Welcome to the Biostar Handbook

Last updated on February 18, 2020

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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.

The Biostar Handbook Collection

The Biostar Handbook is being reworked into separate, more manageable volumes of study.

Access to new books and new content is included with your subscription!

Get notified

A few times a year we send out emails summarizing the changes made to the book

High resolution images

In the web version of the book all images have larger resolution than that shown on the page itself. If you want to see an image in full resolution right-click then select “Open image in new tab”.

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.

How to download the book?

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

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.

Current online courses

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

This course has been launched in September of 2019. The course tracks the 2019 course BMMB 852: Appplied Bioinformatics at Penn State. Slides are provided.


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


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


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.


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.


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?

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