Biovisualization (BCB 4002/502; CS 4802/582)

Term C/D – 2015

Location
SL 104 T F 1:00–2:50pm

Instructor
Lane Harrison
FL–231

Office Hours
T F 3–5

Course Description

In this course we will study the use of interactive data and information visualization to model and analyze biological information, structures, and processes. Topics include the fundamental principles, concepts, and techniques of visualization and how visualization can be used to study biological data at the genomic, cellular, molecular, organism, and population levels.

Learning Goals

After successful completion of this course, you will be able to:

Critically evaluate and deconstruct data visualizations.
Identify application areas for visualization in biological analysis workflows.
Evaluate the characteristics and structure of data you encounter to refine design options.
Use algorithms, aggregation, sampling, and similar techniques to refine and manipulate data.
Apply knowledge of how people perceive and reason with visualizations in your designs.
Design and develop interactive data visualizations for biological data.

Required Text

The text we’re using for readings in this course is Interactive Data Visualization: Foundations, Techniques, and Applications, by Ward, Grinstein, and Keim.

Recommended Texts

If you’re interested in data visualization beyond this class, I strongly recommend Tamara Munzner’s Visualization Analysis and Design. (Many of the figures I use in the class lectures come from this book.)

Assignments

Weekly assignments are the core of this course. Each assignment will focus on a particular type of biological data, such as sequences or phylogenetic trees. The lectures and labs will equip you with the biological background, visualization theory, and technical skills to develop an effective visualization for these datasets.

Labs

The second lecture of every week will include an in-class lab. These labs provide an opportunity for you to learn more about visualization design, data analysis, and technologies.

Programming Language

There are two preferred language choices for this course: Processing and JavaScript using d3.js.

Processing is a programming language that sits above Java and facilitates rapid development of graphics applications. If you’re experienced with Java, Processing is a good choice.

If you’re familiar with web programming, you may use JavaScript and d3.js. JavaScript can be confusing, however, so proceed with caution.

If you want to program in a language other than Processing or JavaScript, please see me before you start your projects to insure the language has the appropriate graphics support. Depending on your choice of languages, I may not be able to provide much help in debugging.