Mastering Perl for Bioinformatics

Features

• Cover Type: Paperback with 377 pages
• Published by: O'Reilly Media, Inc.
• Edition: 1st Edition June 2003
• Written in: English
• ISBN 10 Number: 0596003072
• ISBN 13 Number: 978-0596003074
• Book Dimensions: 9.1 x 7 x 1 inches
• Weighs: 1.5 pounds

Product Description
Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis.

"Mastering Perl for Bioinformatics" covers the core Perl language and many of its section extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with "Beginning Perl for Bioinformatics," forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics.

The range of topics covered in "Mastering Perl for Bioinformatics" prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as:

Gene finding

String alignment

Methods of data storage and retrieval (SML and databases)

Modeling of networks (graphs and Petri nets)

Graphics (Tk)

Parallelization

Interfacing with other programming languages

Statistics (PDL)

Protein structure determination

Biological models of computation (DNA Computers)

Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their extreme proficiency of this versatile languagewill appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.

About The Author
James Tisdall has worked as a musician, a programmer at Bell Labs (where he programmed for speech research and discovered a formal language for musical rhythm), and as a bioinformaticist at Mercator Genetics in Menlo Park, California, and at Fox Chase Cancer Center in Philadelphia. He has a B.A. in mathematics from the City College of New York and an M.S. in computer science from Columbia University; he is working towards a Ph.D. in computer science at the University of Pennsylvania. In his spare time, Jim teaches computer music at the Settlement Music School in Philadelphia. He is also the author of O'Reilly's Beginning Perl for Bioinformatics.

Reader Reviews
This first half of the book focuses entirely on Object-Oriented(OO) Perl. The second half follows up with a general survey of various perl implementations of particular programming issues involving databasing, cgi, graphics, modules, etc, and BioPerl. This book does a good job of applying Perl in OO for Biology in the first half of the book. In the second half he overviews a few broad topics in bioinformatics; he doesn't go super specific, but its a sufficient overview and for me sparked more interest in understanding how I can use perl to handle my informatics issues. In the first half, the author does an excellent job on detailing the ins and outs of perl references and how to construct complex data structures. Indeed they are a bit strange looking at first, but the author breaks it down really good so pretty much anyone can understand it. For me the most intriguing part of the book was in the second half, which included relational databases, graphics, and bioperl. In particular, the chapter that covers Perl DBI and DBD::mysql was really cool. That secion was very helpful for me because I am familiar with php/mysql, but have not ever used Perl to interact with Mysql before. I especially liked the gif draw aka GD chapter. I had no idea how cool GD is. But moreover how it can be integrated with Perl to generate really cool looking plots. Before this book I always used gnuplot. But Tisdall shows you how to get to work with GD pretty good using basic practical examples. The chapter on BioPerl was especially helpful as well. In particular, he shows you what he did to install the beast. He shows you how to use the CPAN shell and again its really beneficial to read through. It motivated me to pursue other topics in bioperl and how I can use it to query different ncbi databases for example. Overall, the text provided a good overview on OO Perl and on various other topics involving Perl for Bioinformatics in general. I am glad I bought it. It was really very practical/useful - I refer to it all the time actually! Comment | | (Report this)