Effective Python Development For Biologists

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Effective Python Development For Biologists

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Author : Martin Jones
language : en
Publisher: Createspace Independent Publishing Platform
Release Date : 2016-09-26

Effective Python Development For Biologists written by Martin Jones and has been published by Createspace Independent Publishing Platform this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-09-26 with categories.

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."

Computing For Biologists

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Author : Ran Libeskind-Hadas
language : en
Publisher:
Release Date : 2014

Computing For Biologists written by Ran Libeskind-Hadas and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with Biology categories.

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.

Python For Biologists

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Author : Martin Jones
language : en
Publisher: Createspace Independent Publishing Platform
Release Date : 2013

Python For Biologists written by Martin Jones and has been published by Createspace Independent Publishing Platform this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with Biology categories.

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.

Mastering Python For Bioinformatics

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Author : Ken Youens-Clark
language : en
Publisher: "O'Reilly Media, Inc."
Release Date : 2021-05-05

Mastering Python For Bioinformatics written by Ken Youens-Clark and has been published by "O'Reilly Media, Inc." this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-05-05 with Computers categories.

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()

Advanced Python For Biologists

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Author : Martin O. Jones
language : en
Publisher: Createspace Independent Publishing Platform
Release Date : 2014

Advanced Python For Biologists written by Martin O. Jones and has been published by Createspace Independent Publishing Platform this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with Biology categories.

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.

Python Programming For Biology

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Author : Tim J. Stevens
language : en
Publisher: Cambridge University Press
Release Date : 2015-02-12

Python Programming For Biology written by Tim J. Stevens and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-02-12 with Science categories.

This book introduces Python as a powerful tool for the investigation of problems in computational biology, for novices and experienced programmers alike.

Computing For Biologists

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Author : Ran Libeskind-Hadas
language : en
Publisher: Cambridge University Press
Release Date : 2014-09-22

Computing For Biologists written by Ran Libeskind-Hadas and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-09-22 with Science categories.

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.

Reproducible Bioinformatics With Python

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Author : Ken Youens-Clark
language : en
Publisher: O'Reilly Media
Release Date : 2021-08-17

Reproducible Bioinformatics With Python written by Ken Youens-Clark and has been published by O'Reilly Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-08-17 with Computers categories.

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()

Python For The Life Sciences

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Author : Alexander Lancaster
language : en
Publisher: Apress
Release Date : 2019-09-27

Python For The Life Sciences written by Alexander Lancaster and has been published by Apress this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-09-27 with Computers categories.

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

Managing Your Biological Data With Python

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Author : Allegra Via
language : en
Publisher: CRC Press
Release Date : 2014-03-18

Managing Your Biological Data With Python written by Allegra Via and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-03-18 with Science categories.

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.