See the full article at Science Advances website.
How to use/interact with the programs
Each program has a Graphical User Interface (GUI) with menus
and submenus in the interface. To create excitations anywhere
in the tissue in 2D applications,
use the mouse/touchpad Click/Drag, whereas in 3D applications,
use Ctrl+click/drag with PCs and
Command+click/drag with Mac OS.
In the lattice-Boltzmann simulations, mouse clicks can be used to
add or remove obstacles based on the clicker type that can be chosen from
the simulation menu.
The main menus in the GUI are as follows.
- Simulation: press Solve/Pause to start or stop a simulation
or Initialize to reinitialize the problem. Change the click
radius and more.
- Model parameters: change interactively at any time. For
example, it is possible to block or enhance currents or
Some programs have predefined sets of parameters that can
be chosen from a drop-down menu.
- Solver parameters: time integration variables, domain size
- Display parameters: change the frame rate throttle to slow
down or speed up the simulation according to graphics card
or visualization speed needs. Colormaps
and signal probe location visibility can also be changed,
tip-trajectory options can be set through a sub-menu, and
- Save Canvas: save a visualization result as a png image.
- Interval caller: make interactive calls to functions; for
example, type in env.savePlot2D() in the
3-Variable Minimal Model
to save the canvas automatically at a set interval.
- More complex models have many more menus and options.
For example, the OVVR model has extensive menus to
change the current multipliers, time coefficients, and
cell types; record signals; display various currents; save and
load parameters, etc.