If you are into biking, running or any other outdoor activity in can be quite entertaining/helpful to record your activities with a GPS. The resulting tracks (in .gpx format) are easily obtainable from for example Garmin devices or the Strava app. Routinely these tracks are overlayed with maps such as Google Maps or Open Streetmap, but it is also possible to take the latitude, longitude and altitude information out of these GPX tracks and plot them in 3D.

Here’s an example how to do this in MATLAB (you need the Mapping Toolbox).

First, add the .gpx file into the MATLAB path folder, here I call it “Bergankunft.gpx”.

Now tell MATLAB to read the .gpx file, extract latitude, longitude, and elevation and plot the obtained information:

route = gpxread(‘Bergankunft_with_Niklas.gpx’);
x = route.Latitude;
y = route.Longitude;
h = route.Elevation;
plot3(x, y, h, ‘b’, ‘LineWidth’, 8)
grid on

Now you have your track as 3D figure and you can manually turn it and study your efforts in 3D 😉

In order to make a video of the whole thing download a MATLAB function created by Alan Jennings which allows you to create a video of any rotating 3D ‘lot (https://ch.mathworks.com/matlabcentral/fileexchange/41093-create-video-of-rotating-3d-plot?s_cid=ME_prod_FX).

I used the following settings:


CaptureFigVid([-180,10;-360,20;], ‘Bergankunft3D’,OptionZ)

Please also check out Alan’s instructions in order to understand what the variables mean. Most important are frame rate, the total duration, and the angles at which the plot is turning and captured.

The resulting small video (MP4) will be saved in your MATLAB path folder and you can watch it with any media player.

In my case (a trailrun from Lauterbrunnen to the Gspaltenhornhütte in Switzerland) the result looks like this:


Yes we can image mRNA

October 18, 2013


Hello Basel!

August 30, 2013

BaselStay tuned for my next exciting project!

Designing a poster

August 1, 2013

Presentation time. In order to attract a few people to my talk I designed this poster with the freely available GIMP software. It takes a while, but the possibilities that GIMP has to offer are astonishing. The software is great for creative outbursts. And wouldn’t it be nice if scientific posters could become more appealing to the eye in the future? The Biology Department of the University of North Carolina at Chapel Hill is already quite good at it: http://www.flickr.com/photos/biologyposters/.


Crossing 45° North

April 13, 2013


Partly painted walls – Boston


Enjoying some liquid sugar – Boston


Winter swimming (no pictures) – Somewhere in the woods


The Atlantic – Rockport


Freeclimbing or something like that – Rockport


Gone fishing – The Atlantic


Mont Royal РMontr̩al




A house in Montréal


A factory in Montréal


More houses in Montréal (it’s a beautiful city though, photos are selective)




Montréal at night (on top of Mont Royal)


Parking lot






Québec and its frozen river/part of the sea


See above


White Mountains hiking


Random impressions

February 7, 2013

No biology today, just photos from Boston. Click here for a little soundtrack and click the individual photos for higher resolution.

28 12 13 14 15 16 17 18 19_b 20 22 23 24 25 26 27

Getting visual

December 9, 2012

My current project explained in a short video. For biological science beginners and only in German. My apologies for these restrictions!

Check the video HERE.

Building a Single Speed

September 5, 2012

Mine is done. Now construct your own Single Speed bike. Here’s what you’ll need:

  1. Everything starts out with a nice frame. I would suggest a 1970s/80s steel frame, but that’s basically a matter of taste. Buy a new one (expensive!), buy a used one, or use that old dusty frame from your garage. Some things you should care about when deciding for a frame: (A) Think about the size you need. This table gives you an overview. Mentioned is the height in centimeters of the seat tube. (B) Check whether a headset and a bottom bracket is still part of the frame, since both are quite expensive parts and relatively difficult to mount. If you can check/ask for the quality (smooth movements, no slackness). (C) Next thing on the list is to check what kind of back dropouts the frame has. For a single speed bicycle horizontal dropouts are best because they allow you to adjust chain tension. I have a frame with vertical dropouts you’ll need an extra chain tensioner later (which kind of destroys the great look of your new bike). (D) The last thing is to check is in what state the frame finishing/paint is. Make sure there is no rust in the headset and bottom bracket area.
  2. If your frame has a bottom bracket already just buy a fitting crankset. If a chainring is attached already make sure that it’s not too large. A 53-tooth chainring is definitely too large for a single speed bike and pedalling will be quite heavy. For me a 46-tooth chainring is perfect. In case your frame doesn’t have a bottom bracket, you should first find out which standard-type you need.This mainly depends on the diameter and the width. Here’s an overview. For the headset there’s basically only one standard. Mounting both parts into your frame is quite complex and if you are not an experienced bike mechanic you should seek the assistance of your favourite bicycle shop.
  3. Now the hardest part is over and you can start searching for the essential parts of your bike that actually make the frame look like a bike: The wheels. Since a single speed bike is not a fixed-gear bike you can use a freehub. I think it’s a bit more comfortable and safer for a beginner. Best thing is to use 28” (inch) diameter rims. For the back wheel just remove the cassette from the freehub and replace it with a single speed conversion kit. Once you have it it’s about 15 minutes work to set it up. I am using a 18-tooth sprocket in combination with the already mentioned 46-tooth chainring in front which is perfect for flat cities and longer journeys. So choose your sprocket size wisely.
  4. For the likely case that you have horizontal dropouts: Be aware that back wheels with quick release skewer might slip if you are a strong guy. I recommend to replace the quick release axle with a standard axle with nuts. If you can find a solid axle with the same diameter and thread pitch and a couple of nuts it will work. Remember that your  new axle should also be at least 4 cm longer than the old (quick release) hollow axle. You need some special tools for it, but you local bike shop can probably assist you.
  5. Now buy some tires. This might seem a bit early, but it’s good to buy them now because you need to check whether they fit your brakes and frame. I’m using 28 mm wide Continental Grand Prix Four Season tires because I think they are fast and comfortable at the same time. Get some high quality inner tubes as well.
  6. It’s time for brakes now. Mounting them is not difficult, just have a look at an existing bike. However, sometimes some fiddling is necessary to get them parallelly aligned.
  7. Next, organize yourself a seat post and a saddle. It’s very important that the diameter of the seat tube exactly matches the diameter of the seat post. Otherwise, you’ll always have fun with a slightly down-sliding seat post. Also find a handlebar now that fits your needs and you think is comfortable.
  8. A bike is nothing without the chain. I would buy a new chain to prevent slipping issues. A special single speed chain is not necessary. To shorten the chain you need a special tool that you can again find in your favourite bike shop (or borrow one from a friend). Concerning the chain: Shimano offers a system called “Quick Link” which makes closing the chain, after having adjusted the length, very easy.
  9. Last, but not least get some pedals. If you cannot decide whether you want to use bike shoes with cleats or not, just buy pedals with a regular and a cleat side.

Parts you should consider to buy new include bottom bracket and headset, as well as front chain ring, sprocket and a chain. New rims and tires are nice, but not necessary. As I wrote, sometimes you will probably need the assistance of an experienced bike mechanic. Probably you will also have to pay him or her, but I definitely think you can have a very beautiful and good working single speed bicycle for around 200€. Well, I think that’s it. Have fun. For more info there is also the famous single speed/fixed-gear bible by the late Sheldon Brown. His “Bicycle Technical Info” page supplies with everything you need to know. If you are from Groningen, you should also pay a visit to Fietsje, a great bike shop with many useful single speed accessories.

Something about my current OOLP! – an out-of-lab-project:

This is an absolutely not biology or biophysics related blog entry. And that is because once in a while its nice to do something completely different, but in contrast to the Python’s I’d like it to be visible. I like sports, but since Groningen is not the best place in the world to go running, it is pretty awesome to go biking. Also the city itself offers some nice possibilities. So it was only a question of time to start an out-of-the-lab-project including the construction of a bike. I chose a total bottom-up approach. Buying, finding or asking for every part. Some progress so far, can be seen below:


First I wanted to construct a real fixie, meaning a bike with no brakes and one single and even fixed gear. That means you have to pedal constantly. It’s as simple as you can get it. It gives you the perfect feel for the road. It’s Gods first bike. However I decided not to construct a real fixie. I wanted brakes. Somehow it felt safer that way. However, this bike will still be a pretty basic bike. The brakes are the highest level of technology you will find on this bike. It’s based on a 1980 Ludo frame from Belgium. In 1964 Eddy Merkx became world champion on such a frame. Of course we’re talkin’ steel frame here. Durable, plain simple. And a bit heavy. But when you’re building a bike with no gears you shouldn’t complain about cycling becoming a bit difficult once in a while.


After having to cut new screw threads at the headset and the bottom bracket (the bike dealer did that), finally a 46er chain ring and some cranks could be mounted. Also a handlebar is part of the ensemble now. Oh yeah and my dad luckily assisted on adding some brakes. Nice old Shimano’s which had to be modified quite a bit in order to fit the world champion frame. I hope during the next weeks I’ll find a nice back wheel (and front wheel). The rest are only details. And then the cruising begins. Until I stop.

The Experiment

December 19, 2011

“[…] One reaction tube contains much more bacteria than the other one and they want to know why. In their own discussion the students conclude that something went wrong during the procedure. The experiment failed. […] But there is no course with the title “How to do proper Science”. […] Daring to make your own conclusions […]. […] Realizing what you have learned over the years […]. […] It sounds so simple, but it is a giant leap. […] Tomorrow we will do a new experiment. An experiment with an unknown result. Educational objective: There will come a day on which you can beg for an explanation of your results, but your teacher will also not know the correct answer. There will come a day on which you will have to figure it out yourself.”

by Rosanne Hertzberger (excerpt from her column in the Dutch newspaper NRC next, December 19th 2011)