Gernot Plank1, Axel Loewe2, Aurel Neic3, Christoph Augustin4, Yung-Lin Huang5, Matthias A F Gsell4, Elias Karabelas6, Mark Nothstein7, Anton J Prassl4, Jorge Sánchez7, Gunnar Seemann8, Edward J Vigmond9. 1. Gottfried Schatz Research Center, Division of Biophysics, Medical University of Graz, Graz, Austria. Electronic address: info@opencarp.org. 2. Institute of Biomedical Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. Electronic address: info@opencarp.org. 3. NumeriCor GmbH, Graz, Austria. 4. Gottfried Schatz Research Center, Division of Biophysics, Medical University of Graz, Graz, Austria. 5. Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg. Bad Krozingen, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany. 6. Institute of Mathematics and Scientific Computing, University of Graz, Graz, Austria. 7. Institute of Biomedical Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. 8. Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg. Bad Krozingen, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany. Electronic address: info@opencarp.org. 9. Liryc Cardiac Modeling Institute, Fondation Bordeaux University, Bordeaux, France. Electronic address: info@opencarp.org.
Abstract
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.
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.
Authors: Cristobal Rodero; Stefano Longobardi; Christoph Augustin; Marina Strocchi; Gernot Plank; Pablo Lamata; Steven A Niederer Journal: Ann Biomed Eng Date: 2022-10-21 Impact factor: 4.219
Authors: Elias Karabelas; Matthias A F Gsell; Gundolf Haase; Gernot Plank; Christoph M Augustin Journal: Comput Methods Appl Mech Eng Date: 2022-03-31 Impact factor: 6.756
Authors: Daniel J Blackwell; Michela Faggioni; Matthew J Wleklinski; Nieves Gomez-Hurtado; Raghav Venkataraman; Chelsea E Gibbs; Franz J Baudenbacher; Shiaoching Gong; Glenn I Fishman; Patrick M Boyle; Karl Pfeifer; Bjorn C Knollmann Journal: JCI Insight Date: 2022-02-08