The mission of the Bioinformatics booth is to introduce prospective students and parents to an emerging interdisciplinary field that is focused on handling large datasets and computational problem solving, in order to address complex biological problems. Such outreach is valuable to the scientific community as a whole, because it advertises the accomplishments in the field, and the dedication of the scientists and engineers involved. The two activities proposed for the 2016 San Diego Science Festival Expo are described below; both of these activities are based on challenging concepts foundational to bioinformatics, yet are presented in an easy to grasp puzzle-like form.
Eulerian Path Problem: Frequently in bioinformatics, abstraction of biological problems lends itself to a solution. For example in DNA fragment assembly, the overall objective is to obtain an organism’s genome; this involves solving the Eulerian path problem. To physically demonstrate the Eulerian path problem, we will use a 3D maze that recreates a graph in which a Eulerian circuit exists. Employing a small remote control car, the user will be tasked with passing over every “bridge” exactly once while traveling from a starting position to an ending point. To motivate the problem, we will also clearly diagram the process, goals, history, and application to genome assembly.
DNA Alignment by hand: Much of modern day genetics research relies on short read sequencing technologies that generate millions of small fragments that need to be mapped onto a larger reference sequence. To perform this mapping process, we use computers to identify the “best” location for the read to a corresponding reference (referred to as alignment). Once aligned we can find differences between the two sequences that might have biological implications. To learn about this alignment process, the participants will receive a piece of paper with a colorful DNA sequence that can be folded into an origami helical DNA molecule. They will then be tasked to find the best location along a “reference” sequence for their DNA fragment. The reference sequence will be displayed on a large poster. The participants will be able to keep their folded DNA molecule.
