Last Post?

Hello lovely readers,

The final two days of my internship are upon us, which also means that the final post in this blog is here.

I know I haven't posted an update for week 7 and 8, but that's frankly because there wasn't much to tell.

In terms of my project, I fixed pretty much any issue I could find (which did take quite some time), after which the application worked as intended. I would go into detail about this process, but suffice to say that I used a couple loops (I love me some good loops, I even eat loops for breakfast! Honey Loops, if you're curious. They're quite good!) and a whole lot of trail and error to get the result I desired. Apart from a single bug which sometimes happens and sometimes doesn't, but does not break the code or the stop the application from working properly in any way, the application works as intended.

With my work now completed, I've been "focusing" on the very boring and tedious process of completing my administration. Log sheets, portfolio's, self-reflection,... that kind of thing. I hated every second of it, and my productivity levels went into the negative. I also had to present my project to my internship mentors. I got a lot of feedback, which I have incorporated into version 2. Am I prepared for the actual presentation? No. However, I am getting to it. Currently, I'm reading articles and vignettes to familiarize myself with just about everything I think they will ask a question about, just in case.

Not necessarily the most pleasant activity, but it needs to be done. I'd rather do this than fill in the paperwork.

Outside of the work hours I have not done a whole lot, really. I have been feeling really tired after dinner. Is this what being an adult is like? Where did all my energy go? Please send help. Someone save me from this dreadful existence!

Also I'd been invited by someone I met at the Local Game Store to come play D&D with him and his friends in their apartment. The contrast with playing out in the open is immeasurable, and I had a lot of fun. The plan was that I'd join them every so often, however, since I have to go back to Belgium soon, that idea went up in smoke. Still, I was rather flattered, and if possible I'd love to play with them again.

I think I'll check if there's an Adventurer's League near my home back in Belgium.

Anyway, I think I can sum up my experience here in Leiden as Very Positive. I've had a lot of fun, and though I didn't go to as many parties as I'd planned (mainly due to not having anyone to go with), I've had fun doing other things.

So, bye Leiden! I will miss you. Probably. At least the first few weeks!

And goodbye to you, lovely readers, and thanks for sticking with me.

Sincerely,

Tibbert

Sixth Week

Hello again, lovely readers.

Week 6 is now behind us, and the end of my internship is quickly coming into view.

Despite its short length, week 6 was quite productive. I have more or less finished developing my project. What I mean by that is that all the basic functions and the functions my supervisor wanted to see included are now working properly. Needless to say, I am quite pleased with myself. A lot of pressure has fallen of off my shoulders, and I can relax a little as I go about adding in some final touches. It is a double-edged sword, though, as I am a procrastinator by nature, and need a certain amount of time pressure to actually focus and be productive. I am looking for a package I could include into the application as well, but as you might expect that is tedious work I do not enjoy doing. As a result, my levels of productivity are about as high as they were at the start of the internship, when I had to slog through a bunch of written tutorials.

I much prefer coding, but right now I there's no more coding to be done until I find another package for DE analysis that's popular enough to be included into the application. That's a job for next week, however.

Because of the Ascension Day on Thursday, and the bridge day on Friday, week 6 only featured 3 work days. I got to enjoy a long weekend, which I made good use of. Kind of. I have mentioned before that every Wednesday is International Students Night at the Einstein pub. Having a free day to recover in case I'd need it, I was very hyped for this party. I could drink without having to worry about work the next day.

However, I'd been expecting a start to the party like last week. Which was a slow start, where I joined the members of the board who organize these parties for a drink at a table. You know, laid back, just sitting, chatting, and having a drink. My preferred way of getting warmed up for a party. Unfortunately, none of that happened this week. Instead, I found myself in a crowd where I didn't know anyone, didn't feel all that at ease, and I didn't know what to do.

I did find some members of the board after an hour or so, and it was fun for a while. Still, I wasn't having as good a time as last week, and I didn't stay very long.

Nevertheless, I wasted half of the next day by lying in bed for no reason other than laziness.

Saturday and Sunday a couple friends from Belgium came over to have check up on me. I bought some drinks, and we toured the city for a while. Then we found a spot at the park near the Museum Volkenkunde - the national museum of ethnology with a nice view of one of the canals, where we sat down to enjoy some drinks together in the sun.

In the evening we then were looking to enjoy the Leiden party scene, but one of my friends had already had too much to drink, so we took it easy instead. Still, it was a very fun couple of days.

I think that's it for this week.

I'll see you again in the next post,

Tibbert

Fifth week

Hello lovely readers.

This week was very productive for me. In hindsight, it doesn't feel like I have done a whole lot, but I do think I have accomplished quite a bit. I had to do a lot of testing, debugging, more testing, rewriting parts of code, adding new parts, testing, and debugging. However, I managed to finish the implementation of edgeR into my application. Then I went through the same process again to calculate GC-content for the different samples and display it into a different datatable. The application now reads all fasq files in a user-specified directory, and then makes the calculations. I'm quite proud of it, especially so since the basic functions of the application are now complete. I can now move on to less important parts, such as improving on the download buttons, adding in a few new functions, etc.

I have also been applying for a couple different jobs this week. I have written several letters of motivation (which takes a long time), and will have to write a lot more still. However, I feel like I am at the start line of the rest of my life, and I want to not fumble when the start signal jumps from red to green.

In other news, I have found out there is an International Student Network here in Leiden, and every Wednesday they organize a party for the internationals. As a person who's not too keen on interacting with people I don't know, I was a bit apprehensive about going as I didn't know what to expect. I went anyway, and I had a very good time. The board members were very friendly and fun people, and I stayed a bit longer and drank a bit more than I had been planning to. I will go there again next week.

Also, I cannot believe I forgot to report on this last week, but my roommate has finally arrived. His name is Malik. He's a PhD student from Senegal, and we get along quite well. Because his first language is French, he's not used to speaking English, and it's a bit difficult to understand him from time to time. Currently there is only one thing I don't like about Malik, and that's that he doesn't clean up after himself when he's used the kitchen. I am starting to understand where my mom is coming from when she's nagging about having just cleaned and the floor already being filthy again. I do think she overreacts a bit, since I don't spill as much food and peels on the floor as Malik does.

Pretty sure my mom would get an aneurysm if she was in my position.

But yeah, I will have just vacuumed in the afternoon, and after Malik has prepared his food, it's just as dirty as it was before. I'm starting to think that cleaning the kitchen is a Sisyphean task.

I should probably tell Malik to be a bit more aware of the mess he makes.

Anyway, that's all for this week. I will see you all again in the next post!

Tibbert

Fourth Week

Hello lovely readers,

Week 4 has flown by, and thus a new blogpost is required. This week was a short one for me, as I spent Monday and Tuesday at home.

It felt good to be back home for a couple days. I wasn’t feeling homesick or anything, though. Here in Leiden I have to pay attention to how I speak so people can actually understand me, so it felt great to be able to speak like I normally would. The Flemish accents all around were a breath of fresh air after a bit more than 3 weeks of Dutch.

I returned to Leiden Tuesday evening, stepping off the train around 12pm. The very next day I went back to my internship a bit tired from the long-ish train journey.

In terms of work, I have added more download buttons, so all datatables can be downloaded in two formats. There are still some kinks to be hammered out, but they do work. So I think I’ll focus on the more important aspects of my application. One of which was the calculation of several values, which, as it turns out, was not correct. I went through my code to edit some parts, and I noticed I had not changed some of the objects in the calculations for one of the options. As such, it used the objects of another option to calculate values, and produced faulty results. Trying to fix this made me realize that the way I was doing it now wasn’t going to work.

I’ve spent a lot of time searching the internet for ways to fix my code and calculations, but couldn’t really find anything concrete I could use. I browsed sample workflows to find solutions, but none of them had something convenient I could just put into my code to make it work. However, there were some bits and pieces scattered around, and if I could combine them, I would get my desired result.

Thus, I read the workflow, entered the code in a different file, and ran it with my data to see what exactly what effect the different lines had. Everything was going pretty well, until I hit a roadblock. The code wanted to calculate the dispersion of my samples, but my data had none. The code needed dispersion to execute further functions. I didn’t know what to do, and went back to Prof. Dr. G. Oogle for advice. Sadly, nothing I thought might help worked, and I was out of ideas. So I reread my code another three times or so, comparing the sample workflow with my own.

And then I saw it. The problem. A stupid mistake. I had been following the workflow too closely, not completely understanding how they had organized their samples, and had messed up with my own samples. As such, I had ended up with 16 groups (1 for each sample) instead of 4, and eliminated the dispersion by accident. I quickly fixed the issue, and lo and behold! I had data to work with.

The difficult part is also the part where this week’s work ends. With the workflow I could calculate the logFC, the logCPM and the Pvalue for a sample, but I still needed the contrasts and the meanCPM and the feature names from my previous block of code. I was fairly sure I could write all of the parameters into a table with the help of some loop structures, but it would take a while to figure out. Last I managed before the end of the week was using the loops to create half of the datatable I wanted.

The weekend felt short, but I had some fun. I went to a jazz café Friday evening. The beer was expensive (granted, it was craft beer, but in Belgium a special beer is still cheaper than what I paid here) though I did like the taste. The music, of course, was excellent. Saturday was a lazy day. I went swimming in the morning. I thought I would feel more awake afterwards, but when I came home and took a shower, I felt more tired than I had been before. I didn’t end up doing a whole lot afterwards. I did slog through a bit of administration I’d been neglecting (and overwrote one of the documents, so I had to fill it out again), so that’s at least something. On Sunday I went to the local game store to play Adventurers League during the afternoon, and created a new jank deck on MTG arena. I don’t think it’s viable, but it is fun to pull off the combo.

Anyways, that’s it for this week. I’ll see you in the next post!

Tibbert

Third week

Hello lovely readers,

I know its been a while. I also know I'm about 4 days late with this post, but I've had a relatively busy weekend, so this kind of slipped my mind.

First things first though, so here's my report of week 3.

Truthfully, there is not a whole lot to tell. My experience with bioinformatics is that it takes a long time to do little work. When I think back to the work I've done on a day by day basis, I'm not all that impressed, since it's usually tweaking the code a little, or adding some UI elements. However, with all the testing and troubleshooting, those things that feel like they should only take a few minutes eat up a couple hours with ease.

Either way, I have integrated EdgeR into the application, though it doesn't work completely yet. Currently, the application calculates the normalized values (in CPM), the p-values, the fold change and logCPM. I need to do more testing, since I am not sure whether those last three are the correct values. I have also added in a download button for the generated RNAseq data. Clicking it lets you download the data in either a .tsv or .csv format. I wanted to autogenerate a title for the document, but I cannot get it to work.

I have also placed the two buttons into one row, which was a lot more trouble than I expected. For some reason the buttons refused to be placed right next to each other, one was always on a different row. I don't know how that happened, since I only added in 1 row. Eventually I tried a different approach. I created a table and placed the buttons inside of it, and that did work.

Lastly, I spent some time writing up a basic template for the front page of the application. As part of that process, I tried to come up with a decent name for the application, but I am rubbish at naming tools, characters or pets, so nothing good came out. I asked my supervisor for some input, but all he said was that he would like for the name to have "differential expression" included in it.

During the weekend I went back home to Belgium. I took the train at 5:30pm on Friday, and I arrived at 9:45pm that same day. Surprisingly, the journey went by faster than I thought it would. Perhaps it had something to do with me having to study on the train, which made it easy to lose track of time.

There are two reasons I went home. The first is that I have applied for a job in a laboratory, which required me to take a multiple choice test to test my knowledge. I wasn't sure what kind of knowledge it would test, so I refreshed some of the courses of the last few years. Turns out most of the questions were insight-based (eg: "In this situation, do you do A, B, C, D or E?") but a couple required me to calculate concentrations, or did test some basic medical knowledge. Most were questions that I feel are easier to answer if you've had some workplace experience.

The second reason would be family. It was Mother's day last Sunday, and my mum had asked me whether I would come home for the weekend. Now, I was glad that the day of my test was on Tuesday after Mother's day, so I asked for a couple days of leave from work. Since the train journey is on the longer side, I didn't want to go home for just 1 full day, and then have to leave again on Sunday evening, but with the leave granted to me so I could go take the test, I had 3 full days to spend in Belgium. That made the journey worth it, of course.

 And that's all for this week's post!

See you in the next post,

Tibbert

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

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