The past years I have been bridging the fields of behavioural ecology with mechanistic perspectives of collective behaviour research. I have recently started to use these concepts to set up some projects to understand how fish populations deal with environmental change, including field work in the Spanish Pyrenees focused specifically on the role of individual heterogeneity in the context of severe effects of floods and droughts.
I have just returned from York where I have presented some of my ideas at the BES conference Impacts of extreme climatic events on ecosystems. It was a great meeting, with many in-depth group discussions about the effects of climatic events on different ecosystems and it was nice to be able to present and discuss my research plans with the broad diversity of people attending. Good to be back in the UK for a couple days as well!
At the ASAB Summer Conference in Konstanz this year, which was focused on new frontiers in the Study of Animal Behaviour, I gave a half-day workshop about automating behavioural experiments with Raspberry Pi’s.
After a general introduction, I discussed its use in animal behaviour research, how to set up, work with, and remotely control a raspberry pi, how to work with the rpi camera system, and finally how to automate recording, including via my own pirecorder software.
I started working with these amazing machines during my PhD, which where then still quite difficult to set up and quite slow, but now with the newest model for almost the same low price, so much is possible!
It was great to see so many people (120) interested in this great open-source technology for their own work, and many told me soon afterwards they immideately started setting-up their own systems.
Due to the interest and enthusiasm I am planning to give more and more hands-on workshops in the near future. Stay tuned!
After chairing one of the sessions at the ASAB Summer Conference in Konstanz today it was time to give a talk myself. I presented an exciting project that explores the role of Schistocephalus parasite infection on individual movement and social interactions. Using experiments and individual-based modelling we show mechanistically this fascinating parasite strongly impairs mobility, with large cascading effects for animal groups.
Today my latest paper came out in Animal Behaviour, one of my favourite journals. It is titled “Personality, plasticity and predictability in sticklebacks: bold fish are less plastic and more predictable than shy fish“. In this paper, which is a result of a collaboration with Neeltje Boogert and Yimen Araj-Ayoy and a MSc project of Helen Briggs, we present an extensive experimental study focused on better understanding the sources of behavioural variation among individual animals.
In short, we tested 80 three-spined sticklebacks repeatedly on their boldness across a 10-week testing period and automatically tracked their movements. We then employed advanced statistical model techniques (GLMMs and DHGLMs) to use this large behavioural dataset to investigate the potential links between the personality (consistent differences in average behaviour), the plasticity (how individuals change their behaviour over time/contexts), and predictability (the remaining intra-individual variation after accounting for personality and plasticity differences) in behaviour.
Besides detecting large consistent individual differences in boldness and the extent to which fish changed this behaviour over time (temporal plasticity), we found that boldness personality and plasticity were negatively linked, with bold fish changing little in their behaviour over time. Interestingly, there were still large individual differences in the remaining behavioural variation, with bold fish showing much less behavioural variation and thus behaving more predictable than shy fish. Importantly, these results suggest that boldness, plasticity and predictability may be fundamentally linked and form part of the same behavioural syndrome.
Jolles, J. W., Briggs, H. D., Araya-Ajoy, Y. G., & Boogert, N. J. (2019). Personality, plasticity and predictability in sticklebacks: bold fish are less plastic and more predictable than shy fish. Animal Behaviour, 154, 193–202.
The paper, which was one of the Editor’s Choice papers for August 2019, can be found here.
I am happy to say I have taken on the role as Head of Animal Facilities at the University of Konstanz Limnological Institute. With this new role I am the main responsible of animal ethics and holding at the institute and oversee the different facilities and projects to make sure they conform to the guidelines of the Animal Welfare Regulation Governing Experimental Animals.
From today you can stay up to date about my research and get a glimpse into the life of a Behavioral Ecologist on my new instagram account: @jollewjolles!
Not only do I think it is great to provide the outside world a glimpse into the scientific process, I also really enjoy showing all the different components of my research, from catching fish and calibrating cameras to late night grant writing and attending conferences, that all together eventually culminate into my academic papers.
Over the Christmas break I couldn’t resit playing around with some detailed stickleback photos I took for one of our experiments, and created my first full-size non-academic poster! It just arrived and I am very excited about the result:
My first non-academic poster: an array of close-up photos of 33 experimental sticklebacks.
The poster shows the 33 individual sticklebacks that we used for an experiment in which we investigated consistent individual differences. As is clear from the poster, despite the fish being size-matched for the experiments, the fish have a beautiful range of colour and shading patterns. Let’s see if I’ll continue doing this for all my future experiments..!
When you start working with Python it is great practice to create isolated Python environments to work on your specific projects.
The standard python environment is used by a large number of system scripts and therefore best to leave alone. In addition, when working on different projects, those projects may have different and conflicting dependencies and therefore should ideally be installed in their own python environments. The ability to create different python environments can also be really beneficial when developing your own python packages and thereby test its installation and performance in different versions of python.
Below I guide you through the basic steps of installing and working with python virtual environments.
I was honoured to be invited for an interview in Humboldt Kosmos magazine a couple months ago. Great to now see the full two-page article out in print! Had fun with the photoshoot in my chest wader ;) You can read the full article by clicking the image below.
Installing OpenCV has never been easy and always required a lot of careful usage of the command line to build from source. This was especially painful when working with a Raspberry Pi as building and installing OpenCV took a lot of time on the RPi, especially on the older models. Luckily this has changed very recently as it is now possible to install OpenCV with pip!
Below I guide you through the basic steps that I think are necessary to get opencv to work nicely on Mac, Ubuntu and Raspberry Pi. If you want more background information, see the excellent article by Adrian Rosebrock from PyImageSearch.com.
FFmpeg is a great little program to help convert more or less any media format. I previously wrote an article how to install ffmpeg on the Raspberry Pi. This short tutorial will help you install ffmpeg on Mac, which is luckily a lot simpler!
The easiest way to install ffmpeg is to use HomeBrew a package manager for Mac. If you don’t have homebrew installed on your mac already, run the following command using terminal:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Once you have Homebrew installed, you can now simply install ffmpeg from terminal with the following command:
brew install ffmpeg
To install ffmpeg with specifical modules, instead of running the above command run below command or remove those modules you do not need:
brew install ffmpeg --with-chromaprint --with-fdk-aac --with-fontconfig --with-freetype --with-frei0r --with-game-music-emu --with-libass --with-libbluray --with-libbs2b --with-libcaca --with-libgsm --with-libmodplug --with-librsvg --with-libsoxr --with-libssh --with-libvidstab --with-libvorbis --with-libvpx --with-opencore-amr --with-openh264 --with-openjpeg --with-openssl --with-opus --with-rtmpdump --with-rubberband --with-sdl2 --with-snappy --with-speex --with-tesseract --with-theora --with-tools --with-two-lame --with-wavpack --with-webp --with-x265 --with-xz --with-zeromq --with-zim
I am very excited to say that, as a fellow of the Zukunftskolleg at the University of Konstanz, I have recently started a one-year position as part of the Executive Committee, the central decision-making body of the Zukunftskolleg.
What makes the Zukuntskolleg quite unique as an Institute of Advanced Science is that the EC committee is not only made up of the directory, Vice Rector for Research and Academic Staff Development at the University, but also representatives of the fellows. In this way us fellows can ourselves play an important role in the management and decision-making of the Zukunftskolleg. A really great opportunity for me to help improve this great community.
This is a repost of an article I was invited to write for the Academic Life Histories Blog, a great collection of articles about navigating academia. See it here.
I always knew in the back of my mind I wanted to have children. However, I never really thought about when that would be. About halfway through my PhD that started to change. Work was progressing well and I was really enjoying the freedom of being able to dive deep into my own research interests. I was fortunate to have my own scholarship and a great supervisor who gave me all the freedom I wanted but was also there for me for long chats about science and academia. I was making my own plans and working according to my own schedule, which wasn’t exactly always nine to five. After some time, I suddenly started to realise that these conditions were actually pretty ideal for having a child and that, as I wanted to have children anyway at some point, why wait?
Towards the end of my third year as a PhD student my son was born. As I was doing my doctorate in the UK, that unfortunately also meant that I only had a few months of funding left. I took a couple weeks of paternity leave and, when my son was about five weeks old, flew with my family to Southern Germany for a job interview. I was lucky to get offered a postdoc position. I still had my PhD to finish though…
To save a jupyter script as an executable .py script you can use the
nbconvert command in terminal:
$ jupyter nbconvert --to script [NOTEBOOK_NAME].ipynb
Make sure to either
cd into the directory where the ipynb file is located or to paste the complete path of the file. But even better is to call the command directly in a jupyter notebook by prepending
!, which will run bash code inside any jupyter script:
!jupyter nbconvert --to script [NOTEBOOK_NAME].ipynb
In this way you can save your .ipynb file to .py file in an easy and fast way and only when you need it, such as when pushing a commit to github, saving time compared to when using auto convert.
The last couple days I have been in Florence for the SEB conference. What a great location to have a conference! Where else can you have pizza for breakfast?
On Tuesday I gave a talk about a mechanistic framework I am developing with Shaun Killen to understand the role of individual heterogeneity in collective behaviour. The sessions this year are all really relevant to me and saw lots of great talks and posters and nice to bump into academic friends from around the world. Too many new project ideas! But I think some nice new collaborations will come from it as well.