Year in review: final year as a PhD student

This post is a summary of 2014, the last year of my PhD. I am writing it a whole year later due to my difficult relationship with blogging. There are two reasons for this: a recent conversation about blogging on Twitter, with this result, and the fact that the summary of my third PhD year played an important role in me deciding to resurrect this blog.

As 2013 was a year of submitting papers, I expected that 2014 would be a year of paper resubmissions. That guess was quite accurate. But 2014 had more challenges in store for me. The year didn’t start out great for me for personal reasons. I am not sure I will ever discuss the details online, so let’s just leave it at “life changing event”. Up until that point, I was sure I would finish my PhD on time. But, with so many things changing so rapidly, I started having serious doubts about my progress.

Writing and staying motivated

Despite the personal chaos, I continued to work on the revisions of my rejected papers. In February, I resubmitted Paper 1. That was tough, so I didn’t want to touch the other rejected papers for a while. Besides, I had other activities lined up, such as a research visit to Copenhagen, where I wrote a conference paper about the work I had done the year before. The visit was a great experience, both professionally and personally! Unfortunately, I received a rejection, adding yet another thing to the revise-resubmit list. On top of that, I was rejected for the Anita Borg scholarship for the third and final time. But there was also a bright side: for example, around the same time I gave my first invited talks, which was a much-needed boost for my confidence.

In June, I finally received the coveted “We would be happy to publish your manuscript” email about Paper 1. This gave me the needed motivation to continue with the other revisions. In July, I resubmitted Paper 2, and in September, Paper 3, which by then had already been rejected at two different journals. Again, it was very helpful to be involved in other activities, such as organizing a workshop and teaching, to stay motivated.

With one accepted journal paper and two others under review, I again started hoping that I would submit my thesis by the end of the year. The thesis requires at least four chapters, each based on a “publishable” paper. My supervisors agreed, so I spent the last months working on Paper 4. Paper 4 described recent results, and was therefore very refreshing in the midst of all the revising. I finished it on time and submitted it to a conference in December. And then, with three papers “in limbo”, both 2014 and my PhD contract, ended.

Take-aways

My year of revisions had a few successes and several disappointments. However, the more important successes were the things that these experiences taught me. I…

  • …became a seasoned reviser-and-resubmitter
  • …learnt how to stay confident as a researcher despite a lot of disappointments
  • …realized even more deeply how important it is to have colleagues who believe in you, who support you, and who are up for a grabbing a beer (or a Spa rood), whether it is to celebrate or offer a shoulder to cry on.

My relationship with blogging

I have a love-hate relationship with blogging. I have always enjoyed having some sort of website. When I was 10 or so, my dad showed me how to build websites in HTML, and I made a website about the Spice Girls. There was no original content on the website, but the fact that I had a website and could update it if I wanted, that’s what counted for me. Of course, when I got a bit older and became embarrassed by my choice of music, the website stopped existing. In high-school, I got a bit more interested in webdesign. Blogs were becoming popular, and since I didn’t have any particular hobbies, I made a website with a blog about what was happening in my life. You can already probably guess what happened… I got older, decided my problems from a year or two before were very silly, and that website disappeared as well. Which is too bad, because now I would find it interesting to see how I thought about things in 2004.

In university I had a break from websites and blogging, probably because my desire to “do something with websites” was satisfied by my part-time job. But when I started working on my MSc thesis, something started nagging at me again. I was learning more about doing experiments, reading and writing papers, and wanted to share my thoughts. Perhaps that was the first time I felt that I had content worth sharing, so I started a blog again. In the end, I often felt obliged to post “something”, which resulted in rather uninteresting posts. This also happened during my PhD – I got inspired by website such as PhDTalk, but my attempts were never really quite successful, because I didn’t spend enough time on them. Again, my earlier posts just seemed silly to me, especially after some major changes in my life. My website was offline once again.

As a postdoc, I’ve started reading more and more academic blogs, and since a few months, I even have a Twitter account. So again, I want to have a blog, and I regret not doing a good job with the other ones. But a difference between regretting getting rid of your website in 2004, and getting rid of your website in 2014, is that I’ve been with the same host for the past 5 years or so, and could recover any content that I posted. So, I have decided to resurrect my blog a little bit, including posts from earlier editions. I’m not making any promises about how often I will post this time, but I will try to keep myself from going through the whole delete-regret cycle. Stay tuned!

Year in review: third year as a PhD student

As I mentioned before, it’s important to keep track of your successes and disapointments. Since I do have a list of sorts, I decided to share my summary of 2013 here.

Writing

2013 was definitely a year of journal papers. Or at least, of long overdue journal paper submissions. Here are the totals! I submitted four times in total (one paper twice, and two papers once). Two of these were rejections, one “revise and resubmit” and one still under review. So, 2014 probably will be a year of journal paper resubmissions.

Reviewing

Next to paper writing, there was also paper reviewing. In the beginning of last year, I was getting worried that I was not invited for reviews, but this worry turned out to be unfounded. I guess this goes together with submitting journal papers (and getting into the system) and meeting more people, who have more reviews than you, but are also more busy. I want to believe in review-karma: by writing good reviews, I hope to get good reviews. By good, I mean objective and constructive, not necessarily an “accept”.

Funding

2013 was also a year in which I tried to apply for scholarships to finance my conference visits and the trip to Tuebingen. For the second time (the first time being in 2012), I did not get the Anita Borg scholarship. I did get the ACM-W / Microsoft Research grant to go to a conference in China, which was awesome! The application that I spent quite a lot of time on, for the short-term fellowship from EMBO to go to Tuebingen, unfortunately got rejected (after I returned from Tuebingen already). However, I was able to get some financial support through my university, which was not a competitive application, but very helpful.

Research visit

And of course, 2013 was the year I went on a research visit, for which I have not (yet?) been able to write an overview. In short, the three months went by really fast and I had a great time. What everybody says about research visits is true. It is really helpful to experience a different place and get an idea of how people do research there. I think it’s a must for all PhD students, especially from smaller labs. It probably doesn’t even need to be a lab in a different country to get an impression of “how things are done” and to pick up useful research skills. I already have my next short visit planned, what about you? Did you / will you do a research visit during your PhD?

On recording your progress

It’s been almost a year since I started to blog alongside my PhD. I’m not sure whether I mentioned this a year ago, but my initial goal was to write something every week, which quickly deteriorated into writing something every month. With this post, I have been able to keep the latter promise up.

Although I had many moments of “oh, this is something I could write a post about!”, only few of them actually made their way from my thoughts into a digital version. The main reasons for this are, I think:

– too little practice: I really do find it difficult to write something that’s not directly about my research

– too little privacy: there are some issues I would not want to discuss online because my name is linked to my blog and I don’t want my opinions to always be “out there” somewhere. Many of the blogs I find very interesting (not just the ones that are linked on this page) are actually blogs that discuss such issues, and for 95%* these are anonymous.
* I initially wrote 95\% which amused me quite a lot.

– too little expertise: I like posts which contain advice on how to do something better, such as never worrying about poster transport again. The truth is, however, that there are not a lot of things I feel I’m more knowledgeable about than other researchers with blogs.

– too little information: I am, of course, knowledgeable about what I do on a daily basis (submitted this, got rejected for that). Of course, this is mostly relevant to me and not to readers in general. I am aware this is my blog and I can post whatever I like, but I am less motivated to spend time writing something that is not helpful to others. Also, I

What I recently realized is that I would have enjoyed to have more of these “progress” posts, just for myself. In my first attempt at blogging, I wrote about how I submitted my first paper and how a few months later, I got the email that started with, “We are pleased to inform you…”. Or about how I reviewed the paper for the first time, and it turned out to be horrible. It’s nice to remember how I felt then, what my goals were, and how I generally thought about research.

My advice (this is actually a helpful post!) if you are a PhD student: write your successes and disappointments down somewhere. Not necessarily in a blog. Maybe it’s even better if it’s not a blog, you might spend less time worrying about how to write it down, and who is going to read it. But sometime later, you will enjoy reading about these experiences, and what they tell you about your progress. Happy writing!

How to print your posters on fabric

The Problem

Probably all PhD students face this problem in their career: the poster presentation, and bringing the poster with you to the conference. This usually means you need one of those poster tubes to keep your poster all neat until the poster session. Not too bad if you are going to a local conference, but more annoying when you are going to, say, Japan, where I attended the International Conference on Pattern Recognition in 2012.

poster

I was determined to go to Japan with just a carry-on bag, something I have never attempted on trips longer than 3 days. Of course, I would also have a “personal item”: my regular bag for my laptop and valuables. I really, really did not want to add an extra piece of luggage (the poster tube) to the list of the things I had to bring with me. So I decided to look for a solution: posters that would fit into my carry-on!

The solution

For paper, this would mean either a very small poster, a poster with fold lines, or a poster consisting of several small parts. Neither of these seemed very appealing, so my material of choice became fabric. After some searching, I settled on this product, in particular the “vlaggendoek” or “flag sheet” variety. This material weights just 115 grams for 1m2, which is conveniently almost the same size as an A0 (841mm × 1189mm). Printing + delivery costs just over 20 euros, which is actually cheaper than an A0 paper poster with a plastic coating. That’s not all: apparently the material is fire retardant, because you never know when fire could break out at a conference.

But the best thing of all? You can fold it and it still looks great when you unfold it! Here are my two posters folded a few times:
poster folded

These did not only fit into my carry on, they even fit into my purse (and made a great padding for my mini laptop).

I received a lot of compliments (about the content too of course 😉 ) and heard a lot of  “I should have known this earlier!” during the poster sessions. So this is me, telling you: print your conference posters on fabric! If you are in the Netherlands, you are welcome to stop by to see the real thing.


Where else to get it

France: Easyflyer (thanks to @cazencott!)

Belgium: UniversityPress (thanks to @dan_marinazzo!)

Germany: Diedruckerej (thanks to @chrshmmmr

UK: SciencePosters (thanks to @IAugenstein!)

US: Spoonflower (thanks to @jengolbeck!) and Postersmith (thanks to @astent!)

If you know of any more companies not in these countries, please let me know (comment below or via Twitter) and I’ll add it to the list! As of July 2017, I’m still updating the list.

 

Bonus

You can get your textile poster repurposed into a piece of clothing or accessory at REpost Science. See my newest blog post about this.

 

 

 

 

Firsts: preparing for a lecture, part 2

“>Here I started preparing for my first lecture and describing my experiences. Now that the lecture is over, I have a few more things to share about the whole process.

In the end, I think I spent 20 hours preparing (not 30 as I estimated previously). At some point I felt I was satisfied with my story and I didn’t feel I could change anything until actually trying it out. In terms of the “how to”, I found a teaching course on Blackboard, and looked through the first teaching lesson. There are some useful tips there on keeping the attention level of the students high, and on structuring the lecture, such as providing summaries. With this in mind, I revised my slides one final time, for a total of around 30 slides for each 45 minute lecture.

During the lecture, a few things went differently than I originally planned. For instance, I included short summary/overview slides for transitions between different topics. However, every time I felt that I already explained this twice, so I did not put too much emphasis on it. In the end, it turns out that I should have done it anyway, against my intuition :). For other slides, I realized that I could have explained something in a different way, or linked the topic more to something students are already familiar with. I received some helpful tips about this from my supervisor, so I hope I can apply these in the future.

Another thing that didn’t go exactly as planned was the timing. I am very happy that I was using the presenter mode in Powerpoint where you can see the time and your notes on the laptop screen. I was too involved with the lecture to actually look at my notes, but the time was very helpful. I realized that I started too quickly, so later on in the lecture I tried to go a little bit slower. In the end, both lectures were finished in under 45 minutes.

Overall, I think the lecture was quite a nice experience! I was not too nervous about it, and although there were some silences (such as after a “Are there any questions about this”?), there was also student participation after some of my other questions and examples. That was very nice, especially because students started thinking of how to apply the method to their own PhD research. And that’s what the course is all about!

Firsts: moving for an internship

Exactly three weeks ago I got on a train to Tuebingen, Germany, and right now I feel I can say that I’m settled in, which means it’s time for a post.

One of my goals when coming here was to concentrate on the project that I am here for. Therefore I wanted to spend as little time as possible on “settling in”, and although I can’t say I was 100% successful, I learned a few things that might be useful when moving to a different country (even if it’s just from the Netherlands to Germany).

Luckily, I was able to arrange a room beforehand, and the room was furnished. I assumed I only needed to get bed sheets, so I ordered those at IKEA and had them delivered to the house before I arrived.  However, “furnished” does not mean “you have everything you need”. Here are a few things I did not really think about, and really missed in my new room:

– A sofa. A bed (though very comfortable) is just not exactly right if you want to read, watch a movie or relax without falling asleep.

– A coffee table. For the laptop that is getting too warm, or food and drinks to go with the movie.

– A coat rack and hangers. I’m not too organized when it comes to my closet, but hanging things up is easier than folding, and a few items (coat, bath robe) just don’t belong on a shelf.

– An electric kettle and a coffee machine. Tea and coffee are basic necessities and specialized tools definitely beat heating up water in a pot on the stove or in the microwave.

– Laundry “accessories”. There is a washing machine in the building, but laundry needs to be stored and dried somewhere as well.

About half of these things I bought second-hand (through Facebook groups or at flea markets), the other half from convenience stores. Now life is more comfortable 🙂 A few other things that I arranged as soon as possible, and that have been very helpful, are:

– A prepaid SIM card with internet. I’m using with my dual SIM phone. I would recommend Alditalk (great value for money), but not so much the phone (dual SIM is great, but it’s quite slow compared to my deceased HTC Desire S).

– A bank account. I did not really want to get one for the few months that I’m here, but the German bank card-operated washing machines thought otherwise.

– A bus pass. I only need to worry about which bus I get and where to get off, not about having the right amount of fare.

– A bike! For all the times that a bus is not that convenient, AND it feels just a bit more like the Netherlands now 🙂

 

Firsts: writing a grant proposal

Despite my previous post about having a whole month to myself to write a journal paper, things went a little bit differently. A fellow PhD student pointed out these short-term fellowships and I decided it would not hurt to try to apply, so I could finance the second half of my visit to the Max Planck Institute in Tübingen. Because I already had a few scholarship applications lying around (such as for the Anita Borg scholarship, which I applied for twice, unsuccessfully), I thought a new application would not cost me more than 2 days. In the end, I spent around 2 weeks working on the new application and neglecting my journal paper, but I still believe it was time well-spent!

One thing that was different about this application is that it was not focused on me, but on the project. Of course, I already had an idea about what I would be working on at the MPI and how that fits together with my PhD topic. What I underestimated, is that I suddenly had to explain all of these machine learning problems to people with a different background – I assume molecular biology, as that is the core subject of the organization providing the fellowships.

What really helped me with writing, was a successful proposal, which was on a different topic, for a different fellowship, from a different organization, kindly provided to me by a colleague. It was a good example of HOW to write for a different audience, rather than WHAT exactly to write about. Here are some of my findings:

  • Don’t assume a term that you use every day is obvious to everybody else. Provide a short explanation and an example. If possible, use pictures in your explanation.
  • Provide references, even if something is common knowledge in your field.
  • Use short, clear sentences in the active voice (“We will conduct experiments…” rather than “Experiments will be conducted…”), here is a good post on how to do this.
  • Avoid words that make you sound unsure, such as “probably”.
  • Include questions which your project will address, such as “What is the cause of X?” or “Is it possible to do Y?”
  • Don’t be afraid to use bullet points for lists, this is probably easier to read than a paragraph of text that does not really fit together.
  • Be explicit about how your previous work is going to be helpful in this project, it might not be obvious to the reviewer that your list of publications is related to the research topic.
  • Ask others (especially people outside your lab) to read your proposal.
  • If possible, use examples (both successful and unsuccessful) of other proposals.
  • Don’t underestimate the time that you will need for writing 😉

I will only get the results of my application in a few months, but I hope these tips can be helpful to other PhD students that are in a similar situation.

Update: the proposal was not funded, but I received funding for my internship from another source, so it was a good experience overall

Firsts: preparing for a lecture, part 1

I’m very proud of it and very scared at the same time – next week I’m going to give a lecture for the first time. The lecture is a part of the Advanced Pattern Recognition course for PhD students and my own lecture will be about the dissimilarity representation and multiple instance learning – topics I should be familiar with 🙂

Right now I’m spending a lot of time in preparing for the lecture. I’m guessing that 30 hours will be a good estimate for how much time I will spend in total. Right now I will try to explain my progress and how many of these hours I am spending where.

I spent an hour or two searching for information on how to prepare your first lecture. I found helpful tips here and here. The main messages for me is: pick a few core topics and explain them well, rather than skipping over all the possibilities.

With that in mind, I started thinking about the actual content. Although the topic is very related to what I’m doing in my PhD, I want to talk more about the general techniques rather than the specific parts that I am doing. Therefore, I could not use the typical structure of my conference presentations. I started out with a mind map (or at least, a bunch of words with arrows between them) of both topics to see what exactly I would need to cover. In my head, I was already preparing the connections between different topics and thinking of nice examples, so in the end, this process costed me about 2 hours.

Then I looked at which topics I feel comfortable explaining (most related to my own research), and which topics I don’t have experience with / haven’t tried explaining to others. For instance, with a dissimilarity representation, there are two main possibilities to improve upon nearest neighbor classification: embedding the dissimilarities, or training a classifier in the dissimilarity space. In my research, I only do the latter, and although I understand the concept behind embedding, I don’t feel as comfortable with it. Yesterday I spent most of the day reading about it and at the same time trying to revise last year’s slides so I could actually use them in my own explanation. This turned out very time-intensive (+/- 7 hours), but also very helpful.

I still need to prepare the slides for my more “comfortable” topics, revise the whole story and practice. I’m not really into practicing the whole thing before presentations, but here I’m especially worried about the timing, because I have never talked for 1.5 hours before. Also, as my lecture is only on the fourth day of the course, I plan to attend the other lectures and see how the experienced people are doing it. So, probably I will revise a few things after that as well.

The last, somewhat more optional part, is to go over the exercises that “go” with my lecture. Because the content and slides that I’m using changed from the previous years, I have to check whether the exercises are still useful, and update them if necessary. I’m actually very looking forward to this, but I’m afraid I won’t have the time to come up with my own exercises, test the code, etc, so I might have to leave that for next time 🙂

To be continued!

Firsts: visiting a lab for an internship

Last week I visited the Machine Learning & Computational Biology group in Tuebingen. It’s difficult to summarize everything, but Tuebingen is a nice city, the institute is a great place to do research, and there are a lot of friendly people there! Therefore I am looking forward to my longer (few months) visit in the fall of 2013 🙂

At the group, I gave a presentation about my work, attended other talks, and discussed the project that I would be working on. The project is still being defined, but it is probably involve classifying brain data, and in particular, the connections in these brains. For instance, it could be the case that healthy people have different connections in their brains, than people suffering from neurological diseases. I hope to find out more about this very soon.

I also have to find out more about living in Tuebingen, and getting financial support to do so. So far, most grants seem to be for MSc students, PhD students who do not get any salary (but they are also supposed to be in the Netherlands, where PhD students DO get a salary… confusing), or more senior researchers. There are a few things I have to investigate further, so I hope something will come up :). It’s amazing (and unfortunate) how much time this search is costing me, though.

Another thing to think about is learning German. I don’t think it’s really necessary for a short visit, but I enjoy learning languages and I’m curious how quickly I could pick it up. There are no courses in Delft (they do have Chinese though, how awesome is that!), but there is a language exchange program. You pair up with somebody who can teach you a language, and who can learn a different language from you. I’m going to try that, and maybe also just start by myself. There must be an app for it!

Let me know if you have any experiences with exchange scholarships for PhD students, or with learning German 🙂

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