Matlab-based IPython notebooks

21 February 2018, update: the new JupyterLab was just released, and according to this tweet is really easy to integrate with Matlab. Probably worth checking out instead of the reasonably outdated instructions below!

I really like Python’s philosophy, but over the last years I haven’t been able to switch the code for my research from Matlab. At this point, the transition costs are too high for me, but it’s a move I have planned for some point in the future.

Now, Python has the awesome Jupyter (formerly IPyton notebook) feature, that allows for comments, code, and most importantly graphical output (i.e. figures you’ve just generated) to be shown in one document. This is a great way to share and explain the code you’re writing, since the reader immediately sees how output is generated without having to run all the analyses themselves.

Continue reading “Matlab-based IPython notebooks”

Decision-making in ten minutes

During the Montenegrin Open Science Days in 2014, I gave a short talk on models and neural bases of decision-making. A video of the talk is now online, so check it out if you’re interested in a crash course on how psychologists and neuroscientists think about the process of decision-making. If you’re interested in the slides, don’t hesitate to get in touch. And while you’re at it, check out the other talks by Nuno, Elena, Merina and Nikola!

Talking to Torsten Wiesel: lessons in science

Perhaps the highlight of the Lindau Nobel Laureate meeting for me was meeting Torsten Wiesel who, together with David Hubel won the Nobel Prize in 1981 for their discoveries on the response properties of neurons in early visual cortex. Wiesel gave a talk in which he gave an overview of his work with Hubel. There wasn’t much time left for discussion that afternoon, but Jolien and I had the chance to talk to him in person the day after, on a very sunny terrace overlooking for Bodensee. Here’s some of the lessons I took from our conversation. Tip of the day: a short email requesting a meeting can really make your week.

10357129_10152206152553231_8343460608684748262_n 59002_10152206152513231_3942944254677863624_nContinue reading “Talking to Torsten Wiesel: lessons in science”

Peeking over the shoulders of giants

I spent last week in Lindau, at the beautiful Bodensee in the south of Germany. I had the honour to be one of 600 young scientists invited to the 64th Lindau Nobel Laureate meeting in Physiology or Medicine, a fantastic chance to meet 37 Nobel Laureates in the field and get a huge boost of inspiration and enthusiasm for doing science. The week was too full for a complete overview, so I’ll restrict this post to my personal highlights of the week. If you feel jealous that you didn’t know about this meeting or had to miss out, don’t panic; the Lindau Mediatheque collects video recordings of most talks.

In 1951, two German physicians convinced the count of Lindau to start inviting Nobel Laureates and students to their island for a week of discussions and talks. The main goal of these first meetings was to rebuild German science and strengthen international collaborations which had suffered during the war. During the 64th meeting this year, the focus on Germany is long gone. Young scientists from 80 countries, working in fields from psychology to physics and oceanography to stem-cell biology, came to Lindau to meet 37 Laureates in Physiology or Medecine (although some won their prize in chemistry and physics). The Laureates were the big stars of the meeting, and rightly so – the brightest minds should in my opinion be honoured like all football players and pop singers of this world together.Continue reading “Peeking over the shoulders of giants”

Perceptual decision-making for dummies

This week, Journal of Neuroscience published the Journal Club commentary I’ve written with Tom Pfeffer, in which we discuss this paper by Simon Kelly and Redmond O’Connell. In short, we weigh the pros and cons about an electrophysiological signature of evidence accumulation in humans they claim to have found, and discuss what such a signature should look like in the brain.

Why is this interesting and important? The study of perceptual decision-making deals with the way in which our brain transforms incoming sensory information into an action. This is something you do all day, every day: you check the street for cars to decide if you can safely cross the road, look at a crowd at people and try and recognise your friend before waving at them, or browse through the menu at a restaurant to order the dish you’ll enjoy most. Continue reading “Perceptual decision-making for dummies”

RiSE intern Samara Green

I’m delighted that this summer, Samara Green will join us in Hamburg as a RiSE intern. The RiSE internship program allows undergraduate students from the United States, Canada and the UK to spend three months working with a research group in Germany. Samara just finished her fourth year of the combined Biology and Psychology degree (BSc) at the University of Victoria in Canada. She has been working as a research assistant in the Visual Cognition Lab, where she helped run behavioural and EEG experiments. Samara is also interested in Autism Spectrum Disorder (ASD), and has helped develop an iPad app that helps children with ASD develop skills in identity recognition, eye gaze, and emotion recognition.

This summer, Samara will be assisting with pharmacology and MEG data acquisition, learn more about programming and electrophysiological data analysis, and explore Germany.

Lindau Nobel Laureate meeting

I just heard that I have been selected to attend the 64th Lindau Nobel Laureate meeting in Physiology/Medicine. This annual meeting, which takes place in the South of Germany this summer, brings together Nobel Laureates and around 600 young researchers from 80 countries for a week of discussions, lectures and masterclasses. Topics such as the future of research in physiology, global health and medical care in developing countries will be discussed. Extra cool is that this year is the first time that there are more female than male young scientists invited to the meeting. I am very excited to have been selected for this unique meeting!

Software for (neuro)science

Since I started my PhD a few months ago, I have been thinking about the various bits of software I use for my research. I spend most of my days behind a computer – searching and reading papers, programming and analysing data. Although some pieces of software are widespread and easy to use when collaborating, there are a great many personal choices to make in computer languages and interfaces. So as a re-start to my new blog, here are some personal considerations and bits of computer goodness I tend to use.Continue reading “Software for (neuro)science”