisticated techniques and Python modules that are particularly effective for bioinformatics programming.

Bioinformatics Programming Using Python is perfect for anyone involved with bioinformatics -- researchers, support staff, students, and software developers interested in writing bioinformatics applications. You'll find it useful whether you already use Python, write code in another language, or have no programming experience at all. It's an excellent self-instruction tool, as well as a handy reference when facing the challenges of real-life programming tasks.

• Become familiar with Python's fundamentals, including ways to develop simple applications
• Learn how to use Python modules for pattern matching, structured text processing, online data retrieval, and database access
• Discover generalized patterns that cover a large proportion of how Python code is used in bioinformatics
• Learn how to apply the principles and techniques of object-oriented programming
• Benefit from the "tips and traps" section in each chapter

About the Author: Dr. Mitchell L Model is a computer scientist with a background in philosophy. He specializes in object technology, knowledge representation, user interfaces, distributed computing, and software development and is an inveterate software tool builder. Mitchell held academic appointments at Brown and Brandeis Universities and worked at a number of early-phase startup companies. For much of his career he has been an independent consultant, providing training, mentoring, and support to software development groups learning to use new technologies and practices. He has written and taught many professional programming and technology courses. Mitchell is also the author of one of the first C++-based data structure books -- Data Structures, Data Abstraction: A Contemporary Introduction Using C++, published in 1994 by Prentice-Hall. Since 1993 Mitchell has been working primarily in bioinformatics, becoming captivated by the complexities of the biological phenomena which it addresses. He was the senior technologist in Millennium Pharmaceutical's large bioinformatics department from 1993 through 2001, playing a major role in growing the department and guiding the development of its diverse software portfolio. He was a Visiting Associate Professor with Wesleyan University's Integrative Genomics group. More recently he has been teaching courses in Northeastern University's Professional Masters in Bioinformatics program. Mitchell's first programming experience was writing machine code for an IBM 1620 in 1966, which ignited a lifelong fascination with computing. He traces his interest in data structures and his visual style of thinking about them to the Tinkertoys of his childhood. Lisp was Mitchell's first professional home, Smalltalk his second. He spent long periods of exile in C++ before returning to Smalltalk in the early 1990's. In the last ten years he has worked extensively in Java, JavaScript, and Python, as well as a number of web and database technologies. He particularly appreciates the way Python elegantly combines an easy to read and write syntax, the functional style of Lisp, the object-oriented purity of Smalltalk, well-designed statement constructs, a wonderful library of well-documented modules, and a terrific user community. Mitchell's personal interests include jazz, photography, typography, design, geology, and a host of more obscure scientific subjects. His commitment is to teaching, always seeking new ways to effectively communicate the conceptual beauty of computer science. What gives him the greatest satisfaction is coaching students and professionals in the art of software development to enable them to work more effectively and creatively.

Bibliographic Details

Title: Bioinformatics Programming Using Python: ...
Publisher: O'Reilly Media
Publication Date: 2010
Binding: paperback
Condition: Very Good