Basal Ganglia Center

The Basal Ganglia Modeling Center in Stockholm is co-hosted at the Royal Institute of Technology (KTH) and Karolinska Institute (KI). This modelling Hub facilitates modelling and simulations of the basal ganglia, using a data-driven approach. Modelling is performed at multiple scales, from the molecular, detailed neuron and microcircuit-level, to large scale brain networks and behaviour, where both function and dynamics can be linked between these scales and investigated. 

Emphasis is on allowing the user to set up new or use pre-defined virtual experiments to investigate the basal ganglia and related structures. These virtual experiments can then be directly compared to, or verified by, animal experiments. As the models are refined and allow a test of putative mechanisms for learning and selection of behaviour, this will lead to new insights and reduce the number of animals needed for experiments. 

The Hub is relying on EBRAINS tools and workflows. For example, a software framework, Snudda, can be used to automatically set up a microcircuit model using detailed morphologically reconstructed neuron models, which is then currently simulated using NEURON on either local machines or on supercomputers for the large networks. Also, a toolset for the simulations of subcellular signalling processes, involved for instance in learning is provided. 

Community managers will help users to use and collaborate using the EBRAINS tools and workflows useful for understanding the basal ganglia in health and disease. In addition, some guidance in getting the appropriate HPC allocation for the project will be provided. In summary, the Hub aims at facilitating, for researchers with computational, biological or medical backgrounds and areas of expertise, collaborations around questions regarding basal ganglia function. Tutorials will be provided when needed. Our aim is to create a multidisciplinary community, where scientists help each other, and share their new findings and ideas, forming new collaborations. We will also actively develop open-source tools and improve our modelling pipeline.