Posted 5th July 2018
This summer Jessica Dafflon, a 2nd year neuroimaging PhD student, is taking part in the prestigious Google Summer of Code (GSoC).
GSoC is a global program focused on bringing more student developers into open source software development. Students recieve funding to work on a 3 month programming project during their summer break.
Tell me a little bit about you and your PhD project
I am a 2nd year Neuroimaging PhD student and part of the CDT in Medical Imaging cohort. I am originally from Brazil but I moved to Switzerland to do my undergrads and masters. Although I started my academic path as a biologist with time I developed an interest in the more computational and technical aspects of research.
So, now as part of my PhD, I am using computational models to explore the relationship between the dynamic functional activity of the brain, neural structure, and cognition.
How did the Google opportunity come about?
I went to an amazing summer course neurohackweek in Seattle. While I was there I met a very nice PhD student from Spain, who had worked on a project for the Google Summer of code that summer. He was very enthusiastic about it, he told me how he enjoyed the experience and how he learned a lot during those months. I was immediately convinced that it was the perfect opportunity to spend 3 months coding, pick up a different tool and learn by doing.
What exactly are you working on?
Computational models are becoming more and more popular tools to study the brain’s complexity. However, many of the models used in neuroscience use different programming languages, tools and techniques making it difficult to share and reproduce results among different research groups. To bridge this limitation, NeuroML and LEMS have been introduced to standardise the neuroscientific models’ descriptions and facilitate the shareability and reproducibility of the different neuronal models.
My goal on this project is to implement different Neural Mass models, which simulate the mean activity of many neurons at the macroscopic level, using NeuroML and LEMS. These models will then be easily available to the community at the Open Source Brain repository.
You can find more information about my project here.
What has been the most exciting thing about it?
From a technical perspective, the Google Summer of code is for me a great opportunity to learn tools and to gain a more in-depth knowledge of the dynamics undergoing the simulations. I also like to be part of the open science community, as I am convinced that sharing is the first step to improve quality, accountability and reproducibility of research results and software.
What has been the biggest obstacle?
Time. Three months are not enough time to develop all the wonderful features and work on the all ideas that my mentor and I have in our heads.