The Biostar Handbook: 2nd Edition
Welcome to the Biostar Handbook
Last updated on September 4, 2026, ISBN: 978-0-578-80435-4
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.
If you are new to Bioinformatics start with the Applied Bioinformatics (2026) course.
Online courses
We offer the following online courses:
Applied Bioinformatics (2026) - Learn bioinformatics in the age of AI. This course is currently under development and focuses on integrating AI into the process of learning and practicing bioinformatics. The recommended course for 2026.
FastTrack Bioinformatics (2025) - A comprehensive but more classical course on bioinformatics data analysis. It still uses AI, but in a less integrated way. The course contains presentations and videos.
Applied Bioinformatics (2023) - An old-school approach to teaching bioinformatics from the pre-AI era. Published here for historical purposes … turns out 2023 is now old history! Challenging quizzes come with this course. Try them if you dare.
The courses contain materials for BMMB 852: Applied Bioinformatics, a graduate-level course in Penn State’s Bioinformatics and Genomics program. The course runs from August through December.
Applied Bioinformatics (2026) - Bioinformatics in the age of AI
Under development for 2026. I expect to complete it by the end of the year. Built around AI and agentic methods.
FastTrack Bioinformatics (2025) - A practical approach to bioinformatics data analysis.
Completed course materials for the FastTrack Bioinformatics course as delivered in 2025 for BMMB 852: Applied Bioinformatics (2025).
The Biostar Handbook Collection
The Biostar Handbook is a collection of volumes:
- The Biostar Handbook - An introduction to Bioinformatics as a scientific field.
- The Art of Bioinformatics Scripting - Learn advanced Unix and Bash scripting skills.
- RNA-Seq by Example - Master RNA-Seq data analysis.
- Corona Virus Genome Analysis - Advanced topics devoted to the study of the Corona Virus.
- Biostar Workflows - Create automated bioinformatics workflows
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Get notified
A few times a year we send out emails summarizing the changes made to the book. If you have access to the book, you are already subscribed. No need to sign up again. You can unsubscribe at any time by clicking on the link at the bottom of the email.
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Your book subscription includes access to all of our online courses.
How to download the book?
Use the website whenever possible. The book and the course materials change often; the web version is always the most current.
PDF and eBook downloads lag behind the website. Treat them as high-level reference, not as the source of truth for how an analysis should be performed:
On the website, images are displayed smaller than their full resolution. Right-click an image and choose Open image in new tab to view it at full size.
Shell casting
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:
An old school approach to bioinformatics data analysis.
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.
What is a Biostar?
It is not a what; it is a who. And it could be you.
A Biostar is a mythical creature forged in the chaotic fires of science, wielding the power of a coder, a statistician, and biologist — while occasionally muttering about R vs. Python. Biostars can often be found debating the most efficient way to process large datasets, while secretly googling: what does this error mean?
Visualization inspired by a blog post from 2014 by Anthony Fejes: Who is a bioinformatician?
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