Hovedinstrument

This post might prove a bit boring, but bear with me, I think you might find the conclusion rather funny, but also very frustrating and disappointing.

It all started with my written Danish exam from last week. No, I haven’t got the results for it, but I do have something almost just as good. The exam consists of two main parts: one where you actually have to write and the other where you have to show that you can understand written text. This part is called… reading. The reading is itself divided in three, among which one consists of quickly scanning a long brochure to answer 15 questions in about 25 minutes. The idea behind it is that people should be able to extract information from text fast, without reading it in too many details.

All the reading material that is being used for the exams is real stuff, not things they wrote specifically for it. This time the brochure was about different types of education you can take in Bornholm, an island which is also the most eastern part of Denmark. Among the questions there was one that had to do with some musical education. The question was in the following manner:

In order to apply for the musical education, does one need to be able to play an instrument?

Section from the brochure

The text corresponding to this question basically said that one has to be good in a main instrument (hovedinstrument in Danish, where hoved means head, main, etc). So, pretty obvious, the answer would be yes. But then the silly girl (or not) looked around the text a bit more and noticed that they were also saying that during the education the students will have a main instrument (instrument or voice) and that they will also learn a secondary instrument (piano). So then I started thinking: the question is about playing an instrument, while the text says that you need to have a main instrument, which could either be voice or… an actual instrument. Right? So I answered no. Wrong! Last week I had a small argument with my teacher on this matter, and the main conclusion was that I wasn’t supposed to look around in the text, but just in the section where it was talking about the admission requirements (adgangskrav)…

Anyways, I ended up being very disappointed and deciding that next time, when I will be in a situation like that, I will stop analyzing things too much. But then things suddenly changed yesterday when, after entering the class, my teacher congratulated me. For what? For being right! It seems that another weirdo in the whole Denmark noticed the same thing and they decided to call Bornholm and ask. The answer was that we were correct and everybody else was wrong. They contacted the persons responsible with the tests, who didn’t want to accept the truth until they talked with those in Bornholm themselves. So what is the conclusion now? That for a question with two possible answers, both of them are correct! Not to mention that, apart from this question, there were 5 more where there were ambiguities and there were two alternative answers. Which means that the people who did the test did it very poorly and they wasted everybody’s time!

I am both relieved that I got it right, but also annoyed and frustrated that something like this happened at all…

Oxford

It has been almost 2 years since I spent 6 weeks in Oxford for a summer school. It was the period when I just started this blog and a lot of exciting things happened. It was a great experience and when I was offered the chance to take part in it once more, my answer was… yes!

When I was there last, we were 12 students divided in 4 groups. Each group worked on a project, supervised by some experienced bioinformatics researchers. However the school has been growing with each year and there will be 36 students this summer. Quite a big increase I would say. More students require more people to help them, people which I will call, from now on, supervisors. Of course there are quite a few in Oxford already, some PhD students, post docs and senior researchers, but it is generally the case that the PhD students have more time to get involved and help the students. So it was decided that each group (6 in total) should have at least one PhD student for a supervisor…

And this is where I come in! I have started working on my new upcoming role since this winter by making a couple of project descriptions. Now we are finalizing them and setting everything up so the students can start working from the moment they arrive in Oxford.

I find this very exciting but it also made me think a bit more about how things are changing around me. This and my increasingly number of gray hairs (yes, I’m getting old) made me think about me slowly becoming a grown-up and having more responsibilities than liberties. It is a bit scary that I will be, more or less, responsible for 6 students. Hopefully things will go well… Until then, I still have to pass a Danish oral exam…

Verdens bedste lærer

You might remember me talking about changing Danish teachers at the beginning of this year. I was far from being happy back then, but it didn’t take me long to realize that I made a good choice: the new teacher I ended up with is, simply put, amazing.

There are only a handful of teachers that I met in my life which I found to be, more or less, the perfect teachers in their own way. It started with my secondary-school math teacher who, apart from being very good at math, knew how to explain the theory so even the stupidest kid would understand it. He was able, as few are, to find different explanations when the previous failed. Way too many teachers repeat whatever they just said when you tell them you didn’t understand. But not him. And that wasn’t all: he would always tell us interesting news and give us good advice on how to approach exams, etc.

But I think the common characteristic of these few teachers, apart from their thorough knowledge of their topic, is their involvement in what they were doing. You can clearly see they like what they’re doing and that they do it with passion. And because of that, they tell you much more than the topic their teaching. Ania, my current Danish teacher, is exactly like that. She bombards us with information from TV, articles from newspapers, schedules for free or cheap cultural events and even good restaurants. Not to mention that my Danish has improved drastically in the last months.

So when a Romanian classmate told me that it was Ania’s birthday on Tuesday, we decided straightaway we should get her a small present to show her our appreciation. After walking around the city, we realized what the perfect gift would be: a personalized mug. So we bought a mug, paint and brushes and set to work. You can see the results below and I can tell you that she seemed to be very pleasantly surprised by our initiative.

The world’s best teacher

Publishing

I think one of the things I will have to get used to when it comes to being a PhD student and doing research is how the publishing process works. And what I mean by that is how long it takes and how many rejects you have to go through before your article is accepted. At the beginning I was, probably like most, eager to have my first article published and I thought that it surely wouldn’t be that difficult: if your work is good, then everything should be fine.

But it isn’t. There are lots of examples out there of research which has been rejected by big journals such as Nature and which, once published, proved to be of major importance. Not that I am pretending that my work is that mind-blowing, but I am just trying to give you an idea of how difficult it sometimes is to publish.

From my limited experience of two articles and one on the way, I can say that probably, in most cases, publishing takes at least the same time it took to do the work. Let’s take my first article. I started the project in September 2010 and the publication process took from May until December 2011. I sent it to a conference, where it was rejected, and then to a journal, where it went thorough the review process twice. Doing the work took me 8 months, while publishing it took… about 8 months.

Second was the article with the guys from Oxford. I was there almost 2 years ago. We worked on the project since July 2009 and we were mainly done by November same year, when we sent the article to a journal. After going under review 3 times and still not being able to satisfy the reviewers, we dropped it. They simply wanted things from us that were, in our opinion, handled already in a proper manner and we couldn’t really see how we could do anything better. We then submitted to another journal in October 2011 and it was finally published this month. Adding 2 months of work this winter, it adds up to 8 vs 15 months.

The reason I started thinking about this is because of the article I am currently trying to get to the surface: the third one! It has by now been rejected twice for two conferences: a Computer Science one and an European Conference on Bioinformatics. This week we are submitting it to yet another conference and if this fails too, we plan to send it off to a journal. I have to mention that it is generally more difficult to publish in a conference than a journal: for a conference you either get accept or reject, while for a journal you can be asked for a revision, saying that they think it’s interesting and useful, but that you are missing things. Not to mention that conferences can only accept a limited number of articles so they might have to throw away some good ones.

The most annoying thing about this current article is that from all 6 reviews that we got, almost all of them where positive. They contained phrases like:

• The paper is a clear and self-contained presentation
• Experiments are included that show improvements over previous approaches
• I encourage them [the authors] therefore to submit their work to a related conference
• Overall, the paper is well written and discusses an interesting technique concerning HMMs which I believe to be of interest
• I think that this paper considers interesting problems and gives solutions from the view of bioinfomatics
• This is a very nice paper that handles an interesting problem

So what went wrong? I am not sure… But just to go back to counting, this work took about 6 months… and if it will be rejected again, I have no hope of getting it out before the end of the year.

In some way, I think it’s silly we spend so much time polishing words in articles and thinking on how to best present our work, when we should instead spend the time doing research. But on the other hand, I know it is a necessary evil.

Exams

Yesterday I finally had the written Danish exam that I have been waiting for, for so long. While days past and I got closer and closer to it, strong feelings started to set in and the nights became longer and more sleepless than otherwise. This made me think about exams, how we approach them, how they take place and what they mean for us…

When I was younger and in school, I was one of those good kids that studied a lot and had good grades. I was far from being the best one in my class, but I was in top five and I was really good at math. In fact I was that good that I went to school math contests, all the way to the national level where I even won awards. I am not writing about this to brag, but rather to tell you in what way I’ve changed because of it. Most importantly, I learned how to handle exams: every year I attended at least 3 serious contests, which took somewhere between 3 and 4 hours. I gradually learned how to deal with my nervousness and how to best approach it, which really helped when I had the huge end-of-highschool exams and started university. I dare say I had an advantage over the others just because I was more used to exams.

At the beginning I was so nervous that I would get out of the exam room totally red, my hair a mess because I would keep playing with it, and sometimes with recent memories of my heart beating so fast that I thought it wanted to go for a run. However, things changed and now I am nervous just before the exam. But then I get my exam questions, calm down and start doing my job. I do think a certain amount of nervousness does you good, as you get more ambitious and maybe a lit more cautious. Therefore I believe I might have reached my optimum exam-nervousness.

When I came to Denmark, it was a bit different for a while, as all of a sudden I had only oral exams, as opposed to Romania where I had just one unlucky oral exam and everything else was written. But I adapted fast and I started preferring oral over written.

And then… yesterday came. I cannot remember when I was last that nervous about an exam. I think the explanation would be that it’s so different then what I am used to – math, computer science, very precise and well defined things, and then all of a sudden I have to write argumentative texts about God knows what. I have to admit that I always had problems writing (and this blog helped a lot in that regard) and that I often used my mother to do my Romanian homework assignments as a kid.

Nevertheless, my strong experience took over and calmness set in when I received the exam papers.

As for how it went… I think it was decent. I don’t know the results yet and… I am not even sure I will want to share. Maybe they will be so bad that I will have to mourn my language skills afterwards! Until then, I have to prepare for the next stage: the oral.

Råbjerg Mile

Råbjerg Mile

While visiting Skagen, we also took the liberty to see other tourists attractions found in the area. I think most of them can be described by one single word: sand. I have been told that centuries ago there were around 60 migrating dunes in Denmark – a slow but catastrophic natural phenomena. They might be pretty to look at but certainly you wouldn’t be happy if they would bury your house or crops. This is why the Danish government decided to put a stop to it by planting dune grasses and conifers and transforming them to some weird looking hills. However, they did leave one dune behind, to allow future generations to understand the problem of sand dune drift – Råbjerg Mile.

It is the largest moving dune in Northern Europe with an area of around 1 km² and a height of 40 m, containing a total of 4 million m³ of sand. The wind moves it in a north-easterly direction up to 18 m a year. I personally found it to be an amazing site – while still in Denmark, you are completely surrounded by sand, like you where in the desert. It seems to me that most of the north-west part of Denmark – at least the bits I’ve seen – look completely alien. It is nothing like the Aarhus area or Copenhagen. Everywhere you look there are remains of desert-like landscape.

We also visited two of most famous buried attractions – a church close to Skagen and a lighthouse on the north-west coast. The only thing left above the surface is the tip of the buildings – the church tower and the most upper part of the lighthouse. But as they say… a picture says a 1000 words.

The buried church and lighthouse

Skagen

I have been in Denmark for almost three years now, but yet I have only seen Aarhus and Copenhagen. Not much, you might say, and I totally agree. I think it is a bit silly to live in another country and not take advantage of that to travel around. The main problem though is that it is not easy to go places without a car. Trains are insanely expensive and the network, I dare say, does not cover a lot. I remember when we went to Legoland last year, there seemed to be no easy way to get there.

‘Summer Evening on Skagen’s Southern Beach with Anna Ancher and Marie Krøyer’ by Krøyer

Lucky me though, Jesper’s parents kindly offered to show me around Denmark. So last week-end we went to Skagen, the northernmost tip in Denmark. The special thing about it is that it separates two seas – the North sea to the west and Kattegat to the east. If fortunate enough, one can see waves coming from both sides, clashing into each other. Skagen is also known for its painters – a group of Scandinavian artists that gathered there to take advantage of a peculiar light. One of them in particular, by the name Krøyer, is known at international level, while Ancher is probably one of Denmark’s most popular artists. The group’s most important works are gathered in Skagen’s Museum and Ancher’s house.

So while there, I witnessed all that and more. The most exciting things apart from those already mentioned, are Bolcheriet – a sweets shops where one can see the amazing process making of sugar candy, and the Teddy bear museum. If asked I would advise anyone to take some time for a trip there – it is a very picturesque place that shouldn’t be missed when visiting Denmark.

We Bike to Work

Even thought I am not happy with what Danes do with the bikes when they’re drunk, I think it is amazing what they do with them when they are sober. By that I mean, of course, the extent to which Danes bike instead of using a personal car or even public transportation. I was impressed from the first moment I set foot in Denmark and I still am. If I am not wrong, Copenhagen is among the most greenest capitals in the world.

However, the Cyclists Union and the Danish Sports Federation still try, every year, to get as many as possible to bike. One of their approaches is by organising an annual event which spans May, entitled We bike to work and which is Denmark’s biggest motion campaign. The idea behind is that teams join the event, they register on a form every day if they biked and how long and points are accorded on the basis of that. At the end, about 40 teams will receive prizes, such as a vacation for the whole team, bikes and biking gear (gloves, socks, bike racks, etc). It is not very clear to me if they give the prizes on the basis of gathered points or just by random, but either way, I think this campaign is really cool and so I wanted to be part of it!

The Computer Science department put a team together, but there was a problem: even though BiRC is part of the department, we are located in the south of the campus, while CS is in the north. And the form where I would have to mark when I biked was going to be placed, of course, at CS. Instead I suggested to our director that we make a team. My idea went through, we made a team of 8 and now I am the team captain! We are called the BiRCyclists. Very creative, right? :-)

So now I have a new reason to bike everyday. I think it’s a bit silly, I live only 1.5km away from BiRC, but as soon as I got used to biking, I couldn’t imagine myself walking such a long distance – it takes a whole 15-20min to do that! What a waste of time… It is a bit ironic that I am the team captain and I am the one that bikes least, but I don’t really care. I just think it’s fun!

Where is my Bike?

I officially hate the stupid drunk Danes that have nothing better to do than messing up with other people’s belongings!

This morning, while heading for the University, I went to pick up my bike. It wasn’t were I left it yesterday and I got scared: I thought it was stolen. And it was barely two weeks ago that a paid quite a bit to get my front wheel fixed… Jesper was a bit more open minded then me and he spotted it. It wasn’t where I left it, but it was pretty close. However, it was placed somewhere where you wouldn’t really expect a bike to be…

Luckily, I had Jesper with me, otherwise I don’t know how I would have got it down…

Making of Ravioli

Jesper received for his birthday last year a pasta machine (just like the one in the picture). For our adventurous cooking spirit, this only meant more freedom to experiment: I started making pasta and ravioli and Jesper made lasagna with home-made plates… mmm… But there was one thing I didn’t like: the ravioli. They tasted nice, that wasn’t the problem, but making them wasn’t easy. I had a difficult time packing them and I felt like I didn’t really put as much filling inside as I could. So I decided to buy some utensil for it.

I first asked the people I knew. I talked to Jesper’s dad who, even though he never made ravioli himself, just laughed in my face, saying that it can’t be that hard to pack them. Jesper asked at a specialized shop and he had a similar reaction: the guy there told him it was silly and that using two spoons should do the trick. I tried that, but with no success. I took my search further and I starting browsing Amazon, until I came upon the best solution: the ravioli tray! When it finally arrived, I was very anxious to try it out. Several months passed since then and I can honestly say that it’s one of the best buy I ever made: it makes everything so much easier!

This week-end, still taking advantage of the free wild garlic in the forest, I made ravioli filled with spinach, wild garlic, egg and Parmesan. While doing it, I thought it would be interesting to document the process. Unfortunately I had the idea a bit too late, but I still got a couple of shots showing how easy it is to use the tray. So I thought that maybe I will inspire one of you to try some home-made ravioli :-)

PS: I have to work on making the plates wide enough to cover the whole tray… but I will get there!