Effective Python Development For Biologists

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Effective Python Development for Biologists

Author : Martin Jones
Publisher : Createspace Independent Publishing Platform
ISBN 13 : 9781539103035
Total Pages : 300 pages
Book Rating : 4.1/5 (3 download)

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Book Synopsis Effective Python Development for Biologists by : Martin Jones

Download or read book Effective Python Development for Biologists written by Martin Jones and published by Createspace Independent Publishing Platform. This book was released on 2016-09-26 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: Python is rapidly becoming the standard language for many talks in scientific research, and is particularly popular in biology and bioinformatics. One of the great strengths of Python is the ecosystem of tools and libraries that have grown up around it. This book introduces the novice biologist programmer to tools and techniques that make developing Python code easier and faster and will help you to write more reliable, performant programs. Written by a biologist, it focusses on solving the problems that students and researchers encounter every day: How do I make my program run faster? How can I be sure that my results are correct? How do I share this program with my colleagues? How can I speed up the process of writing my code? Chapters include: Environments for development - learn how you can take advantage of different tools for actually writing code, including those designed specifically for scientific work. Organising and sharing code - learn how Python's module and packaging system works, how to effectively reuse code across multiple projects, and how to share your programs with colleagues and the wider world. Testing - learn how automated testing can make your code more reliable, how to catch bugs before they impact your work, and how to edit code with confidence. Performance - learn how to make your code run quickly even on large datasets, how to understand the scaling behaviour of your code, and explore the trade offs involved in designing code. User interfaces - learn how to make your code more user friendly, how to design effective interfaces, and how to automate record-keeping with Python's logging system. About the author Martin started his programming career by learning Perl during the course of his PhD in evolutionary biology, and started teaching other people to program soon after. Since then he has taught introductory programming to hundreds of biologists, from undergraduates to PIs, and has maintained a philosophy that programming courses must be friendly, approachable, and practical. In his academic career, Martin mixed research and teaching at the University of Edinburgh, culminating in a two year stint as Lecturer in Bioinformatics. He now runs programming courses for biological researchers as a full time freelancer. Praise for Martin's previous books "Great, great book. I think this is the perfect book for any biologist to who wants to start learning to code with Python... I didn't know a command-line from a hole in the ground when I first opened up this book, and mere days later I was impressing my colleagues with my own DNA analysis programs." "Zero to writing useful programs in a weekend... Python for Biologists arrived last Thursday, 6/16/16, I spent the whole weekend glued to my laptop in a 2 1/2 day frenzy of coding, and I just finished it -- and came on Amazon to order the next one!" "One of the BEST coding books I've used in a long time. Direct applications in bioinformatics. I bought the advanced python book too." "The most useful guide to Python I've found...I've tried a few Python books, and this is by far the best for me."

Python for Biologists

Author : Martin Jones
Publisher : Createspace Independent Publishing Platform
ISBN 13 :
Total Pages : 248 pages
Book Rating : 4.3/5 (121 download)

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Book Synopsis Python for Biologists by : Martin Jones

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.

Advanced Python for Biologists

Author : Martin O. Jones
Publisher : Createspace Independent Publishing Platform
ISBN 13 : 9781495244377
Total Pages : 0 pages
Book Rating : 4.2/5 (443 download)

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Book Synopsis Advanced Python for Biologists by : Martin O. Jones

Download or read book Advanced Python for Biologists written by Martin O. Jones and published by Createspace Independent Publishing Platform. This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 Programming Using Python

Author : Mitchell L Model
Publisher : "O'Reilly Media, Inc."
ISBN 13 : 1449382908
Total Pages : 526 pages
Book Rating : 4.4/5 (493 download)

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Book Synopsis Bioinformatics Programming Using Python by : Mitchell L Model

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

Python for Scientists

Author : John M. Stewart
Publisher : Cambridge University Press
ISBN 13 : 1316641236
Total Pages : 272 pages
Book Rating : 4.3/5 (166 download)

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Book Synopsis Python for Scientists by : John M. Stewart

Download or read book Python for Scientists written by John M. Stewart and published by Cambridge University Press. This book was released on 2017-07-20 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific Python is taught from scratch in this book via copious, downloadable, useful and adaptable code snippets. Everything the working scientist needs to know is covered, quickly providing researchers and research students with the skills to start using Python effectively.

Mastering Python for Bioinformatics

Author : Ken Youens-Clark
Publisher : "O'Reilly Media, Inc."
ISBN 13 : 1098100859
Total Pages : 457 pages
Book Rating : 4.0/5 (981 download)

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Book Synopsis Mastering Python for Bioinformatics by : Ken Youens-Clark

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()

Practical Computing for Biologists

Author : Steven H.D. Haddock
Publisher : Sinauer
ISBN 13 : 9780878933914
Total Pages : 0 pages
Book Rating : 4.9/5 (339 download)

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Book Synopsis Practical Computing for Biologists by : Steven H.D. Haddock

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.

Python for the Life Sciences

Author : Alexander Lancaster
Publisher : Apress
ISBN 13 : 1484245237
Total Pages : 396 pages
Book Rating : 4.4/5 (842 download)

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Book Synopsis Python for the Life Sciences by : Alexander Lancaster

Download or read book Python for the Life Sciences written by Alexander Lancaster and published by Apress. This book was released on 2019-09-27 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: Treat yourself to a lively, intuitive, and easy-to-follow introduction to computer programming in Python. The book was written specifically for biologists with little or no prior experience of writing code - with the goal of giving them not only a foundation in Python programming, but also the confidence and inspiration to start using Python in their own research. Virtually all of the examples in the book are drawn from across a wide spectrum of life science research, from simple biochemical calculations and sequence analysis, to modeling the dynamic interactions of genes and proteins in cells, or the drift of genes in an evolving population. Best of all, Python for the Life Sciences shows you how to implement all of these projects in Python, one of the most popular programming languages for scientific computing. If you are a life scientist interested in learning Python to jump-start your research, this is the book for you. What You'll Learn Write Python scripts to automate your lab calculations Search for important motifs in genome sequences Use object-oriented programming with Python Study mining interaction network data for patterns Review dynamic modeling of biochemical switches Who This Book Is For Life scientists with little or no programming experience, including undergraduate and graduate students, postdoctoral researchers in academia and industry, medical professionals, and teachers/lecturers. “A comprehensive introduction to using Python for computational biology... A lovely book with humor and perspective” -- John Novembre, Associate Professor of Human Genetics, University of Chicago and MacArthur Fellow “Fun, entertaining, witty and darn useful. A magical portal to the big data revolution” -- Sandro Santagata, Assistant Professor in Pathology, Harvard Medical School “Alex and Gordon’s enthusiasm for Python is contagious” -- Glenys Thomson Professor of Integrative Biology, University of California, Berkeley

Python Programming for Biology

Author : Tim J. Stevens
Publisher : Cambridge University Press
ISBN 13 : 0521895839
Total Pages : 721 pages
Book Rating : 4.5/5 (218 download)

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Book Synopsis Python Programming for Biology by : Tim J. Stevens

Download or read book Python Programming for Biology written by Tim J. Stevens and published by Cambridge University Press. This book was released on 2015-02-12 with total page 721 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces Python as a powerful tool for the investigation of problems in computational biology, for novices and experienced programmers alike.

A Primer for Computational Biology

Author : Shawn T. O'Neil
Publisher :
ISBN 13 : 9780870719264
Total Pages : 0 pages
Book Rating : 4.7/5 (192 download)

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Book Synopsis A Primer for Computational Biology by : Shawn T. O'Neil

Download or read book A Primer for Computational Biology written by Shawn T. O'Neil and published by . This book was released on 2017-12-21 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work. The book is broken into three parts: Introduction to Unix/Linux: The command-line is the "natural environment" of scientific computing, and this part covers a wide range of topics, including logging in, working with files and directories, installing programs and writing scripts, and the powerful "pipe" operator for file and data manipulation. Programming in Python: Python is both a premier language for learning and a common choice in scientific software development. This part covers the basic concepts in programming (data types, if-statements and loops, functions) via examples of DNA-sequence analysis. This part also covers more complex subjects in software development such as objects and classes, modules, and APIs. Programming in R: The R language specializes in statistical data analysis, and is also quite useful for visualizing large datasets. This third part covers the basics of R as a programming language (data types, if-statements, functions, loops and when to use them) as well as techniques for large-scale, multi-test analyses. Other topics include S3 classes and data visualization with ggplot2.

Computing for Biologists

Author : Ran Libeskind-Hadas
Publisher :
ISBN 13 : 9781316054239
Total Pages : 220 pages
Book Rating : 4.0/5 (542 download)

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Book Synopsis Computing for Biologists by : Ran Libeskind-Hadas

Download or read book Computing for Biologists written by Ran Libeskind-Hadas and published by . This book was released on 2014 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computing for Biologists

Author : Ran Libeskind-Hadas
Publisher : Cambridge University Press
ISBN 13 : 1107042828
Total Pages : 219 pages
Book Rating : 4.1/5 (7 download)

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Book Synopsis Computing for Biologists by : Ran Libeskind-Hadas

Download or read book Computing for Biologists written by Ran Libeskind-Hadas and published by Cambridge University Press. This book was released on 2014-09-22 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book teaches life science students how to use Python programming and computational problem-solving in the context of compelling biological applications.

Computing Skills for Biologists

Author : Stefano Allesina
Publisher : Princeton University Press
ISBN 13 : 0691182752
Total Pages : 440 pages
Book Rating : 4.6/5 (911 download)

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Book Synopsis Computing Skills for Biologists by : Stefano Allesina

Download or read book Computing Skills for Biologists written by Stefano Allesina and published by Princeton University Press. This book was released on 2019-01-15 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: A concise introduction to key computing skills for biologists While biological data continues to grow exponentially in size and quality, many of today’s biologists are not trained adequately in the computing skills necessary for leveraging this information deluge. In Computing Skills for Biologists, Stefano Allesina and Madlen Wilmes present a valuable toolbox for the effective analysis of biological data. Based on the authors’ experiences teaching scientific computing at the University of Chicago, this textbook emphasizes the automation of repetitive tasks and the construction of pipelines for data organization, analysis, visualization, and publication. Stressing practice rather than theory, the book’s examples and exercises are drawn from actual biological data and solve cogent problems spanning the entire breadth of biological disciplines, including ecology, genetics, microbiology, and molecular biology. Beginners will benefit from the many examples explained step-by-step, while more seasoned researchers will learn how to combine tools to make biological data analysis robust and reproducible. The book uses free software and code that can be run on any platform. Computing Skills for Biologists is ideal for scientists wanting to improve their technical skills and instructors looking to teach the main computing tools essential for biology research in the twenty-first century. Excellent resource for acquiring comprehensive computing skills Both novice and experienced scientists will increase efficiency by building automated and reproducible pipelines for biological data analysis Code examples based on published data spanning the breadth of biological disciplines Detailed solutions provided for exercises in each chapter Extensive companion website

Parallel Programming with Python

Author : Jan Palach
Publisher : Packt Publishing Ltd
ISBN 13 : 178328840X
Total Pages : 173 pages
Book Rating : 4.7/5 (832 download)

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Book Synopsis Parallel Programming with Python by : Jan Palach

Download or read book Parallel Programming with Python written by Jan Palach and published by Packt Publishing Ltd. This book was released on 2014-06-25 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: A fast, easy-to-follow and clear tutorial to help you develop Parallel computing systems using Python. Along with explaining the fundamentals, the book will also introduce you to slightly advanced concepts and will help you in implementing these techniques in the real world. If you are an experienced Python programmer and are willing to utilize the available computing resources by parallelizing applications in a simple way, then this book is for you. You are required to have a basic knowledge of Python development to get the most of this book.

Hands on Data Science for Biologists Using Python

Author : Yasha Hasija
Publisher : CRC Press
ISBN 13 : 9780367546793
Total Pages : 224 pages
Book Rating : 4.5/5 (467 download)

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Book Synopsis Hands on Data Science for Biologists Using Python by : Yasha Hasija

Download or read book Hands on Data Science for Biologists Using Python written by Yasha Hasija and published by CRC Press. This book was released on 2021 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hands-on Data Science for Biologists using Python has been conceptualized to address the massive data handling needs of modern-day biologists. With the advent of high throughput technologies and consequent availability of omics data, biological science has become a data-intensive field. This hands-on textbook has been written with the inception of easing data analysis by providing an interactive, problem-based instructional approach in Python programming language. The book starts with an introduction to Python and steadily delves into scrupulous techniques of data handling, preprocessing, and visualization. The book concludes with machine learning algorithms and their applications in biological data science. Each topic has an intuitive explanation of concepts and is accompanied with biological examples. Features of this book: The book contains standard templates for data analysis using Python, suitable for beginners as well as advanced learners. This book shows working implementations of data handling and machine learning algorithms using real-life biological datasets and problems, such as gene expression analysis; disease prediction; image recognition; SNP association with phenotypes and diseases. Considering the importance of visualization for data interpretation, especially in biological systems, there is a dedicated chapter for the ease of data visualization and plotting. Every chapter is designed to be interactive and is accompanied with Jupyter notebook to prompt readers to practice in their local systems. Other avant-garde component of the book is the inclusion of a machine learning project, wherein various machine learning algorithms are applied for the identification of genes associated with age-related disorders. A systematic understanding of data analysis steps has always been an important element for biological research. This book is a readily accessible resource that can be used as a handbook for data analysis, as well as a platter of standard code templates for building models.

Expert Python Programming

Author : Michal Jaworski
Publisher : Packt Publishing Ltd
ISBN 13 : 1785884395
Total Pages : 536 pages
Book Rating : 4.7/5 (858 download)

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Book Synopsis Expert Python Programming by : Michal Jaworski

Download or read book Expert Python Programming written by Michal Jaworski and published by Packt Publishing Ltd. This book was released on 2016-05-20 with total page 536 pages. Available in PDF, EPUB and Kindle. Book excerpt: Become an ace Python programmer by learning best coding practices and advance-level concepts with Python 3.5 About This Book Based on the latest stable version of Python (version 3.5) Creating well manageable code that will run in various environments with different sets of dependencies Packed with advanced concepts and best practices to write efficient Python code Who This Book Is For The book would appeal to web developers and Python programmers who want to start using version 3.5 and write code efficiently. Basic knowledge of Python programming is expected. What You Will Learn Conventions and best practices that are widely adopted in the python community Package python code effectively for community and production use Easy and lightweight ways to automate code deployment on remote systems Improve your code's quality, reliability, and performance Write concurrent code in python Extend python with code written in different languages In Detail Python is a dynamic programming language, used in a wide range of domains by programmers who find it simple, yet powerful. Even if you find writing Python code easy, writing code that is efficient and easy to maintain and reuse is a challenge. The focus of the book is to familiarize you with common conventions, best practices, useful tools and standards used by python professionals on a daily basis when working with code. You will begin with knowing new features in Python 3.5 and quick tricks for improving productivity. Next, you will learn advanced and useful python syntax elements brought to this new version. Using advanced object-oriented concepts and mechanisms available in python, you will learn different approaches to implement metaprogramming. You will learn to choose good names, write packages, and create standalone executables easily. You will also be using some powerful tools such as buildout and vitualenv to release and deploy the code on remote servers for production use. Moving on, you will learn to effectively create Python extensions with C, C++, cython, and pyrex. The important factors while writing code such as code management tools, writing clear documentation, and test-driven development are also covered. You will now dive deeper to make your code efficient with general rules of optimization, strategies for finding bottlenecks, and selected tools for application optimization. By the end of the book, you will be an expert in writing efficient and maintainable code. Style and approach An easy-to-follow guide that covers industry followed best practices in Python programming

Perl Programming for Biologists

Author : D. Curtis Jamison
Publisher : John Wiley & Sons
ISBN 13 : 9780471430599
Total Pages : 206 pages
Book Rating : 4.4/5 (35 download)

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Book Synopsis Perl Programming for Biologists by : D. Curtis Jamison

Download or read book Perl Programming for Biologists written by D. Curtis Jamison and published by John Wiley & Sons. This book was released on 2003-07-14 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusable and maintainable scripts that spare the rote repetition of code.