What does the book cover at this time?
Scroll down on the menu on the left to see the sections and the entries associated with them. An section with a label but no articles under it is currently under development and should have content released within a month.
What comes in 2017 and beyond?
We encourage suggestions from readers on the topics they would like to see covered. Our plan currently includes the following:
- Genome and Transcriptome Assembly (early 2017)
- Metagenomics (early 2017)
- Chip-Seq (mid-2017)
- Workbook with assignments, exercises, and answer keys.
- Evaluations and tests. Allow readers to evaluate how well they understand the concepts.
All along we will expand and enrich the existing chapters. New methods and techniques will be added to each methodology. Obsolete approaches will be retired.
How was this book developed?
This book is the result of a multi-year experience of teaching life scientists on how to analyze their data. Almost two years ago we decided to collect the materials into a book called the Biostar Handbook. Along the way, we tossed out a relatively complete version of it as it was deemed inadequate. As Fred Brooks once wrote in the Mythical Man Month "Plan To Throw One Away." And throw away one we did.
Then it occurred to us -- why are we writing a traditional book when the Biostars Q&A and online style works so much better. So we switched to that -- and found that this approach worked spectacularly well for both instructors and students as well!
What was the timeline so far?
- 2010-2013: The proposal for the BMMB Applied Bioinformatics accepted by the Penn State Graduate School. The course offered as an elective course at Penn State sees enrollment over capacity every single year since its launch. The course is practically rewritten from scratch every single year.
- 2013-2015: A transition is made to the web-based distribution of materials. The code is reused from semester to semester and shared through a web repository. The material is enriched and improved every single year. We decide to combine all content into a single traditional book titled The Biostar Handbook.
- Spring 2016: The "first edition" of the Biostar Handbook is completed. It is a monolithic, "traditional" book designed to be printed out. The shortcomings of the model became painfully apparent. Some of the content in the book was already obsolete. The decision is made to transition to a web-based book that can be quickly and efficiently updated.
- Fall 2016: The web-book is launched as a textbook for the BMMB 852: Applied Bioinformatics course. Chapters are completed on week-by-week schedule as they are presented in class.