TheopenCARPSimulation Environment for Cardiac Electrophysiology

Abstract

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. 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.Research in cardiac electrophysiology increasingly relies on computational modeling and simulation. A survey of large parts of the community revealed a current lack of reproducibility, time investment (productivity) and functionality originating from the fact that no community standard for cardiac electrophysiology simulation software has evolved yet. Here, we present the openCARP simulation environment as one solution that could address these needs. openCARP and the Python-based carputils framework allow to develop and share simulation pipelines that automate in silico experiments, including all modeling and simulation steps. Documentation and training material facilitate access and decrease training time for new users. The openCARP user community is supported by tailored infrastructure, interactive support and is aiming for future expansion. 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, simple tissue, organ and body level and finally outline future development potential.

AugmentA: Patient-specific Augmented Atrial model Generation Tool

“…In the pipeline, six Laplace problems for the LA and six for the RA were formulated: with proper Dirichlet boundary conditions Ψ a and Ψ b on the respective boundaries Γ a and Γ b . These partial differential equations were solved using the open electrophysiology simulator openCARP [42]. The domain of the Laplace problems is the atrial mesh.…”

“…In the other 70%, several ionic conductances were rescaled to consider effects of cytokine-related remodeling [50] (-50% g K1 , -40% g N a and -50% g CaL ). The spread of the electrical depolarization in the atrial myocardium was simulated by solving the monodomain equation using openCARP [42] and a time step of 0.02 ms.…”

Comparison of propagation models and forward calculation methods on cellular, tissue and organ scale atrial electrophysiology

“…Therefore, anisotropic and locally heterogeneous conductivities were assigned to five different regions in the atria comprising regular bulk tissue, crista terminalis, pectinate muscles, inferior isthmus, and inter-atrial connections as follows: CVs corresponding to the monodomain conductivities reported in [19] for 0.33 mm resolution voxel models were calculated as described in [18]. Using tuneCV [7,31], intra-(σi) and extracellular (σe) conductivities as well as the monodomain conductivities (σm) were iteratively optimized for the tetrahedral mesh setup described above while keeping the σi/σe ratio fixed. For this purpose, five strand geometries with a length of 10 cm were generated each characterized by a resolution corresponding to the average edge length of one of the heterogeneous conductivity regions in the atria.…”

Pacemaking function of two simplified cell models

“…Later additions to this class include modifications of the HH and FHN models, namely Van Capelle-Durrer (VCD) [8], Aliev-Panfilov [9] (AP), Morris-Lecar [10] and its pacemaking variants [11,12], Fenton-Karma [13], Mitchell-Schaeffer [14] (MS), and its modification by Corrado and Niederer [15] (CN). Most of the above mentioned models are included into the modeling software packages and repositories, such as openCARP [16] and Physiome Project [1,17]. The VDP and FHN models and their modifications are being predominantly used as simple models of natural pacemakers in physiological simulations of different levels of complexity (see, for example, [18][19][20][21][22]).…”

“…The latter two models have been used recently to simulate electrophysiology of atria, spiral wave stability, and ventricular tachycardia inducibility in patient-specific models (see review [20] and references therein). Most of the models mentioned above are included in the modeling software packages and repositories, such as openCARP [21] and Physiome Project [1,22].…”