Summer Course on Bioinformatics

I taught a 7-week course on Bioinformatics at Bosphorus University in Istanbul Turkey, this summer. Although I had previously given guest lectures at Yale, this was the first time I had the responsibility for a whole course. It was an interesting experience at several different levels. 

One interesting challenge was the lab setup. Most bioinformatics tools are designed to run on a Linux/Unix environment but the PCs at the training labs had Windows as their OS. For bureaucratic reasons, it was going to be too complicated to make these machines dual-boot with a Linux option. I ended up requiring all students to bring their own laptops to class and install BioLinux (a Ubuntu flavor with a variety of bioinformatics software pre-installed) on their machine. I gave the students three choices:

  1. A dual boot system, with Biolinux as one of the selections.
  2. Install Oracle Virtual Box, then install BioLinux in it.
  3. Reboot the PC from a USB stick with BioLinux on it.

Each option had their pros and cons but every students was able to make one of these options work.

The lab exercises were designed to enable students to do an RNA-seq analysis followed by a differential expression analysis and then creating a database to store the data. This meant learning Linux commands at a level to manage data files as well as the awk and sed languages to manipulate the data within the files. They also learned the R language for statistical analysis and graphing. With this foundation, the students processed an RNA-seq dataset using tophat/cufflinks and graphed their data using the cummeRbund. Finally they learned to set up a relational database in MySQL database.

Half of the final grade of the course depended on writing a literature review on a topic of bioinformatics or implementing one of the algorithms learned in class. I had taught them what consititutes plagiarism and the mechanics of using a bibliography management tool (Mandalay), but the actual writing of the papers turned out to be a bigger challenge than I had expected. Most of the student had had no paper writing experience until then and they could not decide on a topic or how to write one. After I pointed them to a list of papers submitted for a Bioinformatics course similar to ours (http://biochem218.stanford.edu/Projects.html), they were able to proceed.

All in all I think this was a valuable experience for my students. I hope I will get the opportunity to give this course one more time in order to improve on it.

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