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Including gap junctions into distributed neuronal network simulations
KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
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2016 (English)In: 2nd International Workshop on Brain-Inspired Computing, BrainComp 2015, Springer Publishing Company, 2016, p. 43-57Conference paper, Published paper (Refereed)
Abstract [en]

Contemporary simulation technology for neuronal networks enables the simulation of brain-scale networks using neuron models with a single or a few compartments. However, distributed simulations at full cell density are still lacking the electrical coupling between cells via so called gap junctions. This is due to the absence of efficient algorithms to simulate gap junctions on large parallel computers. The difficulty is that gap junctions require an instantaneous interaction between the coupled neurons, whereas the efficiency of simulation codes for spiking neurons relies on delayed communication. In a recent paper [15] we describe a technology to overcome this obstacle. Here, we give an overview of the challenges to include gap junctions into a distributed simulation scheme for neuronal networks and present an implementation of the new technology available in the NEural Simulation Tool (NEST 2.10.0). Subsequently we introduce the usage of gap junctions in model scripts as well as benchmarks assessing the performance and overhead of the technology on the supercomputers JUQUEEN and K computer.

Place, publisher, year, edition, pages
Springer Publishing Company, 2016. p. 43-57
Keywords [en]
Computational neuroscience, Gap junctions, Large-scale simulation, Spiking neuronal network, Supercomputer, Waveform relaxation, Benchmarking, Brain, Neurons, Signal encoding, Supercomputers, Large scale simulations, Spiking neuronal networks, Neural networks
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
URN: urn:nbn:se:kth:diva-201828DOI: 10.1007/978-3-319-50862-7_4Scopus ID: 2-s2.0-85007305475ISBN: 9783319508610 (print)OAI: oai:DiVA.org:kth-201828DiVA, id: diva2:1074975
Conference
Second International Workshop, BrainComp 2015, Cetraro, Italy, July 6-10, 2015
Note

QC 20170216

Available from: 2017-02-16 Created: 2017-02-16 Last updated: 2017-02-16Bibliographically approved

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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf