DOI: 10.6084/m9.figshare.23994354.v1
title: Source data for paper by Ochs & Boyle (CAMB, 2023)

description: This data repository is published concurrently with the following paper: Ochs AR, Boyle PM. Optogenetic Modulation of Arrhythmia Triggers: Proof-of-Concept from Computational Modeling. Cell Mol Bioeng. 2023. doi: 10.1007/s12195-023-00781-zResearchers who reuse these data in their own work are kindly asked to cite this study according to the terms of the CC BY 4.0 license. Moreover, please note that the ventricular models included in this dataset were derived from another publicly available dataset (Costa et al. doi: 10.1016/j.hrthm.2019.03.027). See below for more information. This study and dataset should also be cited by groups who reuse the ventricular models.Brief instructions for reproducing the computational simulations described by Boyle & Ochs are provided here. See inline documentation within files in sub-folders for further information.<b>LICENSE INFORMATION</b>Please note: The mesh files included in this repository were derived from the original versions published by Costa et al. (DOI: 10.18742/RDM01-570). These data are republished under the terms of the ODC-By license, a copy of which can be viewed here: https://opendatacommons.org/licenses/by/1-0/The original versions of this file can be found here: https://doi.org/10.18742/RDM01-570The associated paper by Costa et al. can be found here: https://doi.org/10.1016/j.hrthm.2019.03.027If you reuse these models in your own paper, please attribute the original source of the data, cite Dr. Costa's paper, and make clear to others that data are being used under the terms of ODC-By.<b>Single-cell simulations</b>1. Install openCARP v8.2 (via https://opencarp.org/) -- to function correctly, the software must be compiled from source with DLOPEN=1 set in my_switches.def2. [IMPORTANT] compile .so files from .model files for dynamic ionic models, e.g.:$ /Software/openCARP/v8.2/bin/make_dynamic_model.sh Single-Cell-Simulations_EADs+Optogx/ORd_custom_oC$ /Software/openCARP/v8.2/bin/make_dynamic_model.sh Single-Cell-Simulations_EADs+Optogx/IGtACR1If this step has worked correctly, you will have created IGtACR1.so and ORd_custom_oC.so; please note the exact locations of these files! (full paths)3. (optional but highly recommended) Install xmgraceoption #1: via package manager like apt or yum (e.g., sudo apt install grace)option #2: via https://plasma-gate.weizmann.ac.il/Grace/4. Edit the main driver script (Single-Cell-Simulations_EADs+Optogx/Reproduce-EAD-SingleCell-Sims.sh)Specify the path where the two .so files compiled in Step #2 can be foundSpecify the path to access the bench executable for openCARP v8.25. Run the main driver script and analyze the results, e.g.:bash -u Single-Cell-Simulations_EADs+Optogx/Reproduce-EAD-SingleCell-Sims.shIf grace has been results, look at images produced via $ eog ORd*pngThese can be compared to reference images in Single-Cell-Simulations_EADs+Optogx/ref_images<b>Organ-scale simulations</b>1. Complete steps 1 and 2 above2. Decompress mesh files by executing the following command: &gt; tar xvjf {04,21,24}-mesh-uvc.tar.bz23. Run simulations using files located in LV-Simulations_PVCs+Optogx/Par-Slurm-Files/Option #1: "à-la carte" simulations directly using .par files. Important: make sure to append all necessary parameters on the command line, as described in the .par file headers); for example: &gt; head -n15 LV-Simulations_PVCs+Optogx/Par-Slurm-Files/SuppressEctopicsGtACR1.par # -simID = ** command line ** -- e.g., SuppressEctopicsGtACR1_[params] # -meshname = ** command line ** -- e.g., 04-mesh-uvc/04-mesh-uvc_r1 # -external_imp[0] = ** command line ** -- path to ORd .so file # -external_imp[1] = ** command line ** -- path to GtACR1 .so file # -imp_region[1].im_param = ** command line ** -- format: "GKr*0.14,blf_ICaL*2.80" # -imp_region[1].im_sv_init = ** command line ** -- to match im_param settings # -adjustment[0].file = ** command line ** -- path to opsin expression .adj file # -adjustment[1].file = ** command line ** -- path to light attenuation .adj file # -stim[0].elec.vtx_file = ** command line ** -- path to file specifying elec stim sites # -stim[1].pulse.strength = ** command line ** -- light irradiance to be usedOption #2: "batch approach" adapt and deploy shell scripts (.slurm extensions).<i>WARNING: This should only be attempted by experienced supercomputer users. The .slurm files </i><i>provided have been tested comprehensively on the UW Hyak system running openCARP v8.2. The</i><i> files should be seen as a starting point, not a "plug-and-chug" solution. YMMV.</i>4. Visualize results in meshalyzer (also available via openCARP website) using provided vm.mshz file,e.g., meshalyzer 04-mesh-uvc/04-mesh-uvc_r1 ProvokeEctopicsChR2_Model1_0.19xGKr_1.80xGCaL_Ee0.100/vm.igb vm.mshz5. [optional] Once all simulations from the included .slurm files have been run, use ProcessResults.sh to elegantly parse the results; this will give information about the global number of activations per simulation, which can be used as a surrogate metric to guide EAD assessment.