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Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics

Author: James Tisdall

Publisher: "O'Reilly Media, Inc."

ISBN: 9780596550479

Category: Computers

Page: 386

View: 781

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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

Beginning Perl

Beginning Perl

Author: James Lee

Publisher: Apress

ISBN: 9781430227946

Category: Computers

Page: 464

View: 574

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This is a book for those of us who believed that we didn’t need to learn Perl, and now we know it is more ubiquitous than ever. Perl is extremely flexible and powerful, and it isn’t afraid of Web 2.0 or the cloud. Originally touted as the duct tape of the Internet, Perl has since evolved into a multipurpose, multiplatform language present absolutely everywhere: heavy-duty web applications, the cloud, systems administration, natural language processing, and financial engineering. Beginning Perl, Third Edition provides valuable insight into Perl’s role regarding all of these tasks and more. Commencing with a comprehensive overview of language basics, you’ll learn all about important concepts such as Perl’s data types and control flow constructs. This material sets the stage for a discussion of more complex topics, such as writing custom functions, using regular expressions, and file input and output. Next, the book moves on to the advanced topics of object-oriented programming, modules, web programming, and database administration with Perl’s powerful database interface module, DBI. The examples and code provided offer you all of the information you need to start writing your own powerful scripts to solve the problems listed above, and many more. Whether you are a complete novice or an experienced programmer, Beginning Perl, Third Edition offers an ideal guide to learning Perl.

Beginning Perl

Beginning Perl

Author: Curtis Poe

Publisher: John Wiley & Sons

ISBN: 9781118235638

Category: Computers

Page: 744

View: 649

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Everything beginners need to start programming with Perl Perl is the ever-popular, flexible, open source programminglanguage that has been called the programmers’ Swiss armyknife. This book introduces Perl to both new programmers andexperienced ones who are looking to learn a new language. In thetradition of the popular Wrox Beginning guides, it presentsstep-by-step guidance in getting started, a host of try-it-outexercises, real-world examples, and everything necessary for a Perlnovice to start programming with confidence. Introduces Perl to both new programmers and experienced oneswho want to learn a new language Provides a host of real-world applications for today'senvironments so readers can get started immediately Covers the new features of Perl but fully applicable toprevious editions Beginning Perl provides the information and instructionyou need to confidently get started with Perl. For Instructors: Classroom and training support materialare available for this book.

Beginning Perl Programming

Beginning Perl Programming

Author: William "Bo" Rothwell

Publisher: Apress

ISBN: 9781484250556

Category: Computers

Page: 202

View: 658

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Perl was originally written by Larry Wall while he was working at NASA’s Jet Propulsion Labs. Larry is an Internet legend, known not just for Perl, but as the author of the UNIX utilities rn, one of the original Usenet newsreaders, and patch, a tremendously useful tool that takes a list of differences between two files and allows you to turn one into the other. The term patch used for this activity is now widespread. Perl started life as a “glue” language for Larry and his officemates, allowing one to “stick” different tools together by converting between their various data formats. It pulled together the best features of several languages: the powerful regular expressions from sed (the Unix stream editor), the patte- scanning language awk, and a few other languages and utilities. The syntax was further made up out of C, Pascal, Basic, Unix shell languages, English, and maybe a few other elements along the way. While Perl started its life as glue, it is now more often likened to another handy multiuse tool: duct tape. A common statement heard in cyberspace is that Perl is the duct tape that holds the Internet together.

Beginning Perl Web Development

Beginning Perl Web Development

Author: Steve Suehring

Publisher: Apress

ISBN: 9781430200895

Category: Computers

Page: 376

View: 718

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* Avoids proof-of-concept examples in favor of teaching readers how to produce well-coded secure CGI applications that will stand up to the demands of being placed into the potentially hostile environment of the Internet. * Takes a holistic approach to web application development and includes instruction on how to use ancillary programs such as Mason and Nagios that the reader will need to be familiar with in order to progress. * The book’s comprehensive scope tackles all the areas of Perl web application development the reader is likely to need in creating their first web applications.

Mastering Perl for Bioinformatics

Mastering Perl for Bioinformatics

Author: James Tisdall

Publisher: "O'Reilly Media, Inc."

ISBN: 9781449390907

Category: Computers

Page: 400

View: 625

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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.

Mastering Perl

Mastering Perl

Author: brian d foy

Publisher: "O'Reilly Media, Inc."

ISBN: 9781449364977

Category: Computers

Page: 400

View: 529

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Take the next step toward Perl mastery with advanced concepts that make coding easier, maintenance simpler, and execution faster. Mastering Perl isn't a collection of clever tricks, but a way of thinking about Perl programming for solving debugging, configuration, and many other real-world problems you’ll encounter as a working programmer. The third in O’Reilly’s series of landmark Perl tutorials (after Learning Perl and Intermediate Perl), this fully upated edition pulls everything together and helps you bend Perl to your will. Explore advanced regular expressions features Avoid common problems when writing secure programs Profile and benchmark Perl programs to see where they need work Wrangle Perl code to make it more presentable and readable Understand how Perl keeps track of package variables Define subroutines on the fly Jury-rig modules to fix code without editing the original source Use bit operations and bit vectors to store large data efficiently Learn how to detect errors that Perl doesn’t report Dive into logging, data persistence, and the magic of tied variables

Practical Text Mining with Perl

Practical Text Mining with Perl

Author: Roger Bilisoly

Publisher: John Wiley & Sons

ISBN: 9781118210505

Category: Computers

Page: 296

View: 541

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Provides readers with the methods, algorithms, and means to perform text mining tasks This book is devoted to the fundamentals of text mining using Perl, an open-source programming tool that is freely available via the Internet (www.perl.org). It covers mining ideas from several perspectives--statistics, data mining, linguistics, and information retrieval--and provides readers with the means to successfully complete text mining tasks on their own. The book begins with an introduction to regular expressions, a text pattern methodology, and quantitative text summaries, all of which are fundamental tools of analyzing text. Then, it builds upon this foundation to explore: Probability and texts, including the bag-of-words model Information retrieval techniques such as the TF-IDF similarity measure Concordance lines and corpus linguistics Multivariate techniques such as correlation, principal components analysis, and clustering Perl modules, German, and permutation tests Each chapter is devoted to a single key topic, and the author carefully and thoughtfully introduces mathematical concepts as they arise, allowing readers to learn as they go without having to refer to additional books. The inclusion of numerous exercises and worked-out examples further complements the book's student-friendly format. Practical Text Mining with Perl is ideal as a textbook for undergraduate and graduate courses in text mining and as a reference for a variety of professionals who are interested in extracting information from text documents.

Bioinformatics for Geneticists

Bioinformatics for Geneticists

Author: Michael R. Barnes

Publisher: John Wiley & Sons

ISBN: 9780470026199

Category: Science

Page: 577

View: 741

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Praise from the reviews: "Without reservation, I endorse this text as the best resource I've encountered that neatly introduces and summarizes many points I've learned through years of experience. The gems of truth found in this book will serve well those who wish to apply bioinformatics in their daily work, as well as help them advise others in this capacity." CIRCGENETICS "This book may really help to get geneticists and bioinformaticians on 'speaking-terms'... contains some essential reading for almost any person working in the field of molecular genetics." EUROPEAN JOURNAL OF HUMAN GENETICS "... an excellent resource... this book should ensure that any researcher's skill base is maintained." GENETICAL RESEARCH “… one of the best available and most accessible texts on bioinformatics and genetics in the postgenome age… The writing is clear, with succinct subsections within each chapter….Without reservation, I endorse this text as the best resource I’ve encountered that neatly introduces and summarizes many points I’ve learned through years of experience. The gems of truth found in this book will serve well those who wish to apply bioinformatics in their daily work, as well as help them advise others in this capacity.” CIRCULATION: CARDIOVASCULAR GENETICS A fully revised version of the successful First Edition, this one-stop reference book enables all geneticists to improve the efficiency of their research. The study of human genetics is moving into a challenging new era. New technologies and data resources such as the HapMap are enabling genome-wide studies, which could potentially identify most common genetic determinants of human health, disease and drug response. With these tremendous new data resources at hand, more than ever care is required in their use. Faced with the sheer volume of genetics and genomic data, bioinformatics is essential to avoid drowning true signal in noise. Considering these challenges, Bioinformatics for Geneticists, Second Edition works at multiple levels: firstly, for the occasional user who simply wants to extract or analyse specific data; secondly, at the level of the advanced user providing explanations of how and why a tool works and how it can be used to greatest effect. Finally experts from fields allied to genetics give insight into the best genomics tools and data to enhance a genetic experiment. Hallmark Features of the Second Edition: Illustrates the value of bioinformatics as a constantly evolving avenue into novel approaches to study genetics The only book specifically addressing the bioinformatics needs of geneticists More than 50% of chapters are completely new contributions Dramatically revised content in core areas of gene and genomic characterisation, pathway analysis, SNP functional analysis and statistical genetics Focused on freely available tools and web-based approaches to bioinformatics analysis, suitable for novices and experienced researchers alike Bioinformatics for Geneticists, Second Edition describes the key bioinformatics and genetic analysis processes that are needed to identify human genetic determinants. The book is based upon the combined practical experience of domain experts from academic and industrial research environments and is of interest to a broad audience, including students, researchers and clinicians working in the human genetics domain.

Mastering Perl/Tk

Mastering Perl/Tk

Author: Stephen Lidie

Publisher: "O'Reilly Media, Inc."

ISBN: 9781565927162

Category: Computers

Page: 746

View: 520

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Covers basic and advanced applications of Perl/Tk, discussing topics including basic Perl/Tk widgets and geometry managers, how to use callbacks and bindings effectively, working with images, and developing a Tk widget in C.

Advanced Perl Programming

Advanced Perl Programming

Author: William "Bo" Rothwell

Publisher: Apress

ISBN: 9781484258637

Category: Computers

Page: 296

View: 492

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William "Bo" Rothwell's Advanced Perl Programming continues where his previous book left off, more or less, as it guides you through advanced techniques of the Perl programming language starting with command-line options, references, and arrays and hashes from advanced data types. Next, you'll learn about typeglobs for symbolic entries. Additionally, you'll see advanced subroutine handling, then packages and namespaces. Furthermore, you'll build advanced modules and install CPAN modules. Unlike Java and C++, modules have been around in Perl for a long time now. Along the way, you'll learn and use POD mark up language for Perl documentation. Moreover, you'll get a survey of the many advanced features and data structures of the current Perl programming language. You'll also get a survey of the new features of the latest Perl 5.x release. After reading and using this book, you'll have the tools, techniques, and source code to be an expert Perl programmer. What You Will Learn Carry out command-line parsing and extract scripts Create references; return values from a reference; work with the ref Function and strict refsWork with advanced Perl data types using arrays, hashes, and hash of hashes Use Typeglobs for symbol table entries Build modules and install CPAN modules Write documentation for Perl using POD Work with the newest features in Perl, including the smartmatch operator, yada yada, automated regex modifiers, the CORE namespace and more Who This Book Is For Those with experience with Perl or who have read Rothwell's prior books, Beginning Perl Programming and Pro Perl Programming.