Best Python books for Bioinformatics

Best Python books for Bioinformatics

The page is a read list of the best books that you can read for many hours of reading and research in different categories. Over 100 good books grouped by category are available for you to read.

This is a list of people who have no time for books of little importance. In each category, I list only the best books to read. You can be sure everybody’s awesome and worth your time.

Bioinformatics is an evolving field and thus has lots of advancements that require languages like python to be learned. Find the list of best books for Python in Bioinformatics:

1. Effective Python Development for Biologists

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.”

2. Python for Bioinformatics (Chapman & Hall/CRC Computational Biology Series)

In today’s data-driven biology, programming knowledge is essential in turning ideas into a 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.

3. Advanced Python for Biologists

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.

4. Python Programming for Biology: Bioinformatics and Beyond

Do you have a biological question that could be readily answered by computational techniques, but little experience in programming? Do you want to learn more about the core techniques used in computational biology and bioinformatics? Written in an accessible style, this guide provides a foundation for both newcomers to computer programming and those interested in learning more about computational biology.

The chapters guide the reader through a complete beginners’ course to programming in Python, with an introduction to computing jargon; descriptions of core bioinformatics methods with working Python examples; scientific computing techniques, including image analysis, statistics and machine learning. This book also functions as a language reference written in straightforward English, covering the most common Python language elements and a glossary of computing and biological terms. This title will teach undergraduates, postgraduates and professionals working in the life sciences how to program with Python, a powerful, flexible and easy-to-use language.

5. Python: – The Bible

Python: – The Bible- 3 manuscripts in 1 book: -Python programming for beginners -Python programming for Intermediates -Python programming for advanced.

6. Bioinformatics Algorithms: Design and Implementation in Python

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.

7. Bioinformatics with Python Cookbook, Second Edition

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 the analysis, population genetics, and more Explore various statistical and machine learning techniques for bioinformatics data analysis Book DescriptionBioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. Best Python books for Bioinformatics

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 proteomics 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.

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.

Best Python books for Bioinformatics

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