Wednesday, 4 September 2013

Getting Animated

Getting Animated by Chris Skinner (@cloudskinner)

The formal presentation of research in academia is pretty traditional. I doubt it has changed much in the last 500 years, if not longer, and for a progressive sector of society it really does not look set to change. Basically, you get your results, write it up as a paper, some experts look it over and request more details or changes, you do them, they pass it, you get published.

The published article then goes into a journal. Most of these are still printed but are available, usually as a PDF file, electronically. This is where the embrace with the modern world ends. I mainly read articles either on my computer or my tablet – most articles are formatted into two columns on a page which makes it very awkward to read off a screen. So optimisation for electronic presentation is not high on publishers’ agendas it would seem.

But are we missing out? A magazine I have been reading since I picked up my first copy in October 1993 has changed many times in the last two decades. It isn’t a science publication but is related to a hobby of mine, and last year they started publishing a version of the magazine optimised for the iPad. They could have just bunged out a PDF of the paper copy, but they knew that the new technology provided them with a platform to support more content. In place of a photo there is an interactive 360ยบ image, instead of a price list for new products there are hotlinks direct to their entry on the online store, plus there’s additional videos, interviews and zoom panels. If the magazine contains typos or erroneous details, it is automatically updated. The company have started rolling out this idea to their other printed materials.

What if these ideas were used in academia? What sort of content could we include? The most immediate thing that springs to my mind is animations. I produce tonnes of them, and conference presentations aside, they rarely get seen outside of my research group. Why do I make them? Because they are useful for very clearly showing how systems work, if your model is operating how it should or demonstrating patterns in data - (*Thanks to @volcanologist for pointing out that animations can sometimes be submitted, and hosted on a publisher's website).

Take for example some work I have been doing on historic bathymetry data from the Humber estuary. Bathymetry data are readings of water depth at the same tide level, and I use the data to create maps that show the shape and elevation (heights) of the bottom of the estuary. To find out more about what estuaries are, take a look at Sally's previous blog.

Provided by ABPMer, the data spans a period between 1851 and 2003 – I processed the data, calculated rates of elevation change between each sampling period, and from this produced yearly elevation maps. By putting these together as an animation I could see the evolution of the data (it is important here to stress the difference between ‘data’ and reality - not all areas of the estuary were sampled by each survey, and the number and locations of reading varied. Much of the change seen in the video is because of this and not because the Humber has actually, physically, changed in that way).


What immediately struck me was the contrast between the middle and the inner estuary. The middle estuary is the part between the Humber Bridge and the sea, where the estuary’s course deviates southwards – it is remarkably stable over the 150 or so years. The inner estuary, from the Bridge towards Goole, sees lots of internal changes – driven by interactions between the river inputs and the tides – but overall very little change. The Mouth of the Humber, the part closest to the sea, looks to see little overall change, but most of the variations seen in the animation are due to differences in sampling point in the data, and not actual changes. Similarly, changes around the banks of the estuary observed in the animation are most likely caused by sampling difference in the surveys, rather than actual elevation changes.

I have recently been continuing work on adapting a landscape evolution model, Caesar-Lisflood, to model the Humber estuary, and a big step towards this is to accurately model the tides as they are observed by tidal stations recording water depths. Numerically we can do this, but it is important to check that the model is representing the tides in a realistic way - this is a very important step in making a model as it has to be able to accurately simulate observed behaviours before you can experiment with them. Again, animations are a really useful tool for doing this.


The video above shows the variations of water depth throughout several tidal cycles, as modelled, with light blues as shallow and dark purple as deep water. The model changes the depth of the water at the right hand edge in line with water depth data recorded from the Spurn Point tidal station near there. The water then 'flows' from there, down the length of the estuary as the depth increases, and vice versa - this simulates the tides going in and out.

From this I can tell that the model is operating well, as the tide is advancing (coming in/going up/getting deeper) and receding (going out/down/shallower) as expected, throughout the whole region and not just at the points where the tidal stations are located. You'll notice that the early part of the animation shows the estuary filling up with water - this is part of something called 'spin-up', where you let the model run for a period of time to get the conditions right before you start the modelling. In this case it is a 'day' as the water levels gradually builds, filling the estuary.

Another check would be the velocity of the flow as the tide floods and ebbs - this is the speed with which the water is moving (both in or out). The velocity should increase as the tide advances or recedes, but slack water (where the water is hardly moving at all) should be observed at high and low waters. If the model is working as expected, the area of slack water should progress from the sea and up the estuary towards Goole. From the video below, this is seen to be the case. Light blue shows low flow speeds, and darker purples higher flow speeds. The video shows the same modelling procedure as the previous video.


This type of content is really useful to me as a modeller. It is also really useful for presentations as I can show a group of people something that takes a few seconds, yet would probably take a lot of slides and quite a bit of explaining. If academic publications were to begin to include enhanced content in peer-reviewed publications, I believe this could advance the communication of research, not only to other researchers but also to the wider public. For now, Blogs, like the GEES-ology one here, are the best outlet. I hope you enjoyed the animations!

1 comment:

  1. Rather ironically, it seems the animations don't work on iPads (I blame Apple). The animations are also on my YouTube channel -