Second Week

Welcome back, lovely readers.

My second week in Leiden was fairly uneventful, all things considered.

I have made significant progress in developing the auxiliary tool to AViDE. Using the original code as a base, I have managed to create a rudimentary user interface with a certain number of tabs. Each of these tabs contains a data table that is calculated when two files are uploaded into the tool. You need a DE sample file, and your count data (in a tab delimited format, though I will try to include options for other formats as well). Lastly, you can also choose which package you want to use for calculating the normalized counts, the RNAseq data, the log2FC data, and the log2CPM data. You can either select edgeR or DESeq2, but at the moment only DESeq2 actually works.

Needless to say, I still need to fix a lot of issues, and make some improvements to this foundation I have laid. With this as a base, however, I am sure I can build a satisfactory tool.

Apart from working, I have done some exploring of the classical cuisine of the Netherlands. The Netherlands are famous for their croquettes, so I decided it wouldn't be right for me to have been here for two weeks now without having had a taste of the local specialty. Honestly, I thought they were quite good. I had two, one was vegetarian --probably made with some kind of mushroom paste instead of ragout-- and the other was a classic meat croquette filled with a ragout of beef. The beef croquette's crust was quite thin and brittle, but that did not make it any less delicious.

Have I mentioned in previous blog posts that I have started swimming? Well, if not, than I have now. I got myself a subscription at the Vijf Meibad, which is one of the three or four swimming pools in Leiden. It's an older building, but it serves its purpose. There are 2 pools there, one is a shallow pool where young children can be taught how to swim and become accustomed to the water, and the other is a pool with a length of 25 meters. I think the width of the pool is 10m or something like that, so it's not a huge pool (and it certainly feels quite cramped when a lot of people want to go swimming at once). I like to have some space when swimming or doing any sport, really, so I am always a bit frustrated with the amount of people when I decide to go swimming. Perhaps it's less busy in the early morning than late at night (which is when I go to the pool currently), but I am sadly not a morning person, so getting out of bed earlier than usual is difficult for me. I will try though, and, who knows, maybe I will get used to it.

Lastly, I've found myself going to the local gamestore a couple times recently. They sell a lot of materials for ... let's say... hobbies more commonly thought of as "nerdy". Things like Warhammer, Dungeons and Dragons, the Pokemon Trading Card Game, and Magic the Gathering. I've found myself pleasantly surprised that a lot of the items are a bit cheaper than in the local game store I used to go to. I've found dice at half the price, and card sleeves at 80% of the price in Belgium. I've bought only what I needed to play here, as I've left my Magic decks and accessories at home. I'll probably keep it that way, but I have no doubt that I will probably stop by the shop many more times during my stay to play some Adventurer's League or a couple games of Magic.

Like I said, there's not a lot to report this week, so that's it for now.

See you in the next post,

Tibbert