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: 3435
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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: 2205
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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.

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: 9673
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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.

Python Programming for Biology

Python Programming for Biology

  • Author: Tim J. Stevens,Wayne Boucher
  • Publisher: Cambridge University Press
  • ISBN: 0521895839
  • Category: Computers
  • Page: 711
  • View: 8155
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This book introduces Python as a powerful tool for the investigation of problems in computational biology, for novices and experienced programmers alike.

Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

  • Author: Tiago Antao
  • Publisher: Packt Publishing Ltd
  • ISBN: 1783558652
  • Category: Computers
  • Page: 306
  • View: 5512
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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.

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: 744
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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

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: 3903
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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.

Python for Bioinformatics

Python for Bioinformatics

  • Author: Jason Kinser
  • Publisher: Jones & Bartlett Publishers
  • ISBN: 1449613071
  • Category: Computers
  • Page: 417
  • View: 1566
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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.

R Programming for Bioinformatics

R Programming for Bioinformatics

  • Author: Robert Gentleman
  • Publisher: CRC Press
  • ISBN: 9781420063684
  • Category: Mathematics
  • Page: 328
  • View: 8649
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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: 9274
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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.

Python for Biologists

Python for Biologists

  • Author: Martin Jones
  • Publisher: Createspace Independent Publishing Platform
  • ISBN: 9781492346135
  • Category: Computers
  • Page: 229
  • View: 6794
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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: 4642
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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.

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: 9200
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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

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: 7992
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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.

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: 9770
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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: 1107008565
  • Category: Computers
  • Page: 338
  • View: 8027
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A hands-on introduction to Unix, Perl and other bioinformatics tools using relevant and interesting molecular biology problems.

Python for Bioinformatics

Python for Bioinformatics

  • Author: Sebastian Bassi
  • Publisher: CRC Press
  • ISBN: 1584889306
  • Category: Science
  • Page: 587
  • View: 9297
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Programming knowledge is often necessary for finding a solution to a biological problem. Based on the author’s experience working for an agricultural biotechnology company, Python for Bioinformatics helps scientists solve their biological problems by helping them understand the basics of programming. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. The book begins with a very basic introduction that teaches the principles of programming. It then introduces the Biopython package, which can be useful in solving life science problems. The next section covers sophisticated tools for bioinformatics, including relational database management systems and XML. The last part illustrates applications with source code, such as sequence manipulation, filtering vector contamination, calculating DNA melting temperature, parsing a genbank file, inferring splicing sites, and more. The appendices provide a wealth of supplementary information, including instructions for installing Python and Biopython and a Python language and style guide. By incorporating examples in biology as well as code fragments throughout, the author places a special emphasis on practice, encouraging readers to experiment with the code. He shows how to use Python and the Biopython package for building web applications, genomic annotation, data manipulation, and countless other applications.

Programming Collective Intelligence

Programming Collective Intelligence

Building Smart Web 2.0 Applications

  • Author: Toby Segaran
  • Publisher: "O'Reilly Media, Inc."
  • ISBN: 0596550685
  • Category: Computers
  • Page: 362
  • View: 8999
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Want to tap the power behind search rankings, product recommendations, social bookmarking, and online matchmaking? This fascinating book demonstrates how you can build Web 2.0 applications to mine the enormous amount of data created by people on the Internet. With the sophisticated algorithms in this book, you can write smart programs to access interesting datasets from other web sites, collect data from users of your own applications, and analyze and understand the data once you've found it. Programming Collective Intelligence takes you into the world of machine learning and statistics, and explains how to draw conclusions about user experience, marketing, personal tastes, and human behavior in general -- all from information that you and others collect every day. Each algorithm is described clearly and concisely with code that can immediately be used on your web site, blog, Wiki, or specialized application. This book explains: Collaborative filtering techniques that enable online retailers to recommend products or media Methods of clustering to detect groups of similar items in a large dataset Search engine features -- crawlers, indexers, query engines, and the PageRank algorithm Optimization algorithms that search millions of possible solutions to a problem and choose the best one Bayesian filtering, used in spam filters for classifying documents based on word types and other features Using decision trees not only to make predictions, but to model the way decisions are made Predicting numerical values rather than classifications to build price models Support vector machines to match people in online dating sites Non-negative matrix factorization to find the independent features in a dataset Evolving intelligence for problem solving -- how a computer develops its skill by improving its own code the more it plays a game Each chapter includes exercises for extending the algorithms to make them more powerful. Go beyond simple database-backed applications and put the wealth of Internet data to work for you. "Bravo! I cannot think of a better way for a developer to first learn these algorithms and methods, nor can I think of a better way for me (an old AI dog) to reinvigorate my knowledge of the details." -- Dan Russell, Google "Toby's book does a great job of breaking down the complex subject matter of machine-learning algorithms into practical, easy-to-understand examples that can be directly applied to analysis of social interaction across the Web today. If I had this book two years ago, it would have saved precious time going down some fruitless paths." -- Tim Wolters, CTO, Collective Intellect

Advanced Python for Biologists

Advanced Python for Biologists

  • Author: Martin O. Jones
  • Publisher: Createspace Independent Pub
  • ISBN: 9781495244377
  • Category: Computers
  • Page: 267
  • View: 9787
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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.

Bioinformatics with R Cookbook

Bioinformatics with R Cookbook

  • Author: Paurush Praveen Sinha
  • Publisher: Packt Publishing Ltd
  • ISBN: 1783283149
  • Category: Computers
  • Page: 340
  • View: 1537
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This book is an easy-to-follow, stepwise guide to handle real life Bioinformatics problems. Each recipe comes with a detailed explanation to the solution steps. A systematic approach, coupled with lots of illustrations, tips, and tricks will help you as a reader grasp even the trickiest of concepts without difficulty.This book is ideal for computational biologists and bioinformaticians with basic knowledge of R programming, bioinformatics and statistics. If you want to understand various critical concepts needed to develop your computational models in Bioinformatics, then this book is for you. Basic knowledge of R is expected.