A NEST-based framework unlocks massively parallel simulation of networks of multicompartment neurons with customizable subcellular dynamics
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
Abstract While the implementation of learning and memory in the brain is governed in large part by subcellular mechanims in the dendrites of neurons, large-scale network simulations featuring such processes remain challenging to achieve. This can be attributed to a lack of appropriate software tools, as neuroscientific simulation software focuses on the one hand on highly detailed models, and on the other hand on massive networks featuring point-neurons. Here, we fill this gap by implementing a framework for the massively parallel simulation of simplified dendrite models with customizable subcellular dynamics. To achieve this, we leverage the NEural Simulation Tool (NEST), the neuroscientific reference with respect to efficient massively parallel simulations of point neuron networks. By co-opting the already existing model descriptions language NESTML, we generate C++ code implementing user-configurable subcellular dynamics. Through benchmarking and profiling, we show that the generated models run efficiently, leading to scalable NEST network simulations. We demonstrate relevant functionalities by showing that a key sensory computation – the association of top-down context arriving at distal dendrites in layer 1 and feedforward sensory input arriving perisomatically – can be achieved in a single shot fashion through apical calcium dynamics. Our work thus unlocks the study of how dendritic processes shape learning, and in particular of how brain-wide communication through long-range, layer 1-targetting connections steers perisomatic plasticity.
Authors 7
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Willem A. M. Wybo corresponding
Affiliation as printed
Forschungszentrum Juelich;
Peter Grünberg Institute 5 – Neuromorphic Software Ecosystems (PGI-5), Forschungszentrum Jülich, Aachen, Germany
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Affiliation as printed
Forschungszentrum Juelich;
Institute for Advanced Simulation (IAS-6), Computational and Systems Neuroscience, Forschungszentrum Jülich, Jülich, Germany
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Forschungszentrum Jülich · Jülich Aachen Research Alliance · Jülich Supercomputing Centre · RWTH Aachen University
Affiliation as printed
Forschungszentrum Juelich;
Department of Computer Science 3 - Software Engineering, RWTH Aachen University, Aachen, Germany
Institute for Advanced Simulation (IAS-6), Computational and Systems Neuroscience, Forschungszentrum Jülich, Jülich, Germany
Simulation and Data Lab Neuroscience, Jülich Supercomputer Centre, Institute for Advanced Simulation, Jülich-Aachen Research Alliance, Forschungszentrum Jülich, Jülich, Germany
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Forschungszentrum Jülich · Jülich Aachen Research Alliance · Jülich Supercomputing Centre · RWTH Aachen University
Affiliation as printed
Forschungszentrum Juelich;
Department of Computer Science 3 - Software Engineering, RWTH Aachen University, Aachen, Germany
Simulation and Data Lab Neuroscience, Jülich Supercomputer Centre, Institute for Advanced Simulation, Jülich-Aachen Research Alliance, Forschungszentrum Jülich, Jülich, Germany
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Istituto Nazionale di Fisica Nucleare · Istituto Nazionale di Fisica Nucleare, Sezione di Roma I
Affiliation as printed
Istituto Nazionale di Fisica Nucleare
Istituto Nazionale di Fisica Nucleare, Sezione di Roma, Rome, Italy
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Istituto Nazionale di Fisica Nucleare · Istituto Nazionale di Fisica Nucleare, Sezione di Roma I
Affiliation as printed
Istituto Nazionale di Fisica Nucleare
Istituto Nazionale di Fisica Nucleare, Sezione di Roma, Rome, Italy
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Forschungszentrum Jülich · RWTH Aachen University
Affiliation as printed
Forschungszentrum Juelich;
Department of Computer Science 3 - Software Engineering, RWTH Aachen University, Aachen, Germany
Institute for Advanced Simulation (IAS-6), Computational and Systems Neuroscience, Forschungszentrum Jülich, Jülich, Germany
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