Health Science Reviews

By Themba Stoep

My journey in bioinformatics has lasted six months thus far, yet it feels as though time has leaped forward with incredible haste. Despite all the haste, these months have been densely packed with learning and growth, making the experience immensely fruitful. My interest in bioinformatics sparked during my second year of study, sparked by the field’s integral role in virtually all biological research, I like to say, its shadow looms large over modern health science research. And in many ways Bioinformatics acts as the unseen force behind the scene, and as a research enthusiast who is a fox, I was naturally drawn to it.

Being accepted into the Bioinformatics Honors program is an opportunity for which I am deeply grateful as part of UCT’s intercalated molecular medicine program. This program has allowed me to interact with, and draw inspiration from, esteemed researchers like Prof. Martin, Houcine, and Sinkala, while also fostering new friendships. I particularly enjoyed the long 2~4 hour debates my colleagues and I often had about various topics and the accompanying research we engaged in to address our deficiencies. I feel debate is an essential element of good science that has strengthened our approach to research. The transition from general techniques to specialized modules was particularly exciting for me because thats where we got the meat of the course. Among the various modules, pharmacogenomics and high-performance computing stood out as particularly enjoyable and enlightening.

I was particularly taken aback when we got given a strategy game as an assignment for the course, but after six months of engaging with it, it has proven to been a strategic experience as Prof suggested it would be, and I now await the next age. Furthermore, the necessity to work on it with other people from many different countries, with differing levels of experience and requiring integration of game set ups for each kingdom to function was a very complex exercise. I haven’t even touched the surface about the fun and intensive management it takes to follow orders, setting alarms for multiple hours a days so as everyone can be online at the same time to wage two-day wars on other kingdoms. I feel Utopia is pragmatic for the kind collaboration we do in Bioinformatics, and that anyone who tried the game would probably play it for life.

I am engaging with two honors projects this year, with my primary being focused on developing a pipeline for a de novo transcriptome assembly, and the secondary being about proving the non-randomness of recombination by using Alphafold to predict protein structures from genes and then running a schema test to predict protein interactions. The former has significantly expanded my knowledge of Linux and various bioinformatics tools, while the latter has me engaged with protein structure prediction and the evolutionary history of COVID-19. The transcriptome assembly in particular has proven to be a dynamic, challenging – and by extension – extremely thrilling project that continuously hones my technical skills and broadens my perspective on computer science applications. I feel there is just something extremely satisfying about being able to pull up a laptop at almost any time you want to immerse yourself in code, tackling complex problems and differentially combining ideas to solve them—a fitting pursuit for an overthinker like myself, who is obsessed in finding efficient solutions to intricate challenges.

Bioinformatics has revealed itself to be an incredibly diverse field, and I feel there is no problem that we have been given this year for which we have not been told to look at web tools or applications capable of addressing the issue. I feel that in the direction in which we are going, that bioinformatics truly encapsulates the revolution undergoing in health industry with the speed of the digital revolution and scale of the industrial, and this will truly transform the world in the coming decades.

In summary, my journey in bioinformatics has been both enriching and eye-opening. The journey is still going to be quite long and it’s nice that even if you get far there will always be more and more to do and learn. And so, in look forward to where and what bioinformatics will lead me into. Afterall, sharks were born swimming.