The Biostar Handbook: 2nd Edition
Last updated on September 18, 2023, 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.
The Biostar Handbook is being reworked into separate, more manageable volumes of study.
- 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
Access to new books and new content is included with your subscription!
A few times a year we send out emails summarizing the changes made to the book
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Access to the online courses is included with the book, for the duration of your subscription.
The course, reworked for the Fall of 2021, tracks the BMMB 852: Applied Bioinformatics graduate-level course at Penn State.
Please note that the following courses are to be considered outdated and are listed here only for reference:
- Learn Bioinformatics in 100 hours (2017)
- Python Programming (2018)
- Bioinformatics Cookbook (2018)
- Learn Bioinformatics the Right Way (2019)
- Bioinformatics data analysis (2019)
Though valuable and contain useful content, the links within our older courses are not kept up to date with the changes in 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.
In addition, in the web version of the book all images have larger resolution than that shown on the page itself. To see an image in full resolution right-click then select “Open image in new tab”.
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.
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.
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.
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 from 2014 by Anthony Fejes: Who is a bioinformatician?
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