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Perl Programming for Medicine and Biology

Author(s): Jules J. Berman, PhD, MD
  • ISBN-13: 9780763743338
  • ISBN-10:076374333X
  • Paperback    407 pages      © 2007
Price: $147.95 US List
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Written for biomedical professionals and hospital practitioners interested in creating their own programs, Perl Programming for Medicine and Biology, discusses and reviews biomedical data resources, data standards, data organization, medicolegal and ethical conduct for data miners, and grants-related data sharing responsibilities. It teaches readers the basic Perl programming skills necessary for collecting, analyzing, and distributing biomedical data and provides solutions to in-depth problems that face researchers and healthcare professionals.


Non-technical “Background” sections open each chapter to help non-programmers easily comprehend programming procedures.   Explanations are provided for the biomedical issues underlying the Perl scripts that follow, and examples of real-world implementation are provided.  Perl Programming for Medicine and Biology will show you how to transform, merge, and examine large and complex databases with ease.


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Features & Benefits

Provides solutions to in-depth problems that face life science researchers and healthcare professionals.

Detailed discussions on biomedical data resources, data standards, data organization, medicolegal and ethical conduct for data miners, and grants-related data sharing responsibilities.

Each chapter begins with a non-technical "Background" section that explains the biomedical issues underlying the Perl scripts that follow.

Basic Perl Programming is covered in Chapters 1 - 3.

Chapter 20 contains every citation within the book with its relevance to biomedicine explained.

Chapters are organized by increasing complexity of biomedical issues, while Perl techniques maintain the same degree of difficulty throughout.

All scripts shown in this book can be downloaded from the Jones and Bartlett website.

Bug notices and corrections are updated as needed.

An extensive Glossary includes Perl commands, demonstration codes, and detailed explanations of specialized terms.

Applicable Courses

This text is appropriate for Biomedical and Hospital professionals, graduate students in Biomedical Informatics Programs, advanced undergraduates in computer science, bioinformatics, or biomedical programs, and researchers.

1. Introduction to Perl Programming
2. Using Perl Modules and Applying Some Fundamental Commands
3. File/Directory Operations and Text Transformations with Regular Expressions
4. Indexing Text
5. Autocoding Biomedical Data with Nomenclatures
6. Searching and Mining Data
7. Cryptography and Deidentification
8. Scrubbing Data
9. Finding and Exchanging Data Through the Worldwide Web
10. Creating, Parsing, and Transforming XML
11. Metadata, Ontologies, and the Meaning of Everything
12. Mathematical Functions
13. Statistics and Epidemiology
14. Modeling Biological and Medical Systems
15. Bioinformatics
16. Network Computing
17. A Quick Peek at Object-Oriented Programming
18. Use-Case: A Digital Image Specification in RDF
19. Use-Case: Data Mining OMIM (Online Mendelian Inheritance in Man)
20. References (Commented)
21. Appendix
22. Glossary
23. List of Perl Scripts
24. Index
25. Nota Bene

Jules J. Berman, PhD, MD

Jules Berman received his bachelor's degrees in Mathematics and Earth and Planetary Sciences from Massachusetts Institute of Technology, his Ph.D. from Temple University, and his M.D. from the University of Miami.  He received post-doctoral training in the Laboratory of Experimental Pathology in the National Cancer Institute, at NIH.  He received residency training at the George Washington University Medical Center and is board certified in anatomic pathology and in cytopathology.  He served as the chief of anatomic pathology at the VA Hospital in Baltimore where he held adjunct appointments at Johns Hopkins Medical Center and the University of Maryland Medical Center.  From 1998 to 2005 he was program director for Pathology Informatics in the Cancer Diagnosis Program at the National Cancer Institute.  Jules Berman has first-authored more than 100 publications.  He is now a free-lance author and the past President of the Association for Pathology Informatics.



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Complete Perl Scripts


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Complete Perl Scripts