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Mastering Perl for Bioinformatics


Mastering Perl for Bioinformatics Cover


Synopses & Reviews

Publisher Comments:

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 module 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 mastery of this versatile language will 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.

Book News Annotation:

A companion volume to Beginning Perl for Bioinformatics, this guide covers advanced topics in Perl programming and relates them to biological research techniques. Among the topics discussed are modular and object-oriented programming, complex data structures, graphic and on-line presentations, and the Bioperl library of modules. Tisdall is a graduate student in computer science at the University of Pennsylvania.
Annotation 2004 Book News, Inc., Portland, OR (booknews.com)


This book, along with "Beginning Perl for Bioinformatics, " forms a basic course in Perl programming. It covers core Perl language and many of its module extensions.

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.

Table of Contents

  • Foreword
  • Preface
  • Object-Oriented Programming in Perl
    • Chapter 1: Modular Programming with Perl
    • Chapter 2: Data Structures and String Algorithms
    • Chapter 3: Object-Oriented Programming in Perl
    • Chapter 4: Sequence Formats and Inheritance
    • Chapter 5: A Class for Restriction Enzymes
  • Perl and Bioinformatics
    • Chapter 6: Perl and Relational Databases
    • Chapter 7: Perl and the Web
    • Chapter 8: Perl and Graphics
    • Chapter 9: Introduction to Bioperl
  • Appendixes
    • Perl Summary
    • Installing Perl
  • Colophon

Product Details

Stein, Lincoln D.
O'Reilly Media
Foreword by:
Stein, Lincoln D.
Stein, Lincoln D.
Tisdall, James
Tisdall, James D.
Sebastopol, Calif.
Programming Languages - CGI, Javascript, Perl, VBScript
Programming Languages - Perl
Perl (computer program language)
CourseSmart Subject Description
Edition Description:
Print PDF
Series Volume:
no. 23
Publication Date:
9.19 x 7 x 0.95 in 1.36 lb

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Related Subjects

Computers and Internet » Computer Languages » Perl
Computers and Internet » Computers Reference » Bioinformatics
Computers and Internet » Operating Systems » General
Science and Mathematics » Mathematics » Biological Sciences

Mastering Perl for Bioinformatics New Trade Paper
0 stars - 0 reviews
$49.99 In Stock
Product details 400 pages O'Reilly & Associates - English 9780596003074 Reviews:
"Synopsis" by ,
This book, along with "Beginning Perl for Bioinformatics, " forms a basic course in Perl programming. It covers core Perl language and many of its module extensions.
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