Search Results for "bioinformatics-programming-using-python-practical-programming-for-biological-data"

Bioinformatics Programming Using Python

Bioinformatics Programming Using Python

Practical Programming for Biological Data

  • Author: Mitchell L Model
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 9781449382902
  • Category: Computers
  • Page: 528
  • View: 4028
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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

Bioinformatics Programming Using Python

Bioinformatics Programming Using Python

  • Author: Mitchell Model
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 059615450X
  • Category: Computers
  • Page: 492
  • View: 7874
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Bioinformatics -- applying information technology to the molecular biology field -- will be extremely hot in the coming years, and this book helps simplify the process. With this book, biologists will learn how to use basic scripting to simplify their computational tasks, and how to write more substantial programs. It will also help programmers who want to learn more about bioinformatics programming. This book includes lots of examples and exercises.

Python Programming for Biology

Python Programming for Biology

Bioinformatics and Beyond

  • Author: Tim J. Stevens,Wayne Boucher
  • Publisher: Cambridge University Press
  • ISBN: 1316194140
  • Category: Science
  • Page: N.A
  • View: 8827
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Do you have a biological question that could be readily answered by computational techniques, but little experience in programming? Do you want to learn more about the core techniques used in computational biology and bioinformatics? Written in an accessible style, this guide provides a foundation for both newcomers to computer programming and those interested in learning more about computational biology. The chapters guide the reader through: a complete beginners' course to programming in Python, with an introduction to computing jargon; descriptions of core bioinformatics methods with working Python examples; scientific computing techniques, including image analysis, statistics and machine learning. This book also functions as a language reference written in straightforward English, covering the most common Python language elements and a glossary of computing and biological terms. This title will teach undergraduates, postgraduates and professionals working in the life sciences how to program with Python, a powerful, flexible and easy-to-use language.

Bioinformatics Data Skills

Bioinformatics Data Skills

Reproducible and Robust Research with Open Source Tools

  • Author: Vince Buffalo
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 1449367518
  • Category: Computers
  • Page: 538
  • View: 7891
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Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, you’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 life’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, you’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

Python for Bioinformatics

Python for Bioinformatics

  • Author: Jason Kinser
  • Publisher: Jones & Bartlett Publishers
  • ISBN: 1449613071
  • Category: Computers
  • Page: 417
  • View: 321
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Bioinformatics is a growing field that attracts researchers from many different backgrounds who are unfamiliar with the algorithms commonly used in the field. Python for Bioinformatics provides a clear introduction to the Python programming language and instructs beginners on the development of simple programming exercises . Ideal for those with some knowledge of computer programming languages, this book emphasizes Python syntax and methodologies. The text is divided into three complete sections; the first provides an explanation of general Python programming, the second includes a detailed discussion of the Python tools typically used in bioinformatics including clustering, associative memories, and mathematical analysis techniques, and the third section demonstrates how these tools are implemented through numerous applications.

Bioinformatics Programming in Python

Bioinformatics Programming in Python

A Practical Course for Beginners

  • Author: Ruediger-Marcus Flaig
  • Publisher: John Wiley & Sons
  • ISBN: 3527644903
  • Category: Medical
  • Page: 428
  • View: 9751
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This first introductory book designed to train novice programmers is based on a student course taught by the author, and has been optimized for biology students without previous experience in programming. By interspersing theory chapters with numerous small and large programming exercises, the author quickly shows readers how to do their own programming, and throughout uses anecdotes and real-life examples from the biosciences to 'spice up' the text. This practical book thus teaches essential programming skills for life scientists who want -- or need -- to write their own bioinformatics software tools.

Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

  • Author: Tiago Antao
  • Publisher: Packt Publishing Ltd
  • ISBN: 1783558652
  • Category: Computers
  • Page: 306
  • View: 7779
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If you are either a computational biologist or a Python programmer, you will probably relate to the expression "explosive growth, exciting times". Python is arguably the main programming language for big data, and the deluge of data in biology, mostly from genomics and proteomics, makes bioinformatics one of the most exciting fields in data science. Using the hands-on recipes in this book, you'll be able to do practical research and analysis in computational biology with Python. We cover modern, next-generation sequencing libraries and explore real-world examples on how to handle real data. The main focus of the book is the practical application of bioinformatics, but we also cover modern programming techniques and frameworks to deal with the ever increasing deluge of bioinformatics data.

Practical Programming

Practical Programming

An Introduction to Computer Science Using Python 3.6

  • Author: Paul Gries,Jennifer Campbell,Jason Montojo
  • Publisher: Pragmatic Bookshelf
  • ISBN: 1680504126
  • Category: Computers
  • Page: 412
  • View: 3930
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Classroom-tested by tens of thousands of students, this new edition of the bestselling intro to programming book is for anyone who wants to understand computer science. Learn about design, algorithms, testing, and debugging. Discover the fundamentals of programming with Python 3.6--a language that's used in millions of devices. Write programs to solve real-world problems, and come away with everything you need to produce quality code. This edition has been updated to use the new language features in Python 3.6.

Managing Your Biological Data with Python

Managing Your Biological Data with Python

  • Author: Allegra Via,Kristian Rother,Anna Tramontano
  • Publisher: CRC Press
  • ISBN: 1439880948
  • Category: Science
  • Page: 560
  • View: 9638
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Take Control of Your Data and Use Python with Confidence Requiring no prior programming experience, Managing Your Biological Data with Python empowers biologists and other life scientists to work with biological data on their own using the Python language. The book teaches them not only how to program but also how to manage their data. It shows how to read data from files in different formats, analyze and manipulate the data, and write the results to a file or computer screen. The first part of the text introduces the Python language and teaches readers how to write their first programs. The second part presents the basic elements of the language, enabling readers to write small programs independently. The third part explains how to create bigger programs using techniques to write well-organized, efficient, and error-free code. The fourth part on data visualization shows how to plot data and draw a figure for an article or slide presentation. The fifth part covers the Biopython programming library for reading and writing several biological file formats, querying the NCBI online databases, and retrieving biological records from the web. The last part provides a cookbook of 20 specific programming "recipes," ranging from secondary structure prediction and multiple sequence alignment analyses to superimposing protein three-dimensional structures. Tailoring the programming topics to the everyday needs of biologists, the book helps them easily analyze data and ultimately make better discoveries. Every piece of code in the text is aimed at solving real biological problems.

R Programming for Bioinformatics

R Programming for Bioinformatics

  • Author: Robert Gentleman
  • Publisher: CRC Press
  • ISBN: 9781420063684
  • Category: Mathematics
  • Page: 328
  • View: 3910
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Due to its data handling and modeling capabilities as well as its flexibility, R is becoming the most widely used software in bioinformatics. R Programming for Bioinformatics explores the programming skills needed to use this software tool for the solution of bioinformatics and computational biology problems. Drawing on the author’s first-hand experiences as an expert in R, the book begins with coverage on the general properties of the R language, several unique programming aspects of R, and object-oriented programming in R. It presents methods for data input and output as well as database interactions. The author also examines different facets of string handling and manipulations, discusses the interfacing of R with other languages, and describes how to write software packages. He concludes with a discussion on the debugging and profiling of R code. With numerous examples and exercises, this practical guide focuses on developing R programming skills in order to tackle problems encountered in bioinformatics and computational biology.

Bioinformatics and Molecular Evolution

Bioinformatics and Molecular Evolution

  • Author: Paul G. Higgs,Teresa K. Attwood
  • Publisher: John Wiley & Sons
  • ISBN: 1118697065
  • Category: Science
  • Page: 384
  • View: 3876
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In the current era of complete genome sequencing, Bioinformatics and Molecular Evolution provides an up-to-date and comprehensive introduction to bioinformatics in the context of evolutionary biology. This accessible text: provides a thorough examination of sequence analysis, biological databases, pattern recognition, and applications to genomics, microarrays, and proteomics emphasizes the theoretical and statistical methods used in bioinformatics programs in a way that is accessible to biological science students places bioinformatics in the context of evolutionary biology, including population genetics, molecular evolution, molecular phylogenetics, and their applications features end-of-chapter problems and self-tests to help students synthesize the materials and apply their understanding is accompanied by a dedicated website - www.blackwellpublishing.com/higgs - containing downloadable sequences, links to web resources, answers to self-test questions, and all artwork in downloadable format (artwork also available to instructors on CD-ROM). This important textbook will equip readers with a thorough understanding of the quantitative methods used in the analysis of molecular evolution, and will be essential reading for advanced undergraduates, graduates, and researchers in molecular biology, genetics, genomics, computational biology, and bioinformatics courses.

Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics

An Introduction to Perl for Biologists

  • Author: James Tisdall
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 9780596550479
  • Category: Computers
  • Page: 386
  • View: 9868
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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

Python for Biologists

Python for Biologists

  • Author: Martin Jones
  • Publisher: Createspace Independent Publishing Platform
  • ISBN: 9781492346135
  • Category: Computers
  • Page: 229
  • View: 9145
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Python for biologists is a complete programming course for beginners that will give you the skills you need to tackle common biological and bioinformatics problems.

Computing for Biologists

Computing for Biologists

Python Programming and Principles

  • Author: Ran Libeskind-Hadas,Eliot Bush
  • Publisher: Cambridge University Press
  • ISBN: 1316061337
  • Category: Science
  • Page: N.A
  • View: 6394
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Computing is revolutionizing the practice of biology. This book, which assumes no prior computing experience, provides students with the tools to write their own Python programs and to understand fundamental concepts in computational biology and bioinformatics. Each major part of the book begins with a compelling biological question, followed by the algorithmic ideas and programming tools necessary to explore it: the origins of pathogenicity are examined using gene finding, the evolutionary history of sex determination systems is studied using sequence alignment, and the origin of modern humans is addressed using phylogenetic methods. In addition to providing general programming skills, this book explores the design of efficient algorithms, simulation, NP-hardness, and the maximum likelihood method, among other key concepts and methods. Easy-to-read and designed to equip students with the skills to write programs for solving a range of biological problems, the book is accompanied by numerous programming exercises, available at www.cs.hmc.edu/CFB.

Practical Computing for Biologists

Practical Computing for Biologists

  • Author: Steven Harold David Haddock,Casey W. Dunn
  • Publisher: Sinauer Associates Incorporated
  • ISBN: 9780878933914
  • Category: Computers
  • Page: 538
  • View: 5793
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To help with the increasingly large data sets that many scientists deal with, this book illustrates how to use many freely available computing tools to work more powerfully and effectively. The book was born out of the authors' experiences developing tools for their research and to fix other biologist's computational problems.

Genomics and Bioinformatics

Genomics and Bioinformatics

An Introduction to Programming Tools for Life Scientists

  • Author: Tore Samuelsson
  • Publisher: Cambridge University Press
  • ISBN: 1107378338
  • Category: Science
  • Page: N.A
  • View: 8648
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With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.

Advanced Python for Biologists

Advanced Python for Biologists

  • Author: Martin O. Jones
  • Publisher: Createspace Independent Pub
  • ISBN: 9781495244377
  • Category: Computers
  • Page: 267
  • View: 3126
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Advanced Python for Biologists is a programming course for workers in biology and bioinformatics who want to develop their programming skills. It starts with the basic Python knowledge outlined in Python for Biologists and introduces advanced Python tools and techniques with biological examples. You'll learn: - How to use object-oriented programming to model biological entities - How to write more robust code and programs by using Python's exception system - How to test your code using the unit testing framework - How to transform data using Python's comprehensions - How to write flexible functions and applications using functional programming - How to use Python's iteration framework to extend your own object and functions Advanced Python for Biologists is written with an emphasis on practical problem-solving and uses everyday biological examples throughout. Each section contains exercises along with solutions and detailed discussion.

HTML5 and CSS3

HTML5 and CSS3

Level Up with Today's Web Technologies

  • Author: Brian P. Hogan
  • Publisher: Pragmatic Bookshelf
  • ISBN: 1680503685
  • Category: Computers
  • Page: 316
  • View: 3665
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HTML5 and CSS3 are more than just buzzwords--they're the foundation for today's web applications. This book gets you up to speed on the HTML5 elements and CSS3 features you can use right now in your current projects, with backwards compatible solutions that ensure that you don't leave users of older browsers behind. This new edition covers even more new features, including CSS animations, IndexedDB, and client-side validations. HTML5 and CSS3 power today's web applications, with semantic markup, better forms, native multimedia, animations, and powerful APIs. You'll get hands-on with all the new features with practical example projects, and find what you need quickly with this book's modular structure. "Falling Back" sections show you how to create solutions for older browsers, and "The Future" sections at the end of each chapter get you excited about the possibilities when features mature. This revised second edition walks you through new features such as IndexedDB, CSS Animations, SVG, and more, along with updated fallback solutions. You'll use HTML5's new markup to create better structure for your content and better interfaces for your forms. You'll work with new form controls and validations, and build interfaces that are accessible to assistive technology and mobile devices. You'll draw with the Canvas and SVG, do simple animations with pure CSS, work with advanced CSS selectors, and make audio and video play natively. You'll bring your web apps to the next level as you use Web Storage and IndexedDB to save data on the client and make applications available offline. And you'll discover how to use web sockets, geolocation, cross-document messaging, and the History API to create even more interactive applications. Today, you have the flexibility that used to be only available through large JavaScript libraries or proprietary plugins. Get ready for today's web. What You Need: You'll need the latest versions of Google Chrome, Firefox, Opera, and Internet Explorer, along with a text editor with good support for HTML5 and CSS3 syntax. Instructions for testing on older versions of Internet Explorer are included in the book.

Developing Bioinformatics Computer Skills

Developing Bioinformatics Computer Skills

  • Author: Cynthia Gibas,Per Jambeck
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 9781565926646
  • Category: Computers
  • Page: 427
  • View: 4576
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Offers a structured approach to biological data and the computer tools needed to analyze it, covering UNIX, databases, computation, Perl, data mining, data visualization, and tailoring software to suit specific research needs.

Bioinformatics for Beginners

Bioinformatics for Beginners

Genes, Genomes, Molecular Evolution, Databases and Analytical Tools

  • Author: Supratim Choudhuri
  • Publisher: Elsevier
  • ISBN: 0124105106
  • Category: Medical
  • Page: 238
  • View: 8690
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Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools provides a coherent and friendly treatment of bioinformatics for any student or scientist within biology who has not routinely performed bioinformatic analysis. The book discusses the relevant principles needed to understand the theoretical underpinnings of bioinformatic analysis and demonstrates, with examples, targeted analysis using freely available web-based software and publicly available databases. Eschewing non-essential information, the work focuses on principles and hands-on analysis, also pointing to further study options. Avoids non-essential coverage, yet fully describes the field for beginners Explains the molecular basis of evolution to place bioinformatic analysis in biological context Provides useful links to the vast resource of publicly available bioinformatic databases and analysis tools Contains over 100 figures that aid in concept discovery and illustration