DOI: 10.5061/dryad.kwh70rzh0
title: Population-based computational simulations elucidate mechanisms of focal arrhythmia following stem cell injection

description: This dataset contains the data required to reproduce the computational
 simulations presented in the 2025 paper by Gibbs and Boyle. This dataset
 comprises (1) Geometric descriptions of the simulation domain (whole
 heart, tissue wedge, etc.), with point clouds interconnected by finite
 elements, each of which is associated with a vector encoding
 the local myofiber orientation. (2) Parameter files describing
 functional cell- and tissue-scale properties of different tissue regions,
 perturbations to be applied to the model during the simulation (e.g.,
 electrical stimuli), and numerical solver settings. (3) Initial condition
 state files describing the functional state of the model at the beginning
 of the simulation, if these conditions differ from the cell-scale default
 parameters. All of the above are stored in plain text or binary formats
 compatible with the openCARP framework, which is freely available for
 non-commercial use.
description: # Population-based computational simulations elucidate mechanisms of focal
 arrhythmia following stem cell injection INFORMATION ABOUT THE RELATED
 PUBLICATION Gibbs and Boyle(2025) Population-Based Computational
 Simulations Elucidate Mechanisms of Focal Arrhythmia Following Stem Cell
 Injection (DOI: 10.1016/j.yjmcc.2025.04.010, PMID: 40280466, link:
 [https://pubmed.ncbi.nlm.nih.gov/40280466/](https://pubmed.ncbi.nlm.nih.gov/40280466/)) Please contact Dr. Patrick M. Boyle ([pmjboyle@uw.edu](mailto:pmjboyle@uw.edu)) with any questions, concerns, complaints, or difficulties. This dataset contains data required to reproduce computational simulations presented in the 2025 JMCC paper by Gibbs & Boyle. #### Description of the data and file structure Dryad_Figure3and7.xlsx provides the raw data Graphs of 3A and 7D-F. Raw values are given as percentage of simulations where GHE (graft-host excitation) was observed. Figure 3A summarizes the incidence of graft-host exchange (GHE) observed for two specific grafts — Graft 1 and Graft 2 — and when both grafts are applied together (Graft 1+2). Figure 7D-F: This data presents the proportions of three graft-host exchange (GHE) outcomes — Complementarity (positive interaction or integration between the graft and host.), Cooperativity (arer form of positive GHE in these results, indicating a specific type of synergistic interaction), and No GHE (No observable integration or exchange between graft and host) — across different experimental conditions or connection levels for three different geometries. This can be opened in Microsoft Excel Figure_Graphs.zip is a compressed archive containing all files need to reproduce the graphs found in in Figure 2 D, 3 A, 7 D-F, 8 A-D, and 8 G-I. All .dat files and .txt files will be read in the python script. The python script as both a jupyter notebook and .py file are also included. The following python packages were used: matplotlib 3.3.4 numpy 1.19.5 pandas 1.1.5 scipy 1.5.4 seaborn 0.11.2 sklearn 0.24.2 statannotations 0.6.0 The Figure_Graphs.zip archive looks like this. This file description follows the name AggregateData_200_All.txt AllModels_Doubles_HMean_Binary_False.dat AllModels_Doubles_HMean_Binary_True.dat AllModels_Singles_GraftInfo_Binary_Scar.dat BPMvsAreaAverage.dat Figure_2_and_8_Code.ipynb Figure_2_and_8_Code.py GHE_Singles.dat Model1_GraftExample_host_HostProximity_vs_BTProximity0200.dat **Explanation of each file** AggregateData_200_All.txt : Raw values of Category and Value used to create Fig. 8H AllModels_Distance_NewGHE_False.dat : Raw distance values were no GHE was observed (Fig. 8D) AllModels_Distance_NewGHE_True.dat : Raw distance values were GHE was observed (Fig. 8D) AllModels_Singles_GraftInfo_Binary_Scar.dat : Raw values of GHE, GraftArea, Tortuosity, and Percent Scar used to create Fig. 8 A-C Figure_2_and_8_Code.ipynb : Python Script Jupyter Notebook Figure_2_and_8_Code.py : .py version of above script BPMvsAreaAverage.dat : Average BPM and Area for each graft with GHE (Fig. 8I) Geometry1_GraftExample_host_HostProximity_vs_BTProximity0200.dat : Raw values of Category and Value used to create Fig. 8G GHE_Singles.dat : Raw GHE values as a whole number of all three geometries used to create Fig. 2D Simulations.zip isa compressed archive containing all example model files needed to rerun and visualize simulations in openCARP and Meshalyzer (.pts, .lon, .vec, .elem,. vpts.) The Simulations.zip archive looks like the following Example Simulations/ Meshes/ Tag_1002/ Geometry3_Split0.900_N10* Geometry3_Results/ *Files can be found below Geometry3_1002.par Kernik2019_ModifedByGibbs2023.model Kernik2019_ModifedByGibbs2023_68384.5.sv RunExampleSimulations.sh vm.mshz Geometries/ Geometry1* Geometry2* Geometry3* GenerateMeshes_MultiSplit.sh split_mesh_2D_IslandByIsland_20230810.pl The file GenerateMeshes_MultiSplit.sh is a driver script that can be run from the command line to produce the all finite element meshes with 10% connect graft. Modifications to this script may be necessary to account for local machine settings. See documentation in script for more detail. The file split_mesh_2D_IslandByIsland_20230810.pl is a perl script that is used by the GenerateMeshes_MultiSplit.sh driver script. Specific finite element mesh file types found in the Geometries Folder: ``` .pts: description of points in Cartesian coordinates (spacial unit: microns) .elem: description of how nodes (zero indexed) are interconnected by elements .lon: fiber orientations for each element .mshz: state files for model visualization .taglist: list of all tags present in mesh .tagcombo: List of all possible tag combinations .tags_under: List of all possible tag combinations that can be parsed as a single string ``` Under ExampleSimulations sub-folder the following files can be found The .sv files contain initial conditions for all cell-scale ionic models used in simulation studies. ``` The file .par provides the baseline parameters used to run all simulations in this study. The file RunExampleSimulation.sh is a driver script to run a single example openCARP simulation. The file Kernik2019_ModifedByGibbs2023.model comes from our previous repository DOI:https://doi.org/10.5061/dryad.63xsj3v75. To compile this file into something openCARP can use for simulations be sure to run make_dynamic_model.sh Kernik2019_ModifedByGibbs2023.model where you have openCARP installed. ``` Rerunning the driver script will produce all of the files shown in ExampleSimulation/Geometry3_Results/ subfolder \- electrics.log file include information about the ODE/PDE solvers used \- par_stats.dat file include log information about the parabolic solver \- parameters.par file contain all the options defined for each simulation \- petsc_err_log.txt file contain errors encountered by the PETSc solver. \- protocol.trc file contain information about electrical stimuli applied (none, in the context of these simulations) \- vm_act-thresh.dat file contain activation nodes and times in temporal sequence, measured via threshold crossing (-40 mV) \- vm.igb file contains voltage overtime data that can visualized in meshalyzer Example usage – tested using openCARP v7.0 on Ubuntu 18.04.6 The command below (text following $) can be executed on a properly configured system. ``` $ bash -u GenerateMeshes_MultiSplit.sh; $ bash -u RunExampleSimulation.sh: ``` Data visualization – tested using meshalyzer v5.2 on Ubuntu 18.04.6 The command below can be executed on a properly configure system to visualize the results of a particular simulation; modify the mesh name provided and the path to the relevant vm.igb file to visualize results of different simulations. ``` $ meshalyzer Meshes/Tag_1002/Geometry3_Split0.900_N10.pts Geometry3_Results/vm.igbvm .mshz ``` The first line after the invocation of the visualization program is the path to the .pts file associated with the relevant mesh. The second line is the path to the vm.igb file containing membrane voltage over time. The third line is the path to a meshalyzer state file compatible with v5.2 of the software. **Sharing/access information** All files contained in this repository are published under the Creative Commons CC0 license. Future users are thus allowed and encouraged to distribute, remix, adapt, and build upon the material in any medium or format, with no conditions. Although CC0 does not require attribution, we encourage all parties who reuse this dataset in any way to cite the paper with which it was published (Gibbs et al. 2025, DOI: 10.1016/j.yjmcc.2025.04.010, PMID: 40280466). **Code/software information** openCARP and meshalyzer information can be found at: [https://opencarp.org/](https://opencarp.org/)