Download or read book Mastering Python for Bioinformatics written by Ken Youens-Clark and published by "O'Reilly Media, Inc.". This book was released on 2021-05-05 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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()

Download or read book Reproducible Bioinformatics with Python written by Ken Youens-Clark and published by O'Reilly Media. This book was released on 2021-08-17 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and postdoc researchers who've never learned basic programming skills. This practical guide shows how to exploit the best parts of Python for solving problems in biology while also creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates how to write effective Python code and how to use tests to write and refactor scientific programs. You'll learn the latest Python features and tools--such as linters, formatters, type checkers, and tests--to write documented and tested programs. Create command-line Python programs that document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures (strings, lists, and sets) and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA, FASTQ, and SwissProt Find patterns of text using regular expressions Use higher-order functions in Python like filter() and map()

Download or read book Bioinformatics Programming Using Python written by Mitchell L Model and published by "O'Reilly Media, Inc.". This book was released on 2009-12-08 with total page 526 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Mastering Python for Bioinformatics written by Ken Youens-Clark and published by "O'Reilly Media, Inc.". This book was released on 2021-05-05 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 tools including linters, formatters, type checkers, and tests 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()

Download or read book Python for Bioinformatics written by Sebastian Bassi and published by CRC Press. This book was released on 2017-08-07 with total page 510 pages. Available in PDF, EPUB and Kindle. Book excerpt: In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on the author’s extensive experience, Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. This new edition is updated throughout to Python 3 and is designed not just to help scientists master the basics, but to do more in less time and in a reproducible way. New developments added in this edition include NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development.

Download or read book Bioinformatics Algorithms written by Miguel Rocha and published by Academic Press. This book was released on 2018-06-08 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics Algorithms: Design and Implementation in Python provides a comprehensive book on many of the most important bioinformatics problems, putting forward the best algorithms and showing how to implement them. The book focuses on the use of the Python programming language and its algorithms, which is quickly becoming the most popular language in the bioinformatics field. Readers will find the tools they need to improve their knowledge and skills with regard to algorithm development and implementation, and will also uncover prototypes of bioinformatics applications that demonstrate the main principles underlying real world applications. Presents an ideal text for bioinformatics students with little to no knowledge of computer programming Based on over 12 years of pedagogical materials used by the authors in their own classrooms Features a companion website with downloadable codes and runnable examples (such as using Jupyter Notebooks) and exercises relating to the book

Download or read book Mastering Python Data Visualization written by Kirthi Raman and published by Packt Publishing Ltd. This book was released on 2015-10-27 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Generate effective results in a variety of visually appealing charts using the plotting packages in Python About This Book Explore various tools and their strengths while building meaningful representations that can make it easier to understand data Packed with computational methods and algorithms in diverse fields of science Written in an easy-to-follow categorical style, this book discusses some niche techniques that will make your code easier to work with and reuse Who This Book Is For If you are a Python developer who performs data visualization and wants to develop existing knowledge about Python to build analytical results and produce some amazing visual display, then this book is for you. A basic knowledge level and understanding of Python libraries is assumed. What You Will Learn Gather, cleanse, access, and map data to a visual framework Recognize which visualization method is applicable and learn best practices for data visualization Get acquainted with reader-driven narratives and author-driven narratives and the principles of perception Understand why Python is an effective tool to be used for numerical computation much like MATLAB, and explore some interesting data structures that come with it Explore with various visualization choices how Python can be very useful in computation in the field of finance and statistics Get to know why Python is the second choice after Java, and is used frequently in the field of machine learning Compare Python with other visualization approaches using Julia and a JavaScript-based framework such as D3.js Discover how Python can be used in conjunction with NoSQL such as Hive to produce results efficiently in a distributed environment In Detail Python has a handful of open source libraries for numerical computations involving optimization, linear algebra, integration, interpolation, and other special functions using array objects, machine learning, data mining, and plotting. Pandas have a productive environment for data analysis. These libraries have a specific purpose and play an important role in the research into diverse domains including economics, finance, biological sciences, social science, health care, and many more. The variety of tools and approaches available within Python community is stunning, and can bolster and enhance visual story experiences. This book offers practical guidance to help you on the journey to effective data visualization. Commencing with a chapter on the data framework, which explains the transformation of data into information and eventually knowledge, this book subsequently covers the complete visualization process using the most popular Python libraries with working examples. You will learn the usage of Numpy, Scipy, IPython, MatPlotLib, Pandas, Patsy, and Scikit-Learn with a focus on generating results that can be visualized in many different ways. Further chapters are aimed at not only showing advanced techniques such as interactive plotting; numerical, graphical linear, and non-linear regression; clustering and classification, but also in helping you understand the aesthetics and best practices of data visualization. The book concludes with interesting examples such as social networks, directed graph examples in real-life, data structures appropriate for these problems, and network analysis. By the end of this book, you will be able to effectively solve a broad set of data analysis problems. Style and approach The approach of this book is not step by step, but rather categorical. The categories are based on fields such as bioinformatics, statistical and machine learning, financial computation, and linear algebra. This approach is beneficial for the community in many different fields of work and also helps you learn how one approach can make sense across many fields

Download or read book Bioinformatics with Python Cookbook written by Tiago Antao and published by Packt Publishing Ltd. This book was released on 2015-06-25 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Bioinformatics with Python Cookbook written by Tiago Antao and published by Packt Publishing Ltd. This book was released on 2018-11-30 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discover modern, next-generation sequencing libraries from Python ecosystem to analyze large amounts of biological data Key Features Perform complex bioinformatics analysis using the most important Python libraries and applications Implement next-generation sequencing, metagenomics, automating analysis, population genetics, and more Explore various statistical and machine learning techniques for bioinformatics data analysis Book Description Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries. This book will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data. What you will learn Learn how to process large next-generation sequencing (NGS) datasets Work with genomic dataset using the FASTQ, BAM, and VCF formats Learn to perform sequence comparison and phylogenetic reconstruction Perform complex analysis with protemics data Use Python to interact with Galaxy servers Use High-performance computing techniques with Dask and Spark Visualize protein dataset interactions using Cytoscape Use PCA and Decision Trees, two machine learning techniques, with biological datasets Who this book is for This book is for Data data Scientistsscientists, Bioinformatics bioinformatics analysts, researchers, and Python developers who want to address intermediate-to-advanced biological and bioinformatics problems using a recipe-based approach. Working knowledge of the Python programming language is expected.

Download or read book Practical Computing for Biologists written by Steven H.D. Haddock and published by Sinauer. This book was released on 2011-04-22 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Practical Computing for Biologists shows you how to use many freely available computing tools to work more powerfully and effectively. The book was born out of the authors' own experience in developing tools for their research and helping other biologists with their computational problems. Many of the techniques are relevant to molecular bioinformatics but the scope of the book is much broader, covering topics and techniques that are applicable to a range of scientific endeavours. Twenty-two chapters organized into six parts address the following topics (and more; see Contents): • Searching with regular expressions • The Unix command line • Python programming and debugging • Creating and editing graphics • Databases • Performing analyses on remote servers • Working with electronics While the main narrative focuses on Mac OS X, most of the concepts and examples apply to any operating system. Where there are differences for Windows and Linux users, parallel instructions are provided in the margin and in an appendix. The book is designed to be used as a self-guided resource for researchers, a companion book in a course, or as a primary textbook. Practical Computing for Biologists will free you from the most frustrating and time-consuming aspects of data processing so you can focus on the pleasures of scientific inquiry.

Download or read book Tiny Python Projects written by Ken Youens-Clark and published by Simon and Schuster. This book was released on 2020-07-21 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt: ”Tiny Python Projects is a gentle and amusing introduction to Python that will firm up key programming concepts while also making you giggle.”—Amanda Debler, Schaeffler Key Features Learn new programming concepts through 21-bitesize programs Build an insult generator, a Tic-Tac-Toe AI, a talk-like-a-pirate program, and more Discover testing techniques that will make you a better programmer Code-along with free accompanying videos on YouTube Purchase of the print book includes a free eBook in PDF, Kindle, and ePub formats from Manning Publications. About The Book The 21 fun-but-powerful activities in Tiny Python Projects teach Python fundamentals through puzzles and games. You’ll be engaged and entertained with every exercise, as you learn about text manipulation, basic algorithms, and lists and dictionaries, and other foundational programming skills. Gain confidence and experience while you create each satisfying project. Instead of going quickly through a wide range of concepts, this book concentrates on the most useful skills, like text manipulation, data structures, collections, and program logic with projects that include a password creator, a word rhymer, and a Shakespearean insult generator. Author Ken Youens-Clark also teaches you good programming practice, including writing tests for your code as you go. What You Will Learn Write command-line Python programs Manipulate Python data structures Use and control randomness Write and run tests for programs and functions Download testing suites for each project This Book Is Written For For readers familiar with the basics of Python programming. About The Author Ken Youens-Clark is a Senior Scientific Programmer at the University of Arizona. He has an MS in Biosystems Engineering and has been programming for over 20 years. Table of Contents 1 How to write and test a Python program 2 The crow’s nest: Working with strings 3 Going on a picnic: Working with lists 4 Jump the Five: Working with dictionaries 5 Howler: Working with files and STDOUT 6 Words count: Reading files and STDIN, iterating lists, formatting strings 7 Gashlycrumb: Looking items up in a dictionary 8 Apples and Bananas: Find and replace 9 Dial-a-Curse: Generating random insults from lists of words 10 Telephone: Randomly mutating strings 11 Bottles of Beer Song: Writing and testing functions 12 Ransom: Randomly capitalizing text 13 Twelve Days of Christmas: Algorithm design 14 Rhymer: Using regular expressions to create rhyming words 15 The Kentucky Friar: More regular expressions 16 The Scrambler: Randomly reordering the middles of words 17 Mad Libs: Using regular expressions 18 Gematria: Numeric encoding of text using ASCII values 19 Workout of the Day: Parsing CSV files, creating text table output 20 Password strength: Generating a secure and memorable password 21 Tic-Tac-Toe: Exploring state 22 Tic-Tac-Toe redux: An interactive version with type hints

Download or read book Python for Biologists written by Martin Jones and published by Createspace Independent Publishing Platform. This book was released on 2013 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Mastering Python Scientific Computing written by Hemant Kumar Mehta and published by Packt Publishing Ltd. This book was released on 2015-09-23 with total page 301 pages. Available in PDF, EPUB and Kindle. Book excerpt: A complete guide for Python programmers to master scientific computing using Python APIs and tools About This Book The basics of scientific computing to advanced concepts involving parallel and large scale computation are all covered. Most of the Python APIs and tools used in scientific computing are discussed in detail The concepts are discussed with suitable example programs Who This Book Is For If you are a Python programmer and want to get your hands on scientific computing, this book is for you. The book expects you to have had exposure to various concepts of Python programming. What You Will Learn Fundamentals and components of scientific computing Scientific computing data management Performing numerical computing using NumPy and SciPy Concepts and programming for symbolic computing using SymPy Using the plotting library matplotlib for data visualization Data analysis and visualization using Pandas, matplotlib, and IPython Performing parallel and high performance computing Real-life case studies and best practices of scientific computing In Detail In today's world, along with theoretical and experimental work, scientific computing has become an important part of scientific disciplines. Numerical calculations, simulations and computer modeling in this day and age form the vast majority of both experimental and theoretical papers. In the scientific method, replication and reproducibility are two important contributing factors. A complete and concrete scientific result should be reproducible and replicable. Python is suitable for scientific computing. A large community of users, plenty of help and documentation, a large collection of scientific libraries and environments, great performance, and good support makes Python a great choice for scientific computing. At present Python is among the top choices for developing scientific workflow and the book targets existing Python developers to master this domain using Python. The main things to learn in the book are the concept of scientific workflow, managing scientific workflow data and performing computation on this data using Python. The book discusses NumPy, SciPy, SymPy, matplotlib, Pandas and IPython with several example programs. Style and approach This book follows a hands-on approach to explain the complex concepts related to scientific computing. It details various APIs using appropriate examples.

Download or read book Bioinformatics Data Skills written by Vince Buffalo and published by "O'Reilly Media, Inc.". This book was released on 2015-07 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Command Line Rust written by Ken Youens-Clark and published by "O'Reilly Media, Inc.". This book was released on 2022-01-13 with total page 389 pages. Available in PDF, EPUB and Kindle. Book excerpt: Updated in 2024: A new version has been released that simplifies the programs used in the book, based on changes in the Rust language and crates since original publication. The code has been updated to reflect version 4 of the clap crate. For several consecutive years, Rust has been voted "most loved programming language" in Stack Overflow's annual developer survey. This open source systems programming language is now used for everything from game engines and operating systems to browser components and virtual reality simulation engines. But Rust is also an incredibly complex language with a notoriously difficult learning curve. Rather than focusing on the language as a whole, this guide teaches Rust using a single small, complete, focused program in each chapter. Author Ken Youens-Clark shows you how to start, write, and test each of these programs to create a finished product. You'll learn how to handle errors in Rust, read and write files, and use regular expressions, Rust types, structs, and more. Discover how to: Use Rust's standard libraries and data types such as numbers, strings, vectors, structs, Options, and Results to create command-line programs Write and test Rust programs and functions Read and write files, including stdin, stdout, and stderr Document and validate command-line arguments Write programs that fail gracefully Parse raw and delimited text manually, using regular expressions and Rust crates Use and control randomness

Download or read book Python Algorithms written by Magnus Lie Hetland and published by Apress. This book was released on 2011-02-27 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: Python Algorithms explains the Python approach to algorithm analysis and design. Written by Magnus Lie Hetland, author of Beginning Python, this book is sharply focused on classical algorithms, but it also gives a solid understanding of fundamental algorithmic problem-solving techniques. The book deals with some of the most important and challenging areas of programming and computer science, but in a highly pedagogic and readable manner. The book covers both algorithmic theory and programming practice, demonstrating how theory is reflected in real Python programs. Well-known algorithms and data structures that are built into the Python language are explained, and the user is shown how to implement and evaluate others himself.

Download or read book R Bioinformatics Cookbook written by Dan MacLean and published by Packt Publishing Ltd. This book was released on 2019-10-11 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key FeaturesApply modern R packages to handle biological data using real-world examplesRepresent biological data with advanced visualizations suitable for research and publicationsHandle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analysesBook Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you’ll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you’ll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learnEmploy Bioconductor to determine differential expressions in RNAseq dataRun SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and IndelsUse ggplot to create and annotate a range of visualizationsQuery external databases with Ensembl to find functional genomics informationExecute large-scale multiple sequence alignment with DECIPHER to perform comparative genomicsUse d3.js and Plotly to create dynamic and interactive web graphicsUse k-nearest neighbors, support vector machines and random forests to find groups and classify dataWho this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites.