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Mastering Perl for Bioinformatics

Author : James Tisdall

Publisher : "O'Reilly Media, Inc."

Page : 399 pages

File Size : 31,40 MB

Release : 2003-09-25

Category : Computers

ISBN : 1449390900

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Book Description

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.



Beginning Perl for Bioinformatics

Author : James Tisdall

Publisher : "O'Reilly Media, Inc."

Page : 388 pages

File Size : 45,91 MB

Release : 2001-10-22

Category : Computers

ISBN : 0596550472

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Book Description

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



Perl Programming for Biologists

Author : D. Curtis Jamison

Publisher : John Wiley & Sons

Page : 206 pages

File Size : 42,91 MB

Release : 2003-07-14

Category : Medical

ISBN : 9780471430599

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Book Description

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.



Learning Perl

Author : Randal Schwartz

Publisher : "O'Reilly Media, Inc."

Page : 389 pages

File Size : 27,48 MB

Release : 2011-06-23

Category : Computers

ISBN : 1449303587

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Book Description

The sixth edition of this bestselling Perl tutorial includes recent changes to the language. Years of classroom testing and experience helped shape the book's pace and scope, and this edition is packed with exercises that let readers practice the concepts while they follow the text.



Bioinformatics Biocomputing and Perl

Author : Michael Moorhouse

Publisher : John Wiley & Sons

Page : 506 pages

File Size : 45,13 MB

Release : 2005-09-27

Category : Medical

ISBN : 0470026456

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Book Description

Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today’s bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material. Working with Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease. Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples. Working with the Web presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet. Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.



Mastering Python for Bioinformatics

Author : Ken Youens-Clark

Publisher : "O'Reilly Media, Inc."

Page : 457 pages

File Size : 30,82 MB

Release : 2021-05-05

Category : Computers

ISBN : 1098100859

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Book Description

Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and researchers who've never learned basic programming skills. This practical guide shows postdoc bioinformatics professionals and students how to exploit the best parts of Python to solve problems in biology while creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates not only how to write effective Python code but also how to use tests to write and refactor scientific programs. You'll learn the latest Python features and toolsâ??including linters, formatters, type checkers, and testsâ??to create documented and tested programs. You'll also tackle 14 challenges in Rosalind, a problem-solving platform for learning bioinformatics and programming. Create command-line Python programs to document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA and FASTQ Find patterns of text using regular expressions Use higher-order functions in Python like filter(), map(), and reduce()



Bioinformatics Programming Using Python

Author : Mitchell L Model

Publisher : "O'Reilly Media, Inc."

Page : 526 pages

File Size : 31,50 MB

Release : 2009-12-08

Category : Science

ISBN : 1449382908

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Book Description

Powerful, flexible, and easy to use, Python is an ideal language for building software tools and applications for life science research and development. This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. In a short time, you'll be using sophisticated techniques and Python modules that are particularly effective for bioinformatics programming. Bioinformatics Programming Using Python is perfect for anyone involved with bioinformatics -- researchers, support staff, students, and software developers interested in writing bioinformatics applications. You'll find it useful whether you already use Python, write code in another language, or have no programming experience at all. It's an excellent self-instruction tool, as well as a handy reference when facing the challenges of real-life programming tasks. Become familiar with Python's fundamentals, including ways to develop simple applications Learn how to use Python modules for pattern matching, structured text processing, online data retrieval, and database access Discover generalized patterns that cover a large proportion of how Python code is used in bioinformatics Learn how to apply the principles and techniques of object-oriented programming Benefit from the "tips and traps" section in each chapter



Computational Biology

Author : Röbbe Wünschiers

Publisher : Springer Science & Business Media

Page : 291 pages

File Size : 26,58 MB

Release : 2012-12-06

Category : Science

ISBN : 3642185525

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Book Description

-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



Mastering Perl

Author : brian d foy

Publisher : "O'Reilly Media, Inc."

Page : 397 pages

File Size : 14,88 MB

Release : 2014-01-09

Category : Computers

ISBN : 1449364977

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Book Description

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



Exploring Bioinformatics

Author : Caroline St. Clair

Publisher : Jones & Bartlett Publishers

Page : 309 pages

File Size : 10,16 MB

Release : 2013-12-12

Category : Computers

ISBN : 128402346X

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Book Description

Thoroughly revised and updated, Exploring Bioinformatics: A Project-Based Approach, Second Edition is intended for an introductory course in bioinformatics at the undergraduate level. Through hands-on projects, students are introduced to current biological problems and then explore and develop bioinformatic solutions to these issues. Each chapter presents a key problem, provides basic biological concepts, introduces computational techniques to address the problem, and guides students through the use of existing web-based tools and software solutions. This progression prepares students to tackle the On-Your-Own Project, where they develop their own software solutions. Topics such as antibiotic resistance, genetic disease, and genome sequencing provide context and relevance to capture student interest.