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Research is in my DNA

Tayab Soomro describes his experience working as an undergraduate research assistant working with DNA sequencing technology.

I was just another undergrad doing my 4-year degree in Computer Science, with an ambition to work as a software developer; little did I know that the University of Saskatchewan (UofS) had something way better in store for me. In the summer of 2017, I was unable to find employment after applying for jobs around the city of Saskatoon, and I was bored sitting at home. Having heard that professors often have work for undergraduate students, I decided to email a couple of  professors and ask if they might be looking for an undergraduate research assistant for the summer. I did not have a clue about the kind of work I could be doing, but I figured I might land some sort of odd job like data entry. In January 2017, I received a response from Dr. Matthew Links in the College of Agriculture and Bioresources and he offered me a position as a Student Research Assistant in the department of Animal & Poultry Science. Off the bat, my job was to work with a graduate student and carry out computational tasks, unlike the data entry work that I’d envisioned.

This project was far more sophisticated, and the work more rewarding, than I had anticipated. We were looking at the latest DNA sequencing technology. Using wavelets for denoising nanopore signal data from the MinION DNA sequencer. To understand denoising you can think of a television or radio program that you’re trying to enjoy but with a lot of static going on in the background. Denoising means to reduce the background static to get clearer and an easier-to-understand signal. Although DNA sequencing has become more affordable and accessible these days, accuracy is still a challenge. This is a persistent problem in bioinformatics. Our project sought to increase the accuracy of DNA sequencing by denoising the signal data, hence improving all science that could benefit from DNA sequencing (human, animal and environmental sciences).

In my case, I was in charge of creating the visualizations for the signal data that were generated by the wavelet functions. This was my first exposure to bioinformatics. Bioinformatics can best be explained as a discipline that fuses biology, computer science, and statistics. Coming from a computer science background, I didn’t have much exposure, if any, to biology. I continued the work on this project throughout the summer of 2017, which is when I seriously started considering bioinformatics as my  degree focus. Bioinformatics interested me because of my newfound enthusiasm for the field gained through hands-on research and experiential learning. As such, I transferred to a major in bioinformatics in the following academic year (2017-18).

Building on my first summer of research, this past summer in 2018, I was awarded an Undergraduate Student Research Award (USRA) through the Department of Computer Science. This time the project involved different work but still revolved around the MinION DNA sequencer. In my team, we were developing a web application  to be run with the MinION. This app provides an alerting system through which a scientist performing DNA sequencing runs could be notified through their email or text message. The alerts could be set to respond to any particular sequences of interest arising in their sample. Our team believes that this will enable researchers to use their time more efficiently by allowing them to focus on more important matters in the meantime, rather than waiting around for significant sequences.

Putting the App in Appreciation

It is very common in the kind of projects I have worked on to encounter roadblocks, and I encountered several during the course of my research project.  All of these challenges were related to the functionality of the application. One of the most interesting setback that I encountered was the unexpected behaviour on the  part of my application. I spent days trying to understand why the issue was occurring, and it later turned out that a piece of code was not working as I thought it was meant to. In that moment, I gained an appreciation for the importance of understanding, to the best of your abilities, how everything that you are using works, be it in a wet or dry lab.

I came to rely on several resources to overcome challenges in my research. One of the principle resources that helped me progress during the course of my research was my supervisor. Dr. Links gave me suggestions on how and where to focus my attention and directed me to appropriate online resources for all sorts of problems. When I needed help with web development, my number one go-to resource was StackOverflow, which is an online crowdsourced forum for computer programming help. Other than those sources of help, I also signed up for the poster making session offered by Undergraduate Research Initiative, which gave me guidelines on how to present my work.

I believe that one quality that makes a good researcher is interest and enthusiasm for the topic on which they are conducting research. Being inherently curious and willing to learn about the topic in greater detail is paramount, because at the end of the day, research is about solving problems and you can only solve problems if you fully understand them. One of the most important skills that I have learned during my research, and I am still learning to practice it well, is to learn everything in such detail that I can explain it to anyone not familiar with the topic. This is akin to what Albert Einstein expressed when he said “If you can't explain it to a six year old, you don't understand it yourself.”

Minding the Gap

Since becoming a bioinformatics student, I have learned a lot about DNA, the material present in nearly all living organisms and the carrier of genetic information. In the BMSC 240, Biomedical Sciences: Laboratory Techniques course, I performed a DNA extraction experiment but we never got to do DNA sequencing, which is what one would typically do after extracting the DNA. I believe that my research project bridges the gap in-between classes and original research because I have had a chance to observe closely the DNA sequencing run using the MinION DNA sequences.

I believe that these kind of research projects have helped me to consolidate various skills and expertise that I have learned in classrooms by applying them in real-world settings. In computer science, class projects are designed to help us students get a deeper understanding of the concepts that have been discussed in lectures, and to give us practice on important skills. But, I think that class projects portray simplistic versions of the real-world. Research projects, on the other hand, are mostly open-ended, and your input as a student researcher, in terms of direction of the project, is vital to the success of the project. This condition of thinking and giving input to a project makes research assistantships unlike most class projects where the goal is strictly set by the instructor.

Because of my experiences I remained keen to seek out other ways of bridging the gap between the classroom and the real-world. Recently, I met a couple students in a BINF 200 Introduction to Bioinformatics course who share a common interest in working on bioinformatics projects. We decided to form a group to take on projects much like the one that I was doing over the summer. We call our group the University of Saskatchewan Bioinformatics Team (USBT). We solicit projects from professors and work on them as a team. Thus far, we have also been involved in various activities such as Med.Hack(+) Hackathon, and a project that came out of it, which aims to help make an Operating Room procedure more efficient. If bioinformatics research sounds interesting to anyone reading this, we are still looking for UofS students to welcome to our team of researchers!

 
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