Hi, I’m Torben, and I’m afraid that I am a little late with my blog post (my apologies for that)! Lately, I was introduced by one of my supervisors with the words “He’s one of the cancer guys”. I still find this a little awkward, but I reckon that this expression describes me quite well. I started developing to be a “cancer guy” since working for my master’s project at University of Potsdam where I analysed gene expression data of colorectal cancer samples. I studied bioinformatics in my masters and what fascinated me most was network theory (I hope I can talk about that in future posts).
My project here at Imperial is on the most prevalent type of primary liver cancer, hepatocellular carcinoma (HCC). Since one of my supervisors is heavily involved in a HCC study in West-Africa, I had the chance to travel to Gambia and Senegal. I had never been to Africa before and it was a great experience to see how people actually live there as well appreciate the health system situation is in this country. The project is called “Prevention of liver fibrosis & cancer in Africa”, which you can check out at here, if you’re interested.
Time’s on your side, NOT.
It’s now seven months since I moved to London and started working on my PhD. This is horrifying! Don’t get me wrong, I love my project! But those seven months literally passed by like seven tiny weeks. Seven tiny and intense weeks of a lot of reading, thinking, more reading and harder thinking, plus a bit of lab work and programming. I now realize that three PhD years will go over very fast, so I better stick to my research time table! Time is so subjective (yes, dear Tom, it subjectively accelerates with age as well)!
R vs Matlab!
In my project, I started off with an NMR analysis of urinary samples. It was actually the first time for me doing this. While the sample prep and data acquisition is pretty straightforward and relatively fast, the data analysis is extremely time consuming.
In CMS section here, most of the established NMR data analysis pipelines are Matlab based. Though I never really programmed with Matlab, but with R, I found it quite easy to switch to Matlab. However, I prefer R and here are a few reasons why:
1. It’s free!
2. It’s well documented plus there exist a lot of tutorials online!
3. Various additional packages are available online (www.bioconductor.org)!
4. R has a very active user community!
Obviously, if I would have to choose between R and Matlab, I would choose R. On my desktop, I additionally installed Rstudio, which is an IDE for R, and makes working with R much more convenient.
That’s it for now. I hope I gave you a reasonable good impression about me and my actual work here at Imperial. In my next post, which will be online punctually (I promise), I will talk about network analysis in metabonomics.