Urszula Włodkowska: Building Brains in Canada
The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Urszula Włodkowska, a PhD Researcher at the Nencki Institute of Experimental Biology PAS was awarded an OBF Event Fellowship to attend the University of Waterloo’s Nengo Summer School.
In June of 2024, I had a great opportunity to attend the University of Waterloo’s Nengo Summer School (also known as Brain Camp). This was only possible thanks to the fellowship I received from the Open Bioinformatics Foundation.
Urszula Presenting her project to the group.
This summer school was an important event for many reasons. First, I was excited to learn about the Nengo simulation package (https://www.nengo.ai/), which is a powerful platform for designing cognitive and neural systems. Nengo has recently become open source, and for me, using open tools means having not only a better understanding of how they work but also being able to contribute to and influence their growth. This creates a community of users that give back and support each other. The fact that Nengo is newly open source also provided a unique opportunity to talk to the creators about the challenges of transitioning into that mode.
The Nengo Summer School also provided an introduction to the Neural Engineering Framework. The NEF has been developed by the Computational Neuroscience Research Group led by Chris Eliasmith at the Waterloo Centre for Theoretical Neuroscience as a tool for understanding neurobiological principles through constructing simulations of neural systems. Learning about it provided a satisfyingly complete view of the subject – connecting tools with theory and reasoning behind how the tools have been constructed.
The two weeks I spent in Waterloo were intense. The first week focused on the introduction to the framework and practical tutorials translating theory into code. On top of that, with other participants and TAs we discussed projects that everyone brought with them to work on during the school, looking for common interests and ways to collaborate. During the second week, we worked on our projects and attended tutorials on advanced applications of Nengo. The school ended with project presentations – first, for other participants, and then in an open event at the University of Waterloo.
Tutorial at the Waterloo Centre for Theoretical Neuroscience
My project focused on simulating how a mouse learns to optimally explore the environment while gradually learning the rules governing the behavioral setup. I learned a lot, especially thanks to the help of one of the TAs – Nicole Dumont. I intend to continue working on this project, so the summer school leaves a lasting impression on my research.
But my personal gain was not the only reason I wanted to attend this school. As a part of the Nencki Open Lab initiative (https://nenckiopenlab.org/) that connects young neuroscience researchers from underprivileged regions, I always see the events I attend as an opportunity to share the knowledge and connections I’ve made with others. The Nencki Open Lab events touch on two aspects – teaching people how to use open tools and how to approach research as a part of a bigger picture, connecting theory and practice. The Nengo Summer School helped me grow in both of these areas and I hope to bring the concepts and the people I’ve met there to our own summer schools.
Group photo of this year’s attendees and teachers