Bioinformatics Programming Using Python

Author: Mitchell L Model
Publisher: "O'Reilly Media, Inc."
ISBN: 9781449382902
Format: PDF, ePub, Docs
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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

Author: Mitchell Model
Publisher: "O'Reilly Media, Inc."
ISBN: 059615450X
Format: PDF, Kindle
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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

Author: Tim J. Stevens
Publisher: Cambridge University Press
ISBN: 1316194140
Format: PDF, Kindle
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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 Programming in Python

Author: Ruediger-Marcus Flaig
Publisher: John Wiley & Sons
ISBN: 3527644903
Format: PDF, Docs
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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 for Bioinformatics

Author: Jason Kinser
Publisher: Jones & Bartlett Publishers
ISBN: 1449613071
Format: PDF, Kindle
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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 Data Skills

Author: Vince Buffalo
Publisher: "O'Reilly Media, Inc."
ISBN: 1449367518
Format: PDF, Mobi
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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

Practical Programming

Author: Paul Gries
Publisher: Pragmatic Bookshelf
ISBN: 1680504126
Format: PDF, ePub, Docs
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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.

R Programming for Bioinformatics

Author: Robert Gentleman
Publisher: CRC Press
ISBN: 9781420063684
Format: PDF, ePub, Docs
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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 with Python Cookbook

Author: Tiago Antao
Publisher: Packt Publishing Ltd
ISBN: 1783558652
Format: PDF, ePub, Mobi
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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.

Managing Your Biological Data with Python

Author: Allegra Via
Publisher: CRC Press
ISBN: 1439880948
Format: PDF, Mobi
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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.