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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Use modern Python libraries and applications to solve real-world computational biology problems

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Product type Paperback
Published in Sep 2022
Publisher Packt
ISBN-13 9781803236421
Length 360 pages
Edition 3rd Edition
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Author (1):
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Tiago Antao Tiago Antao
Author Profile Icon Tiago Antao
Tiago Antao
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Table of Contents (15) Chapters Close

Preface 1. Chapter 1: Python and the Surrounding Software Ecology 2. Chapter 2: Getting to Know NumPy, pandas, Arrow, and Matplotlib FREE CHAPTER 3. Chapter 3: Next-Generation Sequencing 4. Chapter 4: Advanced NGS Data Processing 5. Chapter 5: Working with Genomes 6. Chapter 6: Population Genetics 7. Chapter 7: Phylogenetics 8. Chapter 8: Using the Protein Data Bank 9. Chapter 9: Bioinformatics Pipelines 10. Chapter 10: Machine Learning for Bioinformatics 11. Chapter 11: Parallel Processing with Dask and Zarr 12. Chapter 12: Functional Programming for Bioinformatics 13. Index 14. Other Books You May Enjoy

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...

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