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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Solve advanced computational biology problems and build production pipelines with Python and AI tools

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Product type Paperback
Published in Dec 2025
Publisher Packt
ISBN-13 9781836642756
Length 618 pages
Edition 4th Edition
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Author (1):
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Shane Brubaker Shane Brubaker
Author Profile Icon Shane Brubaker
Shane Brubaker
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Toc

Table of Contents (22) Chapters Close

Preface 1. Chapter 1: Computer Specifications and Python Setup 2. Chapter 2: Basics of Data Manipulation FREE CHAPTER 3. Chapter 3: Modern Coding Practices and AI-Generated Coding 4. Chapter 4: Data Science and Graphing 5. Chapter 5: Alignment and Variant Calling 6. Chapter 6: Annotation and Biological Interpretation 7. Chapter 7: Genomes and Genome Assembly 8. Chapter 8: Accessing Public Databases 9. Chapter 9: Protein Structure and Proteomics 10. Chapter 10: Phylogenetics 11. Chapter 11: Population Genetics 12. Chapter 12: Metabolic Modeling and Other Applications 13. Chapter 13: Genome Editing 14. Chapter 14: Cloud Basics 15. Chapter 15: Workflow Systems 16. Chapter 16: More Workflow Systems 17. Chapter 17: Deep Learning and LLMs for Nucleic Acid and Protein Design 18. Chapter 18: Single-Cell Technology and Imaging 19. Chapter 19: Unlock Your Exclusive Benefits 20. Index 21. Other Books You May Enjoy

Technical requirements

It is important to note that, starting around 2020, Apple came out with its own chips instead of using Intel chips – these are referred to as Apple silicon chips. This change caused issues with older versions of Python and with some Python libraries. We should not encounter these in this book since we are using newer versions, but it is something to keep in mind if you ever run into issues. This book was developed on an Apple M2 Pro chip, which is an Apple silicon chip.

The code in this book was developed and tested on a computer with the following specifications:

  • MacBook Pro
  • Chip: Apple M2 Pro
  • RAM: 16 GB
  • OS: Sequoia 15.1
  • Python version: 3.12.2

If you do not have a MacBook, there are several options you could explore using cloud workstations. These options will give you a handy alternative where you can set up the appropriate environment.

If you have an AWS account, you can set up a macOS EC2 instance to use as a cloud workstation. They offer an M2 Mac Pro option matching the computer this book was developed on.

Here are some additional sites you can check out if you want to use a Mac workstation on the cloud:

In the next section, we’ll walk through setting up your system and making sure you have Python and some of the basic libraries you need (we’ll install more libraries as we go).

Free Benefits with Your Book

Your purchase includes a free PDF copy of this book along with other exclusive benefits. Check the Free Benefits with Your Book section in the Preface to unlock them instantly and maximize your learning experience.

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