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

PLoS Comput Biol. 2020 Nov 30;16(11):e1008386. doi: 10.1371/journal.pcbi.1008386. eCollection 2020 Nov.

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 a 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Action Potentials
  • Biophysical Phenomena
  • Brain / physiology*
  • Brain Mapping / methods*
  • Computational Biology*
  • Humans
  • Nerve Net
  • Software*

Grants and funding

This work was funded by the Allen Institute (KD, SLG, YNB, RX, BC, NC, SM, CK, AA), the Norwegian Ministry of Education and Research through the SUURPh Programme (AER), the Norwegian Research Council through COBRA (No. 250128) and IKTPLUSS (No. 300504) (GTE, AJS), as well as NOTUR (No. NN4661K). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.