
This dataset includes the meshes, model parameters, and Alya executable binary for simulating acute and chronic stage post-myocardial infarct using Alya, to replicate the results in the article https://doi.org/10.7554/eLife.93002.1 For each scenario simulated, a baseline simulation folder is provide with all the required meshes, fields, and model parameters necessary to run an Alya simulation. An additional series of models with variability in ionic conductances is also included for each scenario under the folder _pom/, under which 20 simulations are included. For each simulation, only the file describing the ionic conductance scaling factors (ventricular_cell.txt) are included, all other files required to run each particular simulation can be found in the _baseline/ version. The file structure is as follows: Alya executable binary control_baseline control_pom 75%_transmural_scar acute bz1_baseline bz1_pom pom_id_0 ... pom_id_19 bz2_baseline bz2_pom pom_id_0 ... pom_id_19 bz3_baseline bz3_pom pom_id_0 ... pom_id_19 chronic rz1_baseline rz1_pom pom_id_0 ... pom_id_19 rz2_baseline rz2_pom pom_id_0 ... pom_id_19 fast_pacing alternans1 alternans4 The simulation files in alternans4/ was use to generate results Figure 6 of the accompanying article, and alternans1/ was used to generate results Figure 7. The Alya executable binary has been built on ARCHER2 with the following loaded modules: 1) craype-x86-rome 2) libfabric/1.12.1.2.2.0.03) craype-network-ofi 4) perftools-base/22.12.0 5) xpmem/2.5.2-2.4_3.30__gd0f7936.shasta 6) bolt/0.8 7) epcc-setup-env 8) load-epcc-module 9) gcc/11.2.0 10) craype/2.7.19 11) cray-dsmml/0.2.2 12) cray-mpich/8.1.23 13) cray-libsci/22.12.1.1 14) PrgEnv-gnu/8.3.3 15) tk/8.6.13 16) tcl/8.6.13 17) cray-python/3.9.13.118) matplotlib/3.7.2To replicate the study, access to an installation of the code in the Nord supercomputer can be requested to mariano@elem.bio
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