Albert Sun
Albert Sun
Year: 2021
Faculty Advisor: Lukas Mueller

“Analysis and Visualization Tools for BreeDBase”

Project Summary:

Over recent years, traditional phenotypic breeding has shifted to include digital tools such as genetic analysis. Often these tools can be inaccessible or difficult to use, however breed base provides easy access to these tools, and can be simply accessed through the browser. The breedbase website is a massive database of genetic data for a multitude of crops such as musa and cassava. Breedbase allows breeders to input genetic and phenotypic data and then use a multitude of tools to analyze this data. Over the course of this project, I worked on 2 tools, the breeding progress tool and the radar graph tool. The breeding progress tool allows the user to select a trait, then displays the progression of that trait’s values over the course of a specific breeding program. This allows breeders to understand the efficiency of the breeding program by displaying the progress over time. The second tool I worked on is the radar graph tool, which allows breeders to compare the values of traits for several datasets. Both of these tools were built with javascript frontend libraries that were fed data from an AJAX request. The progress tool was built with Vega-JS, a library based on D3.js and the radar graph tool was built with chart.js. The development of analysis tools allows breeders to easily access data and determine the best routes forward.

My Experience:

My summer at the Boyce Thompson Institute has vastly expanded my knowledge on bioinformatics and computing in general. I learned a lot about the web development cycle, starting with a docker image then building up all the way from the database to the frontend. Working on BreeDBase also helped me become more familiar with coding languages such as javascript and perl as well as get more familiar with linux. In addition, the seminars and workshops that were provided expanded my knowledge of the scientific world drastically and helped me learn new skills. Overall, my time at the Boyce Thompson Institute was very positive and helped me develop new skills and expand my knowledge.