Tuesday, 09 January 2018 14:58

New ASM Press author encourages all to enjoy the puzzle-like nature of bioinformatics

Written by 
Published in mBiosphere

Photograph of textbook author Scott Kelley and some letters representing genetic codeScientist and textbook author Scott Kelley

At the intersection of the information and -omics revolutions sits bioinformatics, which uses computational power to reveal patterns in biological data sets, especially DNA, RNA, and protein sequences. In the new ASM Press textbook Computational Biology: A Hypertextbook, authors Scott Kelley and Dennis Didulo provide an introduction to the basics of bioinformatics and present increasingly challenging computational methods to hone skills. This book is more than a textbook, with a host of online ancillary materials and print and electronic components integrated into a complete teaching resource. To understand more about this new textbook, we sat down with author Scott Kelley to pick his brain about the book, the creation process, and what makes computational biology an essential skillset for today’s scientists.


Computational Biology: A Hypertextbook by Scott Kelley and Dennis Didulo


ASM: Can you summarize in one sentence what computational biology is?

Scott Kelley: Computational biology (a.k.a. bioinformatics) encompasses the use of computer methods and databases to study biology.


ASM: What inspired you to write this textbook?

SK: Like a lot of creative efforts, the inspiration arose from a combination of vision and necessity. I came up with the idea for the interactive algorithm teaching tools while teaching bioinformatics to biology students, many of whom were not comfortable with computers. I started with simple in-class pen-and-paper puzzles to teach the concepts behind sequence search methods and other algorithms. Most of the algorithms are intuitive when you break them down into their basic elements, and the students grasped them quickly. I later had an epiphany that my little puzzles would be perfect for touchscreen devices, as use of smartphones started to skyrocket. I also realized that students needed a lot more practice problems and feedback than I was able to give them with paper problems, especially with the more difficult algorithms. Again, the website was a perfect solution: I could generate an infinite number of randomized problems, and the students could get instant feedback on all of them.

For the lab exercise portion of the class, I taught students how to use algorithm-based software (e.g., NCBI BLAST searches, phylogenetic analysis, multiple sequence alignment). The last edition of my favorite lab manual, Bioinformatics for Dummies, was published in 2007 and was badly out of date, so I had to write my own tutorials for the data analysis and database tools we used in class. This led to another epiphany: If I put these tutorials online, I could update them at any time. This is great because, as everyone knows, nerds are always changing websites to improve them.

Once I had a solid vision for the interactive tools and website, I knew that a textbook/lab manual was really needed to bring it all together. Without the biological context and deeper explanations of the algorithms, students would not get much out of the website and teachers would not have a guide for how to teach with it. Moreover, I knew I was the right person to teach a real introductory course on this topic. I had been successfully doing so for years, connecting with biology students who thought computers were not for them as well as with computer science students with little biology background. It was a blast (no pun intended) writing the book, and I think my enthusiasm for the topic really comes through.


ASM: Why is it essential that scientists understand the techniques you teach in Computational Biology: A Hypertextbook?

SK: Computers have become integral to biology (and most other things in our lives). When people ask me what computational biology is I reply, “Are you familiar with the human genome? Well it’s really just 3 billion letters in a computer.” The human brain simply cannot make sense of so much monotonous data. We need computers to make sense of it: Where are the genes? How are they regulated? Where are the mutations? And this is just the tip of the iceberg: next-generation sequencing is generating thousands upon thousands of genome sequences, metagenomes, transcriptomes, you name it. We are also seeing huge proteomic databases, metabolomics and lots of others, which are being used by biologists in every research lab I can think of.

All biologists need to be prepared to use computers in their work for generating or testing hypotheses, and for understanding the output of their favorite analysis program. I cannot tell you how many biology grad students and postdocs come to me and say, “I wish I knew more bioinformatics.” So many mistakes have been made in biological interpretation because the researchers did not understand the principles behind the algorithms or the limitations of databases. Plus, bioinformatics is a hot job market! Students with expertise in computers get great jobs and become invaluable partners in collaborative research.


2018.1.9 Compbio

ASM: How will your textbook meet the needs of instructors and students?

SK: Because the book functions as both a comprehensive course textbook and lab manual, it takes the student all the way from theory to practice in a user-friendly fashion. But more importantly, it automates the most tedious aspect of an instructor’s life: generating exam problems and answers. Not only do we provide multiple problems with answers for every algorithm, but the instructors can use the “print exam” buttons that instantly produce exam (or homework) problems and answer keys for all the algorithms. The tools also provide infinite practice for the students, which helps both instructors and students and reduces the need for midterm practice problems. We also provide chapter problems and answers, lab exercise problems and answers, and PowerPoint image slides as ancillary material for instructors who adopt the book. Finally, the direct and simple nature of the online tutorials makes learning very straightforward. Unlike other lab manuals, we will update the tutorials a few times a year as needed, so both teacher and student are less frustrated by outdated information.

For the student, the book provides a gentle and hopefully fun and inspiring introduction to the field with an emphasis on why everyone should care about computational biology. However, the real strength is in the learning and the practice. The conceptual material in the book helps the students to own the underlying concepts before learning the formal algorithms. Then, the book explanations and the interactive concept modes online lead them through the complex algorithms step-by-step. Most important, the book provides practically infinite practice problems with instant feedback, which can be accessed anywhere: home, school, or at the mall and on any device. Finally, they will also have lots of practical experience in key bioinformatics tools used in research and industry labs around the world, as well as a deep understanding of how these tools work.


ASM: We know from your publication record that you don’t just teach bioinformatics, you are also an active researcher, studying microbes in environments as diverse as the floors of public restrooms, Hawaiian steam vents, and the human mouth.  What’s one of your favorite stories from the field? 

SK: I once collected microbes from scalding hot steam vents in a volcanic park in Italy. Hot steam was shooting out from tiny vents all over the ground, and I spent an hour crouched over a vent condensing microbe-filled steam and trying to avoid burning my toes while answering questions in German from tourists wondering what I was “cooking.” The worst part though was that the nearest cappuccino was over 2 kilometers away.


ASM: If you could give new teachers or students in computational biology one piece of advice, what would it be?

SK: Don’t be afraid! The fundamentals of bioinformatics are very intuitive if you break the algorithms down into their most basics elements. Relax and enjoy the puzzle-like nature of bioinformatics!


Click HERE to learn more or purchase this book.

Click HERE to check out a FREE portion of the textbook

Instructors: Ask for your examination copy today. When you adopt this and other ASM Press textbooks, you receive a code that your students can use to buy the text at a 20% discount at ASMscience.org.

Last modified on Tuesday, 09 January 2018 15:22