Spring 2022: Teaching and Learning

In the spring semester of 2022, our Principal Data Scientist, Dr. Ryan L. Melvin (me), will be teaching INFO-403 Bioinformatics-II (Algorithms) here at UAB. The course serves as an introduction to several computational techniques and forms of algorithmic thinking. Computational topics include dynamic programming, optimization, hidden Markov models, graph algorithms, and unsupervised machine learning.

Bioinformatics Algorithms print edition (online is used for this course). Image courtesy of the authors.

The course structure is modeled after one taught at Carnegie Mellon by one of the textbook’s authors, Phillip Compeau. An UAB-specific special edition of the online, interactive textbook will be the primary resource for content and assignments for those taking the course. Each chapter involves several assigned software/coding challenges that coach students through building famous bioinformatics algorithms from scratch. These assignments are programming-language-agnostic, so students can use whatever scripting or programming language is most comfortable for them. Though, all demos and instructor solutions will be presented in Python, since that is the language the instructor is most comfortable with. 🙂

In terms of in-class meetings, the course has a flipped structure. Each week, the course will meet for one 2.5-hour session. The session will be broken up into roughly five 30-minute segments with a break after the first two. The segments will be questions and troubleshooting/hints from the week’s assigned reading and software challenges, a hands-on activity that connects to a primary biology or algorithm concept from the week, and 3 rounds of discussion questions and graded student presentations.

The hands-on activities are pretty off-beat and will hopefully provide students with a fun, unique experience. For example, one week student groups will play a few rounds of the board game Pandemic. The next week, different groups will conduct a forensic investigation of the game and try to reconstruct the original board state (connecting to the biological concept of disease spread and the algorithmic concept of tree-based methods).

The primary content delivery method is an online, interactive textbook. For the outliers who successfully learn from lectures, recorded lectures are also available. Additionally, the vast majority of students’ final course grades come from interactions with the online textbook. The remaining portion comes from class participation.

For students at UAB taking this course, the online, interactive textbook must be purchased using a link to the UAB-specific special edition. The link is provided in the online syllabus in the course’s Canvas page.