Examples Documentation

The main objective of the tutorials compiled in this section is to provide basic examples for most (ideal all) CARPentry features. This examples are intended to transfer basic user know-how in an efficient way. The scripts for building the tutorials are designed as mini-experiments which should also serve as a basic building block for building more complex experiments.

There is no clear separation between plain and carputils philosophy, the tutorials are intended to teach both aspects. There is a number of tutorials dedicated to teaching plain usage of CARPentry as this is considered necessary fundamental know-how for those who are interested in building more complex experiments from scratch themselves or even for extending pre-existing carputils experiments. However, all the executable tutorials are coded up in carputils to facilitate an easy execution of all experiments without the significant additional time-consuming hassle of assembling long and complex command lines.

Intended use

Most tutorials can be run by simply copying the carputils run command from the tutorial webpages. It is recommended to inspect the generated command lines to understand what the simulation looks like in the plain command line by adding the option --dry to the run script command line. A more detailed background on carputils command line options are given in the Carputils usage section.

To run the examples cd into the respective section relative to the location of your tutorials repository. The structure of the tutorial repository should look similar to the following

├── 01_EP_single_cell
│   ├── 01_basic_bench
│   ├── 02_restitution
│   ├── 02B_APD_restitution
│   ├── 03_state_clamp
│   ├── 03A_voltage_clamp
│   ├── 04_limpet_fe
│   ├── 05_EasyML
│   └── 10_fromCellML
├── 02_EP_tissue
│   ├── 01_basic_usage
│   ├── 02_stimulation
│   ├── 03_study_preparation
│   ├── 03A_study_prep_tuneCV
│   ├── 03B_study_prep_init
│   ├── 03C_tuning_wavelength
│   ├── 03D_conduction_velocity_restitution
│   ├── 04_tagging
│   ├── 05_heterogeneities
│   ├── 05A_Regions_vs_Gradients
│   ├── 05B_Conductive_Heterogeneity
│   ├── 05C_Cellular_Dynamics_Heterogeneity
│   ├── 05D_Region_Reunification
│   ├── 05E_Smooth_Gradient_Heterogeneities
│   ├── 06_eikonal
│   ├── 07_extracellular
│   ├── 07A_augmentation
│   ├── 07B_periodic
│   ├── 08_lats
│   ├── 09_filaments
│   ├── 10_optical
│   ├── 11_discretization
│   ├── 12_tuning_wavelength
│   ├── 13_laplace
│   ├── 14_bidm_rotation
│   ├── 15_bidm_distribution
│   ├── 16_bidm_dogbone
│   ├── 17_bidm_pacing
│   ├── 18_tdr
│   └── 19_Pkje
├── 03_EM_single_cell
│   └── 01_EM_coupling
├── 04_EM_tissue
│   ├── 01_boundary_conditions
│   ├── 02_laplace
│   ├── 03_unloading
│   ├── 04_EM_coupling
│   ├── 05_MEF
│   ├── 06_afterload_fitting
│   ├── 07_constitutive_fitting
│   ├── 08_ring
│   ├── 09_bivslice
│   └── 10_cvsys
├── 05_pre_post_processing
│   ├── 01_basic_mesher
│   ├── 03_Laplace_Dirichlet_Fibers
│   ├── 04_output_restriction
│   ├── 05_igbutils
│   ├── 06_UVC_bullseye
│   └── 07_UVC_applied
├── 06_fluid
│   └── 01_HagenPouseille
└── visualization
    ├── limpetGUI
    ├── meshalyzer
    ├── meshalyzer_adv
    └── paraview

To run the single cell EP tutorials therefore

cd EM_tissue/04_EM_coupling
./run.py --help

The output data from the tutorial persists after the experiment. If meshes were generated with the mesher program, there will be a meshes directory with further subdirectories containing the meshes, each directory name having the date embedded within it. You need to determine which one was used for the last experiment. To be sure of the mesh, you can recursively remove the meshes directory before you run the experiment, or simply run the script with the --clean option.

CARPentry results will be placed in a subdirectory within the experiment directory. The name of the subdirectory may be formed from a combinatio of the date, experiment conditions and number of processes so there may be several. Within each results subdirectory, you should see IGB files (the outputs), possibly intracellular grids, as well as a file parameters.par which has all the parameter settings, encapsulating even the commandline optionss. This file may be used to rerun the simulation from the main experiment directory.

carp.pt +F parameters.par