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.
Today I visited Münster to give an invited departmental seminar at the Institute for Evolution & Biodiversity. It was great to see the nice stickleback labs of Jörn Scharsack and Joachim Kurz and the way in which they are able to experimentally parasitise the fish with Schistocephalus.
Really enjoyed meeting many other members of the department and the very enthusiastic students in the group. I am excited about the possibilities for future collaborations with Jörn to unravel the mechanistic underpinnings of parasite infection and its link to personality variation. Thanks again to Jörn and Nicolle for inviting me!
Today I visited the Institute for Zoology at the University of Bonn. I was invited by Gerhard von der Emde to give a departmental seminar and discuss ideas for investigating individual differences and collective behaviour in weakly electric fish.
Gerhard is an expert on electro-signalling and communicating in weakly electric fish and has been doing great work on unravelling the potential ways that these fish use their electric field. See for example their recent paper in PNAS that shows fish actively use electrocommunication in their interactions.
Yesterday night we had the Konstanzer Lange Nacht der Wissenschaft, a whole evening where scientists present their work to the general public. I was excited to also participate this year and had a couple boards installed with posters and photos about my work, and a big screen that showcased collective moving stickleback shoals with the sophisticated tracking and processing we use projected on top.Read further…
The last couple days Shaun Killen and Lucy Cotgrove from the University of Glasgow visited me in Konstanz to work together on a couple of exciting projects. Shaun and I started collaborating about a year ago to bridge the fields of animal physiology, animal personality, and collective behaviour.
With help of a Zukunftskolleg mentorship grant, we recently started writing an opinion paper on the topic, as well as analysing an exciting experiment with Lucy on the role of individual differences in metabolic rate on collective movement dynamics of schooling fish.Read further…
The last three days I attended the annual von Humboldt conference. It was great fun meeting my fellow research fellows and learning about their (extremely diverse!) work. Quite surprised to learn I was the only Dutch research fellow this year among the many nationalities. Had the chance to present my work during the poster session, which was great fun, and exciting to showcase my new tracking software live using a mobile projector. Got many new ideas these last couple days by chatting with the other researchers at such an inter-discplinary level.
Today French MSc student Pauline joins the lab! She starts a three-month project to investigate the mechanisms underlying the boldness personality trait and will run a range of behavioural experiments with three-spined sticklebacks.
Today is the start of a new research period for me. I was very lucky to be awarded both a von Humboldt postdoctoral fellowship as well as a Zukunfstkolleg fellowship. These fellowships will give me the freedom to fully develop and pursue my own research ideas and set up my own interdisciplinary research program.
The next couple years I will aim to set up a unified framework for investigating the link between consistent behavioural variation, the emergence of collective properties, group functioning, and ultimately individual fitness and between-group dynamics. I will employ a combination of detailed laboratory experiments, field surveys, and computational modelling to study consistent behavioural phenotypes and collective behaviour of three-spined sticklebacks (Gasterosteus aculeatus).
By developing this framework and fully bridging the gap between the fields of Animal Personality and Collective Behaviour, I aim for this project to yield crucial new insights into the ecological and evolutionary implications of consistent behavioural phenotypes and the evolution of sociality.
From swarm to school, stickleback groups differ repeatedly in their collective performance
among schooling fish, groups can have different collective personalities, with some shoals sticking closer together, being better coordinated, and showing clearer leadership than others.
For centuries, scientists and non-scientists alike have been fascinated by the beautiful and often complex collective behaviour of animal groups, such as the highly synchronised movements of flocks of birds and schools of fish. Often, those spectacular collective patterns emerge from individual group members using simple rules in their interactions, without requiring global knowledge of their group.
In recent years it has also become apparent that, across the animal kingdom, individual animals often differ considerably and consistently in their behaviour, with some individuals being bolder, more active, or more social than others.
New research conducted at the University of Cambridge’s Department of Zoology suggests that observations of different groups of schooling fish could provide important insights into how the make-up of groups can drive collective behaviour and performance.
In the study, published today in the journal Proceedings of the Royal Society B, the researchers created random groups of wild-caught stickleback fish and subjected them repeatedly to a range of environments that included open spaces, plant cover, and patches of food.
The last 6 weeks master students Jana and Fe did an exciting project with me to understand if and how fish school under different light conditions, including complete darkness. They did an excellent job and although still preliminary we already got some exciting results, giving insights into what senses sticklebacks use for schooling and how they manage to school even under very low light conditions. More about this soon!
An important aspect of science is the dialogue with the general public. Most public outreach is however rather static, only focused on transferring knowledge, and quite uni-directional. I wanted to find a way to convey my research about collective animal behaviour in a format that people can engage with and appreciate.
An excellent opportunity for more interactive outreach is to bridge science with art. Not only may this lead to a better understanding of science by the general public and more appreciation about the hidden beauty of the world around us, it may also generate new ideas and perspectives about my own work.
I am excited to say that I have been awarded a Zukunftskolleg Intersectoral grant that enables me to set-up a professional collaboration with Toer, a Dutch design studio known for their curiosity-driven work and interactive art installations. This long-term program will bridge the disciplines of science, art, and technology with the aim to not only inform and educate the public about collective behaviour but to inspire and make science accessible in a playful way.
The project is called Under the surface, of which soon we will launch a brand new website at www.under-the-surface.com!
I am excited to have been awarded a Zukunftskolleg Mentorship grant to continue my collaboration with Shaun Killen. Shaun and I started working together last year to unravel the fundamental mechanisms of individual traits in the collective behaviour of animal groups. Besides setting-up some new experiments on fish physiology, personality and collective behaviour, we are writing an opinion paper on this important topic.
As a scientist, I think it is important to contribute to the community. One of the ways I have been doing this the last couple years is by reviewing a fair share of papers (currently 44 reviews for 20 different journals). Even if I am busy I try to accept review invitations if I think I can give a proper assessment of the paper.
I have recently decided to join Publons to have an actual official log of my reviewing activity. After adding my whole backlog of reviews it is now as simple as a simple as forwarding an email to Publons to keep track of my reviews. I think it is great scientists get credit or their reviewing and editorial contributions and think that potentially a website like Publons may help provide further incentive for academics to keep fulfilling this important job.
Today after work I went snorkeling with some friends from work. We decided to start near the heart of Konstanz and swim down the Seerhein for about one and a half kilometer. I must say people looked a bit surprised to see three guys walking in wetsuit across the street. Although the water was not as clear as I hoped we still managed to see a couple groups of huge Carp, a number of single adult Pike of 1m+ at about 5-8m depth on the river floor, and some huge stickleback schools swimming in the shallows.
A huge Carp, my friend Ziga, and a large adult Pike somewhere in the green of the Seerhein
My latest paper on the collective behaviour of stickleback shoals is out today in the journal Current Biology!
Jolles, JW, Boogert, NJ, Sridhar, VH, Couzin, ID, Manica, A. (2017) Consistent individual differences drive collective behaviour and group functioning of schooling fish. Current Biology 27: 1-7. doi: 10.1016/j.cub.2017.08.004 (link).
Highly coordinated school of three-spined sticklebacks swimming in the blue waters of the Bodensee near Konstanz, Southern Germany. Photo: Jolle W. Jolles
New research sheds light on how “animal personalities” – inter-individual differences in animal behaviour – can drive the collective behaviour and functioning of animal groups such as schools of fish, including their cohesion, leadership, movement dynamics, and group performance. These research findings from the University of Konstanz, the Max Planck Institute of Ornithology and the University of Cambridge provide important new insights that could help explain and predict the emergence of complex collective behavioural patterns across social and ecological scales, with implications for conservation and fisheries and potentially creating bio-inspired robot swarms. It may even help us understand human society and team performance. The study is published in the 7 September 2017 issue of Current Biology.
During the lab meeting today Lauren gave a great final presentation today of her Masters project on the effects of the group personality composition on group learning ability in three-spined sticklebacks. Looking forward to her MSc thesis in a month’s time!
This week I visited Shaun Killen in Glasgow and gave a seminar at the Institute of Biodiversity, Animal Health and Comparative Medicine. Three stimulating days with lots of productive discussion and research ideas for collaboration on the relationship between physiology, personality differences and collective behaviour. Really great to meet the Killen lab and drink some proper Ales and Whiskeys. Thanks to Shaun for hosting me!