Preface

Bioinformatics is an incredibly transformative field that is drawing more and more interest in this era of computationally driven science. From its early days of developing the first sequence atlases and alignment tools to the excitement of the Human Genome Project, bioinformatics has always been a highly interdisciplinary field. It draws those passionate about using computation to advance science in ways never before achievable.

This book will teach you practical methods for solving real-world problems in bioinformatics. We will cover all the major topics in bioinformatics to give you a solid foundation in each area. The book will be taught using Python, which has become the predominant language in bioinformatics. In each recipe, we’ll show you the important Python libraries and programming techniques used to solve relevant problems, and give you a wealth of resources to learn more and grow your skills.

We’ll start with a gentle introduction to Python and basic data processing and data science techniques. We will then cover core algorithms in bioinformatics for genome alignment, assembly, annotation, and variant calling.

Next, we’ll dive into the wealth of public databases available for bioinformatics data and learn how to navigate them. We’ll then cover important applications of bioinformatics, such as phylogenetics, metabolic modeling, and genome editing.

We’ll give you a solid introduction to cloud computing and cover the major workflow systems in bioinformatics that are used to orchestrate complex pipelines. Finally, we’ll discuss the growing impact of machine learning in bioinformatics and show you how scientists are using large language models to design new proteins and even entire genomes. We’ll finish by talking about exciting frontier topics in bioinformatics, such as microfluidics, single-cell analysis, and connectomics.

This book provides practical examples of using Python libraries in your work. The book takes an AI-first approach to coding. You will learn how to use AI tools to upgrade, debug, and test your code. Throughout the book, AI tips are provided to help you take your learning further. You will be guided to extensive resources on programming, with an emphasis on practical applications in the workplace. You will also be exposed to many scientific resources to inspire meaningful application of the tools to real-world problems.

This fourth edition has been extensively upgraded with modernized code, new libraries, new approaches and applications, and new chapters on the latest topics.