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Author: Martin Jones Publisher: Createspace Independent Publishing Platform ISBN: 9781539103035 Category : Languages : en Pages : 300
Book Description
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."
Author: Martin Jones Publisher: Createspace Independent Publishing Platform ISBN: 9781539103035 Category : Languages : en Pages : 300
Book Description
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."
Author: Martin Jones Publisher: Createspace Independent Publishing Platform ISBN: Category : Computers Languages : en Pages : 248
Book Description
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.
Author: Mitchell L Model Publisher: "O'Reilly Media, Inc." ISBN: 1449382908 Category : Science Languages : en Pages : 526
Book Description
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
Author: Martin O. Jones Publisher: Createspace Independent Publishing Platform ISBN: 9781495244377 Category : Biology Languages : en Pages : 0
Book Description
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.
Author: Ken Youens-Clark Publisher: "O'Reilly Media, Inc." ISBN: 1098100859 Category : Computers Languages : en Pages : 457
Book Description
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()
Author: John M. Stewart Publisher: Cambridge University Press ISBN: 1316641236 Category : Computers Languages : en Pages : 272
Book Description
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.
Author: Steven H.D. Haddock Publisher: Sinauer ISBN: 9780878933914 Category : Medical Languages : en Pages : 0
Book Description
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.
Author: Shawn T. O'Neil Publisher: ISBN: 9780870719264 Category : Science Languages : en Pages : 0
Book Description
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.
Author: Stefano Allesina Publisher: Princeton University Press ISBN: 0691182752 Category : Computers Languages : en Pages : 440
Book Description
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
Author: John Hunt Publisher: Springer Nature ISBN: 3031403363 Category : Computers Languages : en Pages : 638
Book Description
Advanced Guide to Python 3 Programming 2nd Edition delves deeply into a host of subjects that you need to understand if you are to develop sophisticated real-world programs. Each topic is preceded by an introduction followed by more advanced topics, along with numerous examples, that take you to an advanced level. This second edition has been significantly updated with two new sections on advanced Python language concepts and data analytics and machine learning. The GUI chapters have been rewritten to use the Tkinter UI library and a chapter on performance monitoring and profiling has been added. In total there are 18 new chapters, and all remaining chapters have been updated for the latest version of Python as well as for any of the libraries they use. There are eleven sections within the book covering Python Language Concepts, Computer Graphics (including GUIs), Games, Testing, File Input and Output, Databases Access, Logging, Concurrency and Parallelism, Reactive Programming, Networking and Data Analytics. Each section is self-contained and can either be read on its own or as part of the book as a whole. It is aimed at those who have learnt the basics of the Python 3 language but wish to delve deeper into Python’s eco system of additional libraries and modules.
Author: Martin Jones
Author: Martin Jones
Author: Martin Jones
Author: Mitchell L Model
Author: Martin O. Jones
Author: Ken Youens-Clark
Author: John M. Stewart
Author: Steven H.D. Haddock
Author: Shawn T. O'Neil
Author: Stefano Allesina
Author: John Hunt