Student blogs

Hello from the second year of the MTLS programme at KTH. Also a warm welcome to the new MTLS students who will officially start their courses this week! Just like how the end of August went from a nice warm summer to the cold of autumn, the Stockholm University (SU) semester went by in the blink of an eye. I will be writing about my reflections on the courses, attending a new school, Sweden in the the new year and some advice.

Also, remember to check if any of the courses mentioned here have changed since writing this!

Courses

I had previously described the first semester at Karolinska Institutet (KI) as “a taste of everything”. Now, I would summarize the SU semester as “computational.” Whether it was actual coding, theories, labs or reports, there was a common thread of the courses. The exception would be Methods in molecular life science (BL8064) where we had our sole wet lab experience.

A common question that I get about the programme is “What if I do not have any coding experience?”. The truth is that the programme has a very diverse cohort with varying levels of coding experience. My previous experience primarily was in R and properly learnt Python for the first time here. While I do think the experience in courses like Programming techniques Life Science (DA7066) would differ depending on your experience, I can confirm that it starts from the basics. Certain aspects such as understanding for-loops were familiar but I was surely challenged in later courses. Thanks to Bioinformatics (KB8029) and Comparative Genomics (KB8030), I can say that I have now created a secondary structure predictor using machine learning and neural network theories, aligned sequences and created phylogenetic trees in the terminal.

Memorable course

Rather than asking about my favourite course this semester, I opted for the phrase a memorable course: Bioinformatics. My feelings towards this course teeters between appreciation and flashbacks of difficult times. Neural networks and machine learning were topics that initially felt very out of reach for myself. If you remember the reflection from the last semester, I spoke about the successive course structure where you focus on one course at a time. I hinted at the difficulty I had digesting the material and this was especially magnified for this course. I would read the textbook, watch the lectures, complete the lab but before I could even really comprehend everything, I would need to do it all again for the next topic.

Time didn’t wait for me but, in hindsight, time challenged me to push myself. I’m very proud of the work I put into the secondary structure predictor and now I can chat about the evoformer architecture and the basic workings of some generative AI models.

Starting at a new school

As you might already know, one of the key characteristics of the MTLS programme is the collaboration between the three schools: KI, SU and KTH. Each semester for the first three semesters is at a different school. We waved goodbye to Solna (although not for long) in January and said hello to many new locations and people. My first class ever in SU was at the Albano campus for the Programming techniques for life sciences course. I still remember the sea of people floating through the halls and the sound of chatter and footsteps all around. Statistically, SU has the largest student population out of the three and the first day really embodied that stat.

However, you also get the complete opposite experience. In our second course we travelled back to our familiar Solna in the SciLifeLab building. There you are the only set of Masters students taking classes amidst researchers in their environment. Truthfully, due to this arrangement, I missed the student environment that the SU campus offered. On the flip side, it was the beginning of a relationship with SciLifeLab that I would continue in the summer (more on that in a later post).

Living in Stockholm

Outside of academics, I pushed through the dark winter to the longer days with the sun shining through my windows at 3AM. The hardest months to get through personally was January and February. In early January, I came out of the adrenaline associated with Christmas and had very little festivities to look forward to. Luckily I had a very grand Lunar New Year meal where I made dumplings, wished for fortune in the new year and made new friends. I found enjoying celebrations made me happier and more social despite the cold and dark.

Soon enough (but could be sooner), the temperature slowly rises and flowers start to bloom. The cherry blossoms bloomed in late March and early April and colour entered Stockholm. In the same way I mentioned finding hope in Spring in a previous post, I found myself more settled in my space here in Stockholm. I have my own preferred grocery stores, walking routes, and was more attuned to the daily change in weather. There are places I can get to without consulting my phone and recipes I could cook off the top of my head.

Advice for the me in January

My advice is “It will be all be worth it.”

There will be times when you will struggle whether that it debugging your code or learning the difference between AlphaFold3 and AlphaFold2 architecture. While it might seem obvious, time put in will be worth your effort. The reason I wanted to say something so obvious is that there is often a lot of apprehension associated with coding and computational work. It is easy to compare yourself to the pace of others who have different backgrounds from you but keep yourself steady and focus on your own progress. You can do it.

Similarly, you will have great friends and feel more comfortable in Stockholm eventually. All those times you chose to go out instead of staying inside, all the times you replied to text messages and all the times you explored Stockholm will be worth it.

If you’re looking to come to the MTLS programme in the future or just a first year student wondering what’s in store, I hope that this gave some insight into the second semester.