Community experiments

Overview This repository contains the software used to generate the data in the work "AutoVARP – A framework for automated reproducible inducibility testing in computational models of cardiac electrophysiology" by Seghetti, Gsell, Prassl, Bishop, and Plank (DOI: https://doi.org/10.1016/j.cmpb.2026.109466). The archive documents two numerical experiments performed with auto-VARP, an open-source Python framework that automates the ventricular arrhythmia risk predictor (VARP) protocol over cohorts of computational cardiac models. auto-VARP orchestrates the full simulation pipeline:  prepacing;  S1 stage;  S2 stage;  maintenance (MT) stage. The pipeline relies on an openCARP installation along carputils, and uses forCEPSS as its simulation back-end. See the official openCARP website  and forCEPSS publication for more information. Slab with isthmus experiment We provide the isthmus geometry used to generate Fig. 4 of the publication, to access the full cohort please send an email to PS (paolo.seghetti@medunigraz.at). The archive includes the `auto-varp.py` entry-point script, the VARP sub-module, the planfile and protocols JSON files, the representative subject mesh (`1mmbz.300um.f90`: 1 mm BZ, 300 µm resolution, 90° fibre angle), and Supplementary Movies 1–8 (transmembrane potential animations for all 8 electrodes on that subject). Furthermore, the file 'meshalyzer.mshz' can be modified using meshalyzer to adjust rendering settings. Left ventricle experiment We provide the geometry and uvc file used to generate Fig. 5 of the publication. A single realistic biventricular geometry adapted from Subject 15 of the Strocchi et al. (2020) public cohort (A publicly available virtual cohort of four chamber heart meshes for cardiac electro mechanics simulations), resampled to approximately 350 µm. Pacing sites are defined as uvc coordinates or vertex files to showcase the newly added feature. The archive includes the `auto-varp.py` entry-point script, planfile, electrodes and configurations JSON files, the subject mesh with UVC data, and Supplementary Movies 9–13 (transmembrane potential animations for electrode EL6 across all tested S2 intervals).      All files are structured for direct use with auto-VARP. Issue the commands reported in the publication to reproduce results. Software requirements: the study can be reproduced with a working installation of openCARP and carputils. For visualization purposes, an installation of meshalyzer is needed (usually included in the openCARP environment).   References Strocchi, M., Augustin, C. M., Gsell, M. A. F., Karabelas, E., Neic, A., Gillette, K., Razeghi, O., Prassl, A. J., Vigmond, E. J., Behar, J. M., Gould, J. S., Sidhu, B., Rinaldi, C. A., Bishop, M. J., Plank, G., & Niederer, S. A. (2020). A Publicly Available Virtual Cohort of Four-chamber Heart Meshes for Cardiac Electro-mechanics Simulations [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3890034

This experiment offers the possibility to simulate the Riz et al. (2014) model with an additional K2P/TASK-4 leak current (IK2P) channel. In this experiment the ATP-sensitive potassium current (IKATP) was fixed to 20 % of its basal value, while IK2P is increased from 0 to 1 in increments of 0.01 and the resulting intracellular calcium concentration was analysed.

This is an idealized 2D cardiac infarct model designed with the purpose of replicating the setup used in our study entitled "An automated near-real time computational method for induction and treatment of scar-related ventricular tachycardias" (accepted) Medical Image Analysis (2022).

In silico experiments to study the sinoatrial node characteristics. The experiment script is able to modify several electrophysiological parameters using as an input a vtk file.

An openCARP EMI experiment assigning three different ionic models to individual cells of a cell-resolved cardiac tissue mesh. A circular scar core of unexcitable myocytes (Plonsey) is surrounded by a border zone containing equal parts excitable myocytes (Courtemanche), unexcitable myocytes (Plonsey) and fibroblasts (MacCannell), embedded in healthy Courtemanche tissue. The membrane tag pairs required to assign a per-cell ionic model are derived from the mesh at run time. Core radius, border-zone width and the random assignment seed are set on the command line. The underlying mesh considers realistic cell alignment

Single cell simulations of KCNQ1 mutants using human myocyte models. Use external/runAll.py to launch all simulations.

This experiment simulates the extended sinoatrial node cell models of Severi et al. (2012) and Fabbri et al. (2017) with several [Ca2+]o and [ISO]. The extension of the AC-cAMP-PKA signalling cascade is based on the work of Behar et al. (2016).

This is an example to run the PEERP (Pacing at the End of the Refractory Period, Luca Azzolin et al., https://doi.org/10.3389/fphys.2021.656411) protocol using a monoatrial left atrium (LA) mesh, with fibers and region annotation. The mesh is the mean LA geometry from the SSM (Statistical Shape Model) proposed by Claudia Nagel et al. ([doi:10.5281/zenodo.4309957](https://doi.org/10.5281/zenodo.4309957)) and the fibers and annotations were generated using AugmentA code https://github.com/KIT-IBT/AugmentA (https://doi.org/10.1016/j.compmedimag.2023.102265) by Luca Azzolin et al.