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Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook - Fourth Edition

By : Shane Brubaker
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Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

By: Shane Brubaker

Overview of this book

If you've ever felt overwhelmed by the vast number of Python tools available for bioinformatics, you're not alone. The Bioinformatics with Python Cookbook is a recipe-based guide that explores practical approaches for solving classic bioinformatics challenges, showing you which Python packages work best for each task. You’ll start with the essential Python libraries for data science and bioinformatics, then move through key workflows in sequencing analysis, quality control, alignment, and variant calling. Along the way, you’ll pick up modern coding practices, explore recent advances in bioinformatics research, and gain hands-on experience with libraries such as NumPy, pandas, and sci-kit learn. This book walks you through core bioinformatics tasks such as phylogenetic analysis and population genomics while familiarizing you with the wealth of modern public bioinformatics databases. You’ll learn cloud computing approaches used by researchers, set up workflow orchestration systems for controlling bioinformatics pipelines, and see how AI and the use of large language models (LLMs) are reshaping the field–right down to designing proteins and DNA. By the end of this book, you’ll be ready to apply Python for real bioinformatics work and launch bioinformatics pipelines for your research.
Table of Contents (22 chapters)
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Computer Specifications and Python Setup

We will start by installing the basic software that is required for most of this book. This will include the Python distribution, some fundamental Python libraries, and our Jupyter Notebook environment. We will also set up our GitHub environment and gain access to the repository for the book. As different users have different requirements, we will cover two different approaches for installing the software. One approach is using the Anaconda Python (http://docs.continuum.io/anaconda/) distribution and the other is via Docker (a server virtualization method based on containers sharing the same operating system kernel; please refer to https://www.docker.com/). This will still install Anaconda for you but inside a container.

If you are using a Windows-based operating system, you are strongly encouraged to consider changing your operating system or using Docker via some of the existing options on Windows. On macOS, you should be able to install most of the software natively, though Docker is also available. Learning using a local distribution (Anaconda or something else) is easier than Docker, but given that package management can be complex in Python, Docker images provide a level of stability.

Most modern data scientists use a Mac due to the ease with which you can interact with a native Linux-style operating system. We recommend using a similar computer for this book. In the Technical requirements section, we provide the specifications of the computer and libraries used to develop this book. In most cases, deviations from such a system should work fine with minimal modifications, but if you have trouble, you can try the Docker container. Another alternative could be to use a cloud workstation (some options follow).

In this chapter, we will cover the following recipes:

  • Installing the required software with Anaconda
  • Installing the required software with Docker
  • Introduction to Jupyter Notebook

In this chapter, we will first install some prerequisite software – details of which are given in the Technical requirements section. Each recipe will then take you through the software and the steps that are needed to install it. Each chapter and section might have extra requirements on top of these – we will make those clear as the book progresses. An alternative way to start is to use the Installing the required software with Docker recipe, after which everything will be taken care of for you via a Docker container.

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Bioinformatics with Python Cookbook
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