After the New Year’s break, our battle field shifts from Karolinska to Stockholm University, where we are going to learn bioinformatics now!
A few weeks before, our course teacher Professor Arne Elofsson had already sent us the link to course website. According to the course website, the upcoming course “Introduction to Bioinformatics” will consist of 17 lectures (2 hours each), 9 programming-lab sessions (3 hours each) and 9 bioinformatics-lab sessions (3 hours each). Believe it or not, the whole course is designed to be finished within four weeks! At that time, I was still indulged in my excellent academic results in the first term at Karolinska, and had no idea of how tough the coming 3 months would be and how much I would learn.
My google calendar from 16 Jan to 5 Feb.
1. The course teacher
Our course teacher is Arne Elofsson. He is a full Professor of Bioinformatics at Stockholm University as well as one of the Principal Investigators at Science For Life Laboratory. Arne is specialized in protein structure prediction using bioinformatics tool, and one of his most recognizable achievements is the development of Pcons series for predicting
protein residue contact. Arne is certainly one of the most efficient people I have ever seen: any Email from
students will ALWAYS be replied within one hour. Personally I am impressed by his erudition in the field: he can answer all the questions from us and share his deep insight with us. According to scholar.google, Arne has an H-index of 55.
Unlike any lectures that I had previously in primary, secondary, and undergraduate schools, in the course Introduction to Bioinformatics, all the lecture slides and videos were uploaded to Youtube. Students were required to 1. watch the video, 2. study the slide and 3. put their own questions to the course website before coming to a lecture. Therefore, during the 2-hour lecture, Arne will only be responsible to answer our questions and perhaps explain the core concept regarding to this lecture. In my opinion there are both advantage and disadvantages:
If you don’t understand the lecture, it is always possible to go through the video at any time
It is really a matter of self-discipline. It would be a vicious cycle if you don’t prepare for the lecture!
3. Programming Labs in Python
The most wonderful thing of these labs is that we are assumed to have no background in programming. Hence, the labs are designed so that we pick up the basis in the beginning, and accelerate gradually towards a capable bioinformatician. In the first lab, we started by creating strings, lists and dictionaries and making simple calculation; while in the last one, we were asked to extract the data from a high-throughput biological experiment, integrate them and present them graphically using python, which are all critical and bonus techniques in a modern wet lab.
Plotting thousands of raw data from wet lab experiment
4. Bioinformatics Labs
In parallel with programming labs, the bioinformatics labs integrate our knowledge acquired from lectures to solve bioinformatics problem. The tasks in these labs could be a re-enforcement of the concepts we learned, such as drawing a relation tree for a few species; or dealing with a practical issue confronted by daily researchers such as compare and contrast different database and software tools and select the most suitable for the assigned task, or apply some of the most popular and useful bioinformatics tools on our own.
Finding out the structure of a whole protein from a sequence fragment
No Pain, No Gain
Although it is such a painstaking process, all of our classmates agree on the fact that we learned a lot in the process and it is such a good investment of time and energy. And most importantly, bioinformatics is FUN!
Summary to the links mentioned in the blog:
- Course website of Introduction to Bioinformatics: http://bioinfo.se/courses/introduction-to-bioinformatics/
- Arne’s profiles at Stockholm University: http://www.su.se/english/profiles/aelof-1.181851 Science For Life Laboratory: https://www.scilifelab.se/researchers/arne-elofsson/ and Google Scholar: https://scholar.google.com.hk/citations?user=s3OCM3AAAAAJ&hl=zh-TW
- Arne’s Youtube channel of the course: https://www.youtube.com/channel/UCavIQR6RF5dXiAuNy28yOaw