A novel simulator for extended Hodgkin-Huxley neural networks

Sotirios Panagiotou, Rene Miedema, Harry Sidiropoulos, George Smaragdos, Christos Strydis, Dimitrios Soudris

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review

3 Citations (Scopus)

Abstract

Computational neuroscience aims to investigate and explain the behaviour and functions of neural structures, through mathematical models. Due to the models' complexity, they can only be explored through computer simulation. Modern research in this field is increasingly adopting large networks of neurons, and diverse, physiologically-detailed neuron models, based on the extended Hodgkin-Huxley (eHH) formalism. However, existing eHH simulators either support highly specific neuron models, or they provide low computational performance, making model exploration costly in time and effort. This work introduces a simulator for extended Hodgkin-Huxley neural networks, on multiprocessing platforms. This simulator supports a broad range of neuron models, while still providing high performance. Simulator performance is evaluated against varying neuron complexity parameters, network size and density, and thread-level parallelism. Results indicate performance is within existing literature for single-model eHH codes, and scales well for large CPU core counts. Ultimately, this application combines model flexibility with high performance, and can serve as a new tool in computational neuroscience.

Original languageEnglish
Title of host publicationProceedings - IEEE 20th International Conference on Bioinformatics and Bioengineering, BIBE 2020
PublisherInstitute of Electrical and Electronics Engineers (IEEE)
Pages395-402
Number of pages8
ISBN (Electronic)9781728195742
DOIs
Publication statusPublished - Oct 2020
Externally publishedYes
Event20th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2020 - Virtual, Cincinnati, United States
Duration: 26 Oct 202028 Oct 2020

Conference

Conference20th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2020
Country/TerritoryUnited States
CityVirtual, Cincinnati
Period26/10/2028/10/20

Keywords

  • Biological neural networks
  • electrophysiology
  • extended Hodgkin-Huxley neuron model
  • gap junctions
  • in silico medicine
  • OpenMP
  • parallel processing

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