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:
Methods of data storage and retrieval (SML and databases)
Modeling of networks (graphs and Petri nets)
Interfacing with other programming languages
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.
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.
Our look is the result of reader comments, our own experimentation, and feedback from distribution channels. Distinctive covers complement our distinctive approach to technical topics, breathing personality and life into potentially dry subjects. The animal on the cover of Mastering Perl for Bioinformatics is a North American bullfrog (Rana catesbeiana). It is native to the central and eastern United States, as well as southern portions of Canada. However, this bullfrog has since been introduced as far away from its native habitat as Asia, Europe, and Hawaii.The North American bullfrog is the largest true frog in North America and can weigh over a pound. It can grow up to eight inches in length, although the norm is four to five inches. The gender of the bullfrog is ascertained by comparing the size of the external ear (the tympanum) relative to the size of the eye.Bullfrogs are predators and also are cannibalistic. Their role in the environment is to control the population of insect pests as well as snakes and mice. In fact, the zeal of the North American bullfrog threatens to drive other frog species to extinction.The generic name (rana) comes from the Latin for frog, while the species name (catesbeiana) honors an English naturalist. In the 18th century, Mark Catesby (1683--1749) produced the authoritative and exhaustive record of the flora and fauna found in the New World. Wealthy patrons in England eagerly received Catesby's regular shipments of specimens, including plants, birds, reptiles, insects, and frogs. Mary Anne Weeks Mayo was the production editor and copyeditor, and Marlowe Shaeffer was the proofreader, for Mastering Perl for Bioinformatics. Jane Ellin and Colleen Gorman provided quality control. Marlowe Shaeffer, Mary Agner, and James Quill provided production assistance. John Bickelhaupt wrote the index.Ellie Volckhausen designed the cover of this book, based on a series design by Edie Freedman. The cover image is a 19th-century engraving from the Dover Pictorial Archive. Emma Colby produced the cover layout with QuarkXPress 4.1 using Adobe's ITC Garamond font.David Futato designed the interior layout. This book was converted by Andrew Savikas to FrameMaker 5.5.6 with a format conversion tool created by Erik Ray, Jason McIntosh, Neil Walls, and Mike Sierra that uses Perl and XML technologies. The text font is Linotype Birka; the heading font is Adobe Myriad Condensed; and the code font is LucasFont's TheSans Mono Condensed. The illustrations that appear in the book were produced by Robert Romano and Jessamyn Read using Macromedia FreeHand 9 and Adobe Photoshop 6. The tip and warning icons were drawn by Christopher Bing. This colophon was written by Reg Aubry.
Comments about oreilly Mastering Perl for Bioinformatics:
It is a great second book to beginning perl for bioinformatics. I have only scanned the parts that were interesting to me, but I found mostly what I was looking for. This book goes into practical applications like perl/mysql. perl/web and perl/bioperl and it spends quite a bit of time on object oriented perl. There are very few books out there that explore all these topics. (If Oreilly is reading this. I would like the solution to exercise 7.7 pg 270 chapter 7.) An object oriented database using perl on the web is a personal goal of mine. Also, Oreilly should put up the answers to all the excercises, just like in beginning perl. They were very helpful in learning the material.
Comments about oreilly Mastering Perl for Bioinformatics:
The only reason I gave this a Very Good instead of Definitive is that I bought the book this afternoon and have only made it through the first 70 pages - so I can't say what my opinion on later chapters will be...but so far, so excellent! This is a great book. It contains the information key to being able to use Perl well for bioinformatics, and has really good listings for further reading and documentation. The only negative is that I can't seem to find any sample answers for the exercises. If sample answers were easily available, this book would have had "Definitive" even after only 70 pages.