Computer Science and Software Engineering Capstone Presentations
Fall Quarter
December 18, 2020
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Olena Gavrishchuk "Investigation
of Coevolutionary Dynamics Using Muller Diagrams" (UWB CSS Faculty Research) Faculty Advisor: Dr. Wooyoung
Kim |
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Abstract In this project, we investigate coevolutionary
dynamics using muller diagrams. The project is a collaboration between the
UWB CSS department and the biology department. We build a web-interactive
tool intended to be used by Dr. Hillesland's lab at UWB. The research tracks
changes in the genome of two microorganisms, Desulfovibrio
vulgaris and Methanococcus maripaludis.
Sixteen different cultures are grown in a controlled environment with the
intention of studying their coevolution and observing mutations through
genome sequencing analysis. The purpose of the web application is to help
biologists visualize the data produced by the experiment and find notable
trends in it through muller plots. These muller plots are used to visualize
evolutionary dynamics by analyzing frequencies of genes over a timeline of
generations. The initial version of the application generated
muller plots for a single culture and the task at hand was to expand that
functionality for all sixteen cultures. Throughout the quarter, a new
database was integrated into the web application and data analysis
functionality was expanded to all cultures. That data analysis includes data
tables generated for all cultures, frequency tables generated for all
cultures, frequency graphs created for all cultures, frequency graph
filtering capabilities for all cultures and muller plot graphing for all
cultures. On top of that, front-end code was changed and added in an effort to increase security with basic password
protection for the PHP scripts and improve user experience with a simpler
layout. The result is a functional and user-friendly web application that
supports the data analysis of all genomic data of sixteen culture within the
existing database. |
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Updated December 15, 2020