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Perl Programming for Medicine and Biology (Series in Biomedical Informatics) (Englisch) Taschenbuch – 6. April 2007


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After explaining the basics of Perl programming, this guide provides Perl scripts for collecting data, organizing data, searching data, or converting data to a desired format. Berman, formerly a pathologist with the U.S. National Cancer Institute, shows how Perl scripts can automate internet queries, parse data from XML documents, facilitate the in

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Review of Berman's Perl Programming 14. Mai 2007
Von G. William Moore - Veröffentlicht auf Amazon.com
Format: Taschenbuch
I reviewed an early draft of this book for the publisher, for which I received no compensation. I was interested to see whether the author responded to some of my suggestions. He did.

The book begins with a preface, which compares biomedical professionals of the 1970s, who couldn't touch-type, against biomedical professionals today, who lack computer programming skills. In the modern biomedical world, every biomedical professional should be able to do some computer programming. It's not enough to leave this skill to information technology professionals, just as keyboard typing is no longer left to clerks. If you are responsible for a large biomedical database, then you must be able to explore it yourself, both to get a first-hand overview of the data, and to better understand how to benefit from the information technologists with whom you work.

Three computer languages satisfy the minimum requirements for biomedical programming: Perl, Python, and Ruby. These languages are: free; fast; and easy to learn. Each provides a large user community; easy environment for correcting errors; large, available library of specialized modules; built-in pattern recognition commands; and yet are capable of large-scale data-analysis for advanced programmers. This list, enumerated by Dr. Berman and many others, should be chiseled in granite, published everywhere, and yelled from the rooftops. Greater compliance with this list would clear out much of the clutter in the chaotic world of biomedical informatics.

"Perl Programming for Medicine and Biology" covers all the areas of major interest to biomedical researchers, clinical scientists, and healthcare students: (1) how to download a cost-free copy of Perl for personal use; (2) simple Perl programs and troubleshooting; (3) file conversions; (4) file reading, one line at-a-time; (5) pattern-matching; (6) assigning data-arrays; (7) building an index; (8) regular expressions (regex); (9) biomedical nomenclatures; (10) searching and sorting; (11) data management; (12) internet and network protocols and data transfer; (13) cryptography, privacy, and data-scrubbing; and (14) related metadata languages (HTML, XML and RDF). For each data analysis area, the book includes sample problems that are accompanied by complete explanations, and by Perl source code that the reader can copy into his/her own computer and try out. The book makes generous use of publicly available datasets and other resources in these examples, so that the reader can perform his/her own computing experiments on data of genuine biomedical interest.

Several features of this book are particularly valuable for the busy professional reader. First, every chapter begins with a Background section, so that the reader gets an immediate overview of the material to be covered. These Background sections are inviting and insightful: why should the average biomedical professional care about a particular area, and what tasks can be carried out in Perl? Second, the Glossary is one of the highlights of the book. The glossary is reminiscent of Dr. Samuel Johnson's Dictionary of the English Language, or Ambrose Bierce's Devil's Dictionary: included for each term is both a solid definition of what it is, and a personal opinion of why one should know or care about the term. Third, the Reference section isn't just a list of citations; each reference is accompanied by a useful commentary. Finally, the Resource section lists copious on-line resources available to the reader for further, in-depth study.

Some impatient readers, like myself, read the beginnings of a few chapters in a technical book, and then go quickly to the last chapter of the book, to see where it all ends, and whether it seems worthwhile to slog through the whole thing. Such readers are in for a pleasant surprise: the background sections, glossary, and references are reasonably comprehensive, and separate the wheat from the chaff among concepts in Information Technology. You can get a good overview of the whole book in a few hours.

The book is written in a breezy style that cuts through all the usual verbal chatter of more academic publications. This is an easy book to pick up and start reading, and hard to put down.
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