First Week

Hello lovely readers (?),

I’ve been in Leiden for about a week now, so I think it’s about time to report my activities for the past few days.

So, this week was the first week of my internship at the Leiden University College. I went into it not really knowing what to expect, as the building I was instructed to go to wasn’t the actual college building. Turns out it’s a small corridor with a couple labs for biology, bioinformatics, and chemistry (I think). If I’m being honest, my workspace was just as disappointingly normal as I should have expected, but I cannot get the romanticized over-the-top crazy scientist laboratory image out of my head when I think of labs of any kind. In reality though, they’re usually a set of tables with machinery on top of them, nothing too special (except the ‘streets’ used for clinical chemistry, those are actually pretty cool). The bioinformatics workspace wasn’t some kind of shady room filled with computers, and people wearing leather coats and sunglasses, typing away on three keyboards at once while surrounded by half a dozen monitors. Instead I was lead into an ordinary office room. Much to my delight however, someone actually was working with two monitors (one turned vertically, one horizontally), and his own personal laptop. No clichéd hacker outfit, unfortunately.

There are two other interns in the bioinformatics room, both from the Netherlands, and there’s a number of analysts. Usually one or two, but we are sometimes joined by lectors of the college. I haven’t asked what they are working on, so I don’t know why they’re there. Everyone is very friendly and welcoming, so I felt right at home. Naturally though, my supervisor (a very laidback, fun guy) has been cracking jokes about Belgians just about every single day so far. They’re good jokes though, so I couldn’t help but laugh along.

I haven’t done a whole lot just yet. I’m supposed to build a tool in R shiny that will pre-format input data which can then be used as input for AViDA, a tool for differential expression analysis. AViDA has such a function already, but the idea is to separate that part from the program so AViDA can run faster and more efficiently. Also, by building a separate tool for data conversion, the tool can be more extensive than it is now. Basically, the user will input a set of data files, and will get an output file in return, which can then be used as input for AViDA.

For now though, I’m reading up on AViDA, R Shiny and differential expression analysis to prepare myself. I first need to fully understand what the process is, and what I need to implement into my tool. I’m currently slogging through a mock-analysis for that very purpose. By my estimations I should be done with that Monday evening, so I will be able to start mucking about with code on Tuesday.

On a less work-related note, I’ve bought myself a subscription at a local swimming pool. I originally planned to go jogging, but I like to jog through more rural, less bustling areas, like parks or forests, or something like that. I haven’t found anything of the sort yet, though, but I do like swimming a whole lot more than I do jogging, so I figure I won’t be jogging here. That said, I think I was a bit overzealous during my first visit to the pool. My right knee hurts when I bend it, which probably isn’t a good thing. Still, I don’t intend to let it stop me. I paid for that subscription, and I WILL NOT waste that money.

Apparently, this weekend was the King’s birthday, so all of Leiden (and the rest of the Netherlands, I imagine) was celebrating. The actual holiday was on Saturday, and there were a lot of activities to partake in all around the city. The evening before, there were stages everywhere, with artists performing. There were food stalls, mobile bars, DJs, and a whole lot of people everywhere. Basically, all of Leiden had been transformed into one massive party. I joined the festivities for a couple hours, but I don’t really like to go partying on my own, so I didn’t stay that long. I tried, but it just made me painfully aware my friends were not around. I bet that if they’d been there with me, we’d have had a load of fun that night. In fact, if there was one person I knew to go with, I’d have been more at ease. Sadly, none of the other interns live in Leiden, and I don’t have a roommate yet, so…

Lastly, I really miss my electric razor. As always when shaving manually, I managed to cut myself in the usual places above my mouth. I don’t know if it’s because of the razor, or because I’m not dexterous enough. Who knows.

Anyways, I will end this here for now.

Until next post,

Tibbert