How to survive 2 months of programming…!

Hello all! Congratulations to all the students admitted to KI Master’s Programmes! Especially to the ones admitted to Molecular Techniques in Life Science! For more information about the programme, you can check KTH International Students Instagram’s account, since this week my classmate Javier is running it!

Now that we are done with the first two courses of the second semester, I found that I got back some energy and finally decided to write more program-related stuff!

The second semester of Molecular Techniques in Life Science is taught at Stockholm University. We started with the course ‘Introduction to Bioinformatics‘, from mid January to end of February. It was followed by a project course, which we finished last week, where we were assigned with an individual programming-based project.

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Computer lab concentration!
  • Introduction to Bioinformatics, 7,5 ECTS (SU). In this course we learned the basics about bioinformatics, how to use biological databases, how to perform sequence alignments, the basis about machine learning and also how to predict secondary and tertiary structure of proteins. We had 2h/day of lectures and 4h/day of computer lab. In the computer lab we had to prepare assignments based on what we learnt in the lectures and we also learnt to program using Python Programming Language.

Python.png

  • Project in Molecular Life Science, 7 ECTS (SU). The aim of this course is to use the knowledge gained in the previous course to create a secondary structure protein predictor. For example, predict whether an amino acid sequence will fold as an alpha helix or as a beta sheet. The whole predictor was developed by programming in Python. During this course we did not have to attend lectures, but we were welcome to join several lab meetings from research groups in Scilife as well as seminars from the Bioinformatics Club.  Moreover, the assistants where available 2h/day everyday of the week.
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3D protein structure prediction from an amino acid sequence

As you can imagine, this involves hundreds of hours sitting in front of a computer, especially during the second course. First, because programming is extremely time consuming, and second, because the way these courses are taught require a lot of self-learning.

We spend many days (included weekends) in the computer room in SU. Sometimes it felt like we were partly living there. We would arrive in the morning and leave late in the evening. You could also work from home if you prefer, but then you would need to have mac or install Linux in your laptop. It was hard but we all succeeded to create an functional protein structure predictor.

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One of those many late evenings in the conmputer lab

What do you mandatorily and absolutely need to survive programming?

  • Chocolate (several kg!!) and other sugary food!
  • Loads of coffee
  • A bit of craziness… and a lot of patience! An error in your code can take a veeery looong time to be fixed
  • Physical activity to release bad energy (and to keep computers safe!)
  • And of course, the most important thing you need… FRIENDS! I would never have been able to go through this course without the help and support of my amazing classmates.

For more information, read the Bioinformatics course review written by my classmate TinaBioinformatics Course Review

Contact me for any further question!

Email: carolina.savatier-dupre.banares@stud.ki.se

Linkedin: Carolina Savatier-Dupré Bañares

Facebook: Carolina Savatier-Dupré Bañares

Instagram: Carolina Savatier-Dupré Bañare

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