volume 208 pages 106223

The openCARP simulation environment for cardiac electrophysiology

Gernot Plank 1
Axel Loewe 2
Aurel Neic 3
Christoph Augustin 1
Yung Lin Huang 4, 5
Matthias A F Gsell 1
Elias Karabelas 6, 7, 8
Mark Nothstein 2
Anton J Prassl 1
Jorge Sánchez 2
Gunnar Seemann 9
Edward Vigmond 10
Publication typeJournal Article
Publication date2021-09-01
scimago Q1
wos Q1
SJR1.130
CiteScore11.1
Impact factor4.8
ISSN01692607, 18727565
Computer Science Applications
Software
Health Informatics
Abstract
• We present the openCARP simulation environment as a solution that could foster the needs of large parts of the computational cardiac electrophysiology community. • Together with the Python-based carputils framework, openCARP allows developing and sharing simulation pipelines to increase reproducibility and productivity. • openCARP focuses on usability and performance for cardiac electrophysiology simulations. • We provide extensive training material and a community platform as a basis for a vivid user community. Background and Objective: Cardiac electrophysiology is a medical specialty with a long and rich tradition of computational modeling. Nevertheless, no community standard for cardiac electrophysiology simulation software has evolved yet. Here, we present the openCARP simulation environment as one solution that could foster the needs of large parts of this community. Methods and Results: openCARP and the Python-based carputils framework allow developing and sharing simulation pipelines which automate in silico experiments including all modeling and simulation steps to increase reproducibility and productivity. The continuously expanding openCARP user community is supported by tailored infrastructure. Documentation and training material facilitate access to this complementary research tool for new users. After a brief historic review, this paper summarizes requirements for a high-usability electrophysiology simulator and describes how openCARP fulfills them. We introduce the openCARP modeling workflow in a multi-scale example of atrial fibrillation simulations on single cell, tissue, organ and body level and finally outline future development potential. Conclusion: As an open simulator, openCARP can advance the computational cardiac electrophysiology field by making state-of-the-art simulations accessible. In combination with the carputils framework, it offers a tailored software solution for the scientific community and contributes towards increasing use, transparency, standardization and reproducibility of in silico experiments.
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GOST Copy
Plank G. et al. The openCARP simulation environment for cardiac electrophysiology // Computer Methods and Programs in Biomedicine. 2021. Vol. 208. p. 106223.
GOST all authors (up to 50) Copy
Plank G., Loewe A., Neic A., Augustin C., Huang Y. L., Gsell M. A. F., Karabelas E., Nothstein M., Prassl A. J., Sánchez J., Seemann G., Vigmond E. The openCARP simulation environment for cardiac electrophysiology // Computer Methods and Programs in Biomedicine. 2021. Vol. 208. p. 106223.
RIS |
Cite this
RIS Copy
TY - JOUR
DO - 10.1016/j.cmpb.2021.106223
UR - https://doi.org/10.1016/j.cmpb.2021.106223
TI - The openCARP simulation environment for cardiac electrophysiology
T2 - Computer Methods and Programs in Biomedicine
AU - Plank, Gernot
AU - Loewe, Axel
AU - Neic, Aurel
AU - Augustin, Christoph
AU - Huang, Yung Lin
AU - Gsell, Matthias A F
AU - Karabelas, Elias
AU - Nothstein, Mark
AU - Prassl, Anton J
AU - Sánchez, Jorge
AU - Seemann, Gunnar
AU - Vigmond, Edward
PY - 2021
DA - 2021/09/01
PB - Elsevier
SP - 106223
VL - 208
PMID - 34171774
SN - 0169-2607
SN - 1872-7565
ER -
BibTex
Cite this
BibTex (up to 50 authors) Copy
@article{2021_Plank,
author = {Gernot Plank and Axel Loewe and Aurel Neic and Christoph Augustin and Yung Lin Huang and Matthias A F Gsell and Elias Karabelas and Mark Nothstein and Anton J Prassl and Jorge Sánchez and Gunnar Seemann and Edward Vigmond},
title = {The openCARP simulation environment for cardiac electrophysiology},
journal = {Computer Methods and Programs in Biomedicine},
year = {2021},
volume = {208},
publisher = {Elsevier},
month = {sep},
url = {https://doi.org/10.1016/j.cmpb.2021.106223},
pages = {106223},
doi = {10.1016/j.cmpb.2021.106223}
}