Applied bioinformatics, 7.5 credits (ECTS)

Current round: appbio11, period 2, fall semester 2011. This course is known as DD2397 at KTH and DA7021 at SU.

Please note that the course language is English.

Comments from students

Inge Van den Herrwegen

After the 2009 course round, Inge wrote

I should also thank you still for the course: It made finally my fear of programming disappear :)

Burcu Ayoglu

To motivate you for this course, please have a look at what former AppBio student Burcu Ayoglu, participant of "KTH på insidan 2009", had to say about programming in a blog post in the spring of 2009:

Yesterday I have spent almost half a day just to write a small script, which, by looking at certain patterns within the rownames of my big 384×75 matrix, would extract the indices of those data points belonging to MS patient samples and plotting them in a different color than the one used to plot the remaining data points belonging to healthy control samples on each of the 75 plots. It might sound a little stupid that I've spent half a day for something like that instead of doing the same job 'manually' in a much shorter time. But, as a person who took some basic, undergrad computer programming courses and very recently an applied bioinformatics course at KTH, I would be somehow unhappy for doing it manually instead of writing just a nested loop.

While I was taking the programming courses during my undergrad studies, I must honestly admit that I totally hated trying to write programs. I guess the reason is that at that time I was not completely believing in the fact that programming is sooner or later an unavoidable thing for someone who studies science or engineering. I think the applied bioinformatics course I took at KTH (given of course by Lars Arvestad!) made me both accept this fact and stop being somehow afraid of writing programs. Yesterday I saw that I can now at least try my best to write a code for my own little use without giving up, but if I wouldn't have taken that course recently, I would maybe not even dare to do it.

To conclude, I'd like to say that some very basic knowledge of programming is today very crucial no matter what you study, what you do, in which field you work, and, related to this, especially technical universities have great responsibility in designing different levels of computer programming courses (with lab exercises focusing on up-to-date applications) and inserting these courses into the study programs properly.

Rohit Thaper

Rohit was in the same class as Burcu, appbio08, and wrote this in 2009:

I take immense pleasure in writing my feelings about this course. There are very few instances where core biotechnology students get a chance to learn some IT courses. I can confidently say that if you ask any Core Biotechnology student what is a 'query language' 90% of them will not have the answer to it (unless they have taken this course!!). I had a keen interest in IT since the beginning of my college days but I never knew if being a Biotechnology student I could ever get a chance to study IT and especially Databases. After taking this course those big and scary IT words like SQL, Databases, Query language etc etc look like normal day to day words now. What could be more fascinating to tell that out of my six years of biotech study I managed to secure a position on the basis of one course which I just studied in one semester, and that is Applied Bioinformatics. While studying this course I never realised the real potential of this course but soon after finishing this course when I was doing my master' s thesis I realised the true potential of this course as the company where I was doing my thesis was interested in setting up a new Data management unit. And since I was already familiar with SQL from my Appbioinfo course, it took me very less time to understand the technical jargons and to get hold of the whole process. And guess what, today I spend my whole day creating and managing databases which I really enjoy now. I am quiet sure which ever field you choose, the knowledge from this course is definitely going to help you in your future.

I really thank the KTH faculty for introducing this course to the Biotech students and would really thank Lars for his efforts that he has put in to make this course a worth while course for biotech students.

Cheers !!!