Bioinformatics with Python Cookbook is a recipe-based guide that helps you choose from a wide range of Python packages and approaches for classic bioinformatics problems.
Starting with the fundamentals of key Python libraries used for data science and BioInformatics, you will progress through key tasks in sequencing analysis, quality control, alignment and variant calling. Along the way you learn important tips about modern coding practices and recent advances in the field. You will deep dive into core bioinformatics tasks such as phylogenetic analysis and population genomics. You’ll work with practical examples using libraries such as numpy, pandas, & sci-kit learn. The book provides exposure to the wealth of modern public bioinformatics databases available. You'll gain hands-on knowledge of important cloud computing approaches and learn how to set up workflow orchestration systems for controlling bioinformatics pipelines. You will gain an understanding of how bioinformatics is evolving to include AI and we’ll try out new techniques such as Large Language Models to design proteins and DNA.
By the end of this book you will gain a functional understanding of using Python for Bioinformatics and how to launch Bioinformatics pipelines.

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Spis treści

Bioinformatics with Python Cookbook. Solve advanced computational biology problems and build production pipelines with Python & AI tools - Fourth Edition eBook -- spis treści

• 1. Computer Specification and Python Setup
• 2. Basics of Data Manipulation
• 3. Modern Coding Practices and AI generated Coding
• 4. Data Science and Graphing
• 5. Alignment and Variant Calling
• 6. Annotation and Biological Interpretation
• 7. Genomes and Genome Assembly
• 8. Nucleic Acid Database
• 9. Protein Databases
• 10. Phylogenetics
• 11. Population Genomics
• 12. Metabolic Modeling and Other Applications
• 13. Genome Editing
• 14. Cloud Basics, Infrastructure as Code, and Containers
• 15. Workflow Systems
• 16. Machine Learning, Deep Learning, and LLMs for Nucleic Acid and Protein Design
• 17. Single Cell Technology and Imaging Data