Book Image

Bioinformatics with Python Cookbook - Third Edition

By : Tiago Antao
Book Image

Bioinformatics with Python Cookbook - Third Edition

By: Tiago Antao

Overview of this book

Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data, and this book will show you how to manage these tasks using Python. This updated third edition of the Bioinformatics with Python Cookbook begins with a quick overview of the various tools and libraries in the Python ecosystem that will help you convert, analyze, and visualize biological datasets. Next, you'll cover key techniques for next-generation sequencing, single-cell analysis, genomics, metagenomics, population genetics, phylogenetics, and proteomics with the help of real-world examples. You'll learn how to work with important pipeline systems, such as Galaxy servers and Snakemake, and understand the various modules in Python for functional and asynchronous programming. This book will also help you explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks, including Dask and Spark. In addition to this, you’ll explore the application of machine learning algorithms in bioinformatics. By the end of this bioinformatics Python book, you'll be equipped with the knowledge you need to implement the latest programming techniques and frameworks, empowering you to deal with bioinformatics data on every scale.
Table of Contents (15 chapters)

Installing the required software with Docker

Docker is the most widely-used framework for implementing operating system-level virtualization. This technology allows you to have an independent container: a layer that is lighter than a virtual machine but still allows you to compartmentalize software. This mostly isolates all processes, making it feel like each container is a virtual machine.

Docker works quite well at both extremes of the development spectrum: it’s an expedient way to set up the content of this book for learning purposes and could become your platform of choice for deploying your applications in complex environments. This recipe is an alternative to the previous recipe.

However, for long-term development environments, something along the lines of the previous recipe is probably your best route, although it can entail a more laborious initial setup.

Getting ready

If you are on Linux, the first thing you have to do is install Docker. The safest solution...