Clinical phenotypes in acute and chronic infarction explained through human ventricular electromechanical modelling and simulations

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 <scenario>_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 <scenario>_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/1.12.1.2.2.0.0
3) 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/3.9.13.1
18) matplotlib/3.7.2

To replicate the study, access to an installation of the code in the Nord supercomputer can be requested to mariano@elem.bio