Source code for single cell, popoulations, and tissue modeling

H Ni, S Morotti, X Zhang, D Dobrev, E Grandi. Integrative human atrial modelling unravels interactive protein kinase A and Ca2+/calmodulin-dependent protein kinase II signalling as key determinants of atrial arrhythmogenesis. Cardiovasc Res. 2023 Oct 24;119(13):2294-2311. doi: 10.1093/cvr/cvad118. Link

• Compiler: intel icpc
• Dependencies: CVODE and zlib
• Data analysis: Python & Matlab
• Data visulization: Paraview

Dependencies and complilers

• compiler: C++ with CXX=mpiicpc (tested with intel mpi for parallel computing on clusters)
• CVODE with Sundials (tested with Version 5.7)
• zlib (for tissue geometry input)

Folders

• Single_Cells: source code for single cell modeling
• Populations: source code for population simulation, DAD analysis, and logistic regression analysis
• 2D_Tissue_modeling: source code for 2D simulations
• 3D_Spatial_Myocyte_modeling: source code for running 3D spatial cell modeling
• PV-like_Populations: source code for simulating PV-like myocytes
• Matlab_Single_Cell: a copy of single cell model implemented in Matlab