Beginning Perl For Bioinformatics

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Beginning Perl for Bioinformatics

James Tisdall
Beginning Perl for Bioinformatics Book PDF

Author : James Tisdall
Publisher : "O'Reilly Media, Inc."
Page : 388 pages
File Size : 42,6 Mb
Release : 2001-10-22
Category : Computers
ISBN : 9780596550479

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Beginning Perl for Bioinformatics by James Tisdall Pdf

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 for Bioinformatics

James Tisdall
Beginning Perl for Bioinformatics Book PDF

Author : James Tisdall
Publisher : "O'Reilly Media, Inc."
Page : 384 pages
File Size : 54,9 Mb
Release : 2001
Category : Computers
ISBN : 9780596000806

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Beginning Perl for Bioinformatics by James Tisdall Pdf

This book shows biologists with little or no programming experience how to use Perl, the ideal language for biological data analysis. Each chapter focuses on solving a particular problem or class of problems, so you'll finish the book with the skills to tackle more advanced bioinformatics programming.

Mastering Perl for Bioinformatics

James Tisdall
Mastering Perl for Bioinformatics Book PDF

Author : James Tisdall
Publisher : "O'Reilly Media, Inc."
Page : 399 pages
File Size : 40,6 Mb
Release : 2003-09-25
Category : Computers
ISBN : 9781449390907

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Mastering Perl for Bioinformatics by James Tisdall Pdf

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.

Perl Programming for Biologists

D. Curtis Jamison
Perl Programming for Biologists Book PDF

Author : D. Curtis Jamison
Publisher : John Wiley & Sons
Page : 206 pages
File Size : 40,6 Mb
Release : 2003-07-14
Category : Medical
ISBN : 0471430595

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Perl Programming for Biologists by D. Curtis Jamison Pdf

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.

Beginning Perl For Bioinformatics

James D Tisdall
Beginning Perl For Bioinformatics Book PDF

Author : James D Tisdall
Publisher : Unknown
Page : 390 pages
File Size : 47,5 Mb
Release : 2001-01-01
Category : Plant diseases
ISBN : 8173663955

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Beginning Perl For Bioinformatics by James D Tisdall Pdf

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.

Beginning Perl

James Lee
Beginning Perl Book PDF

Author : James Lee
Publisher : Apress
Page : 453 pages
File Size : 51,9 Mb
Release : 2010-06-14
Category : Computers
ISBN : 9781430227946

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Beginning Perl by James Lee Pdf

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.

Developing Bioinformatics Computer Skills

Cynthia Gibas,Per Jambeck
Developing Bioinformatics Computer Skills Book PDF

Author : Cynthia Gibas,Per Jambeck
Publisher : "O'Reilly Media, Inc."
Page : 452 pages
File Size : 41,5 Mb
Release : 2001
Category : Computers
ISBN : 1565926641

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Developing Bioinformatics Computer Skills by Cynthia Gibas,Per Jambeck Pdf

This practical, hands-on guide shows how to develop a structured approach to biological data and the tools needed to analyze it. It's aimed at scientists and students learning computational approaches to biological data, as well as experienced biology researchers starting to use computers to handle data.

Learning Perl

Randal Schwartz,brian foy,Tom Phoenix
Learning Perl Book PDF

Author : Randal Schwartz,brian foy,Tom Phoenix
Publisher : "O'Reilly Media, Inc."
Page : 389 pages
File Size : 43,7 Mb
Release : 2011-06-23
Category : Computers
ISBN : 9781449303587

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Learning Perl by Randal Schwartz,brian foy,Tom Phoenix Pdf

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.

UNIX and Perl to the Rescue!

Keith Bradnam,Ian Korf
UNIX and Perl to the Rescue Book PDF

Author : Keith Bradnam,Ian Korf
Publisher : Cambridge University Press
Page : 429 pages
File Size : 41,7 Mb
Release : 2012-07-19
Category : Computers
ISBN : 9781107000681

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UNIX and Perl to the Rescue! by Keith Bradnam,Ian Korf Pdf

An accessible guide to learning the key features of Unix and Perl, written with the non-programmer in mind.

Beginning Perl For Bioinformatics

James Tisdall
Beginning Perl For Bioinformatics Book PDF

Author : James Tisdall
Publisher : Unknown
Page : 128 pages
File Size : 47,5 Mb
Release : 2001-01-01
Category : Computers
ISBN : 0613911970

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Beginning Perl For Bioinformatics by James Tisdall Pdf

Discusses the ties between biology and computer science, how to program, basic PERL programming concepts, and how to use PERL to perform tasks including analyzing genetic codes.

Bioinformatics Biocomputing and Perl

Michael Moorhouse,Paul Barry
Bioinformatics Biocomputing and Perl Book PDF

Author : Michael Moorhouse,Paul Barry
Publisher : John Wiley & Sons
Page : 506 pages
File Size : 47,9 Mb
Release : 2005-09-27
Category : Medical
ISBN : 9780470026458

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Bioinformatics Biocomputing and Perl by Michael Moorhouse,Paul Barry Pdf

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.

Perl for Exploring DNA

Mark D. LeBlanc,Betsey Dexter Dyer
Perl for Exploring DNA Book PDF

Author : Mark D. LeBlanc,Betsey Dexter Dyer
Publisher : Oxford University Press, USA
Page : 296 pages
File Size : 55,5 Mb
Release : 2007
Category : Computers
ISBN : STANFORD:36105123393030

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Perl for Exploring DNA by Mark D. LeBlanc,Betsey Dexter Dyer Pdf

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BLAST

Ian Korf,Mark Yandell,Joseph Bedell
BLAST Book PDF

Author : Ian Korf,Mark Yandell,Joseph Bedell
Publisher : "O'Reilly Media, Inc."
Page : 363 pages
File Size : 49,5 Mb
Release : 2003-07-29
Category : Computers
ISBN : 9780596002992

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BLAST by Ian Korf,Mark Yandell,Joseph Bedell Pdf

This is the only book completely devoted to the popular BLAST (Basic Local Alignment Search Tool), and one that every biologist with an interest in sequence analysis should learn from.

Perl Programming for Medicine and Biology

Jules J. Berman
Perl Programming for Medicine and Biology Book PDF

Author : Jules J. Berman
Publisher : Jones & Bartlett Learning
Page : 428 pages
File Size : 47,6 Mb
Release : 2007
Category : Biology
ISBN : 076374333X

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Perl Programming for Medicine and Biology by Jules J. Berman Pdf

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.

Bioinformatics Data Skills

Vince Buffalo
Bioinformatics Data Skills Book PDF

Author : Vince Buffalo
Publisher : "O'Reilly Media, Inc."
Page : 538 pages
File Size : 46,6 Mb
Release : 2015-07
Category : Computers
ISBN : 9781449367510

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Bioinformatics Data Skills by Vince Buffalo Pdf

Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, youâ??ll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand lifeâ??s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, youâ??re ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles