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Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits

Kael Dai,Sergey L. Gratiy,Yazan N. Billeh,R. Xu,Binghuang Cai,Nicholas Cain,Atle E. Rimehaug,Alexander J. Stasik,Gaute T. Einevoll,Stefan Mihalas,C. Koch,A. Arkhipov

Published 2020 in bioRxiv

ABSTRACT

Experimental studies in neuroscience are producing data at a rapidly increasing rate, providing exciting opportunities and formidable challenges to existing theoretical and modeling approaches. To turn massive datasets into predictive quantitative frameworks, the field needs software solutions for systematic integration of data into realistic, multiscale models. Here we describe the Brain Modeling ToolKit (BMTK), a software suite for building models and performing simulations at multiple levels of resolution, from biophysically detailed multi-compartmental, to point-neuron, to population-statistical approaches. Leveraging the SONATA file format and existing software such as NEURON, NEST, and others, BMTK offers consistent user experience across multiple levels of resolution. It permits highly sophisticated simulations to be set up with little coding required, thus lowering entry barriers to new users. We illustrate successful applications of BMTK to large-scale simulations of a cortical area. BMTK is an open-source package provided as a resource supporting modeling-based discovery in the community.

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