Data_Sheet_1_Real-Time Simulation of a Cerebellar Scaffold Model on Graphics Processing Units.PDF (261.4 kB)
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Data_Sheet_1_Real-Time Simulation of a Cerebellar Scaffold Model on Graphics Processing Units.PDF

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posted on 07.04.2021, 04:30 authored by Rin Kuriyama, Claudia Casellato, Egidio D'Angelo, Tadashi Yamazaki

Large-scale simulation of detailed computational models of neuronal microcircuits plays a prominent role in reproducing and predicting the dynamics of the microcircuits. To reconstruct a microcircuit, one must choose neuron and synapse models, placements, connectivity, and numerical simulation methods according to anatomical and physiological constraints. For reconstruction and refinement, it is useful to be able to replace one module easily while leaving the others as they are. One way to achieve this is via a scaffolding approach, in which a simulation code is built on independent modules for placements, connections, and network simulations. Owing to the modularity of functions, this approach enables researchers to improve the performance of the entire simulation by simply replacing a problematic module with an improved one. Casali et al. (2019) developed a spiking network model of the cerebellar microcircuit using this approach, and while it reproduces electrophysiological properties of cerebellar neurons, it takes too much computational time. Here, we followed this scaffolding approach and replaced the simulation module with an accelerated version on graphics processing units (GPUs). Our cerebellar scaffold model ran roughly 100 times faster than the original version. In fact, our model is able to run faster than real time, with good weak and strong scaling properties. To demonstrate an application of real-time simulation, we implemented synaptic plasticity mechanisms at parallel fiber–Purkinje cell synapses, and carried out simulation of behavioral experiments known as gain adaptation of optokinetic response. We confirmed that the computer simulation reproduced experimental findings while being completed in real time. Actually, a computer simulation for 2 s of the biological time completed within 750 ms. These results suggest that the scaffolding approach is a promising concept for gradual development and refactoring of simulation codes for large-scale elaborate microcircuits. Moreover, a real-time version of the cerebellar scaffold model, which is enabled by parallel computing technology owing to GPUs, may be useful for large-scale simulations and engineering applications that require real-time signal processing and motor control.

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