Welcome to the Biostar Handbook

Last updated on January 23, 2020


The Biostar Handbook introduces readers to bioinformatics, the scientific discipline at the intersection of biology, computer science, and statistical data analytics dedicated to the digital processing of genomic information.

The Biostar Handbook has been developed, improved and refined over more than a half decade in a research university setting while used in an accredited Ph.D. level training program. The contents of this book have provided the analytical foundation to thousands of students, many of whom have become full-time bioinformaticians and work at the most innovative companies in the world.

News: Shell casting (January 2020)

The book now includes shell casts to demonstrate command line usage. The shell casts are not videos! These animations are textual, captured from a terminal exactly as typed, with sharp visibility, will zoom with your screen font sizes, may be paused at any time, and may be selected for copy-paste from the screen! Here is an example:

Shell casts are only visible via the web. PDF and ebooks do not have these animations embedded in them. Animations are a new feature in 2020. As we re-work the book we will be adding shell casts into each chapter.

News: The Art of Bioinformatics Scripting (November 2019)

The Biostar Handbook has grown huge :-) it is now close to 1000 pages! To manage this complexity we have started reworking the various chapters into independent books.

The reorganization will allow readers to more easily locate the information that they need. It will allow us to design and formulate specific training plans that are customized to specific needs. The first book section that has been reworked covers Unix Scripting and is titled:

Over the next year we will move more content into different volumes of the Biostar Handbook. We will be releasing online courses will target specific domains rather than treating bioinformatics as a single subject.

Access to all new books and materials is included with your subscription!

How to download the book?

The book is available to registered users. The latest versions can be downloaded from:

The book is updated frequently, especially during the Spring and Fall semesters when the book is used as a textbook.

We recommend reading and accessing the book via the website! The web version will always contain the most recent additions and most up-to-date content. A few times a year we send out emails that describe the new additions. Subscribe below to be notified of new developments:

Current online courses

Access to all courses is included with the book for the duration of your subscription.

Course: Learn Bioinformatics the Right Way (Fall 2019)

This course has os launching in September of 2019. The course tracks the 2019 course BMMB 852: Appplied Bioinformatics at Penn State. Slides and audio tracks (with occasional video) will be provided.

Course: Bioinformatics Data Analysis (Spring 2019)

This course has 18 lectures, video presentations. It is our recommended course that follows the 2nd edition of the Biostar Handbook.

Course: Learn Bioinformatics in 100 hours (2017)

The course has 30 lectures, slides, assignments and quizzes (no videos). This course was developed using the 1st edition of the Biostar Handbook.

Course: Bioinformatics Recipes Course (2018)

This course comes with six lectures, video presentations. Some of the materials for this course have been merged into the Bioinformatics Data Analysis (2019) course.

Course: Python Programming (2018)

The course has four lectures with videos, slides, assignments, and quizzes. The course is incomplete and will be rebooted in the fall of 2019 or early spring 2020.

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How was the book developed?

We have been teaching bioinformatics and programming courses to life scientists for many years now. We are also the developers and maintainers of Biostars: Bioinformatics Question and Answer website the leading resource for helping bioinformatics scientists with their data analysis questions.

We wrote this book based on these multi-year experiences in training students and interacting with scientists that needed help to complete their analyses. We are uniquely in tune with the challenges and complexities of applying bioinformatics methods to real problems, and we’ve designed this book to help readers overcome these challenges and go further than they have ever imagined.

How is this book different?

We use a Question/Answer based format to explain concepts and demonstrate methods simply and practically. We found this to be the most efficient training method for the topics that we cover.

Who is a Biostar?

It is not a what; it is a who. And it could be you. It is the person whose responsibilities go beyond clear boundaries. This book is for them.

Visualization inspired by a blog post by Anthony Fejes: Who is a bioinformatician?