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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 & AI tools

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Product type Paperback
Published in Jan 2026
Last Updated in Oct 2025
Publisher Packt
ISBN-13 9781836642756
Length 617 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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Table of Contents (14) Chapters Close

1. Bioinformatics with Python Cookbook, Fourth Edition: Solve advanced computational biology problems and build production pipelines with Python & AI tools FREE CHAPTER
2. Chapter 1: Computer Specifications and Python Setup 3. Chapter 2: Basics of Data Manipulation 4. Chapter 3: Modern Coding Practices and AI-generated coding 5. Chapter 4: Data Science and Graphing 6. Chapter 5: Alignment and Variant Calling 7. Chapter 6: Annotation and Biological Interpretation 8. Chapter 7: Genomes and Genome Assembly 9. Chapter 8: Accessing Public Databases 10. Chapter 9: Protein Structure and Proteomics 11. Chapter 10: Phylogenetics 12. Chapter 11: Population Genetics 13. Chapter 12: Mectabolic Modeling and Other Applications 14. Chapter 13: Genome Editing

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. Containers will be discussed in more detail in Chapter 14, Cloud Basics.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.Conda and Docker are key tools to help maintain software compatibility and reproducibility across different systems and libraries. We’ll discuss reproducibility more in Chapter 15, Workflow Systems.

Note

This recipe is an alternative to the previous recipe. Normally, if...

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