[PDF] The Programming Language Perl For Biologists eBook
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Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusable and maintainable scripts that spare the rote repetition of code.
With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.The book covers: Programming basics and working with DNA sequences and strings Debugging your code Simulating gene mutations using random number generators Regular expressions and finding motifs in data Arrays, hashes, and relational databases Regular expressions and restriction maps Using Perl to parse PDB records, annotations in GenBank, and BLAST output
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.
Document from the year 2015 in the subject Computer Science - Programming, , course: Bioinformatics, language: English, abstract: This book is designed to be useful in theory and practical classes of UG and PG bioinformatics students. Moreover, it will be beneficial to other persons who wish to learn Perl programming language. To explain the Perl jargon, program based approach is used throughout the book. Important points are provided at the end of each chapter along with questions to test the skills. Solutions of find errors are provided at the end of the book. All the programs are tested on Windows 7 with Perl v5.18.1. The book is divided into thirteen chapters which gradually take a reader from basic to advanced Perl. Although the book has been drafted with utmost care, it is quite possible that some errors/misprints might have crept in the book. I request the readers for their valuable suggestions and comments for further improvement of the book.
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.
-Teaches the reader how to use Unix, which is the key to basic computing and allows the most flexibility for bioinformatics applications -Written specifically with the needs of molecular biologists in mind -Easy to follow, written for beginners with no computational knowledge -Includes examples from biological data analysis -Can be use either for self-teaching or in courses
Emphasizing the search for patterns within and between biological sequences, trees, and graphs, Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic
In its first five years of existence, The Perl Journal ran 247 articles by over 120 authors. Every serious Perl programmer subscribed to it, and every notable Perl guru jumped at the opportunity to write for it. TPJ explained critical topics such as regular expressions, databases, and object-oriented programming, and demonstrated Perl's utility for fields as diverse as astronomy, biology, economics, AI, and games. The magazine gave birth to both the Obfuscated Perl Contest and the Perl Poetry contest, and remains a proud and timeless achievement of Perl during one of its most exciting periods of development.Computer Science and Perl Programming is the first volume of The Best of the Perl Journal, compiled and re-edited by the original editor and publisher of The Perl Journal, Jon Orwant. In this series, we've taken the very best (and still relevant) articles published in TPJ over its 5 years of publication and immortalized them into three volumes. This volume has 70 articles devoted to hard-core computer science, advanced programming techniques, and the underlying mechanics of Perl.Here's a sample of what you'll find inside: Jeffrey Friedl on Understanding Regexes Mark Jason Dominus on optimizing your Perl programs with Memoization Damian Conway on Parsing Tim Meadowcroft on integrating Perl with Microsoft Office Larry Wall on the culture of Perl Written by 41 of the most prominent and prolific members of the closely-knit Perl community, this anthology does what no other book can, giving unique insight into the real-life applications and powerful techniques made possible by Perl.Other books tell you how to use Perl, but this book goes far beyond that: it shows you not only how to use Perl, but what you could use Perl for. This is more than just The Best of the Perl Journal -- in many ways, this is the best of Perl.
Too often, healthcare workers are led to believe that medical informatics is a complex field that can only be mastered by teams of professional programmers. This is simply not the case. With just a few dozen simple algorithms, easily implemented with open source programming languages, you can fully utilize the medical information contained in clini