2: Demonstrate that challenges have been undertaken, developing new skills in the process
4: Show commitment to and perseverance in CAS experiences
5: Demonstrate the skills and recognise the benefits of working collaboratively
During the summer, I spent 6 weeks at the University of Hawaii's College of Tropical Agriculture & Human Resources (CTAHR). I worked at a plant bacteriology lab under the supervision of my PI and several grad students. On some days, I gardened and learned lab techniques such as DNA extraction, DNA sequencing, growing bacteria. However, in most other days, I learned to use bioinformatics tools to analyze the recombination of the genome of two bacteria species, Clavibacter and Dickeya. From that data, I created visualizations such as phylogenetic trees and population structures.
A lot of the programs I worked with were command-line based, and on Linux. Prior to this, I had neither interacted with the Linux UI nor familiarized myself with command-line based programs. It was initially hard to adjust, but talking to the grad students about the socioeconomic significance of such research motivated me to keep learning the commands and practicing using the programs. In hindsight, I’m glad I pushed myself to go outside of my comfort zone; I feel I’ve developed a new type of computer literacy where I can now understand and use software that was otherwise too technical for me in the past.
Along the way, I also read papers about the construction and underlying mechanism of the bioinformatics tools fastGEAR and ClonalFrameML. I was amazed to see the amount of math involved in quantifying and comparing genetic sequences. Furthermore, it was a new side of math I had never learned about. School math consisted of nicely behaved functions, elegant solutions, and basic or special case applications. But here, it was used for processing countless numbers efficiently for the sake of practicality. Still, in the end these results became insightful when expressed using visual representations.
Here are some of the diagrams I created.
Working in the plant bacteriology lab gave me a glimpse into the work of a researcher and the current landscape of research, which will most likely be relevant for my future. I experienced the interdisciplinary nature of research, where biology, math, and computer science mixed. It helped me gain a new appreciation of the role of math in the information age where there is an overwhelming amount of data. Likewise, the execution of complicated scientific and mathematical models is only possible with computer software. From this, I am now more eager to use computer science to aid my work in math, and hopeful that I can apply my math knowledge across different fields.
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