Applications Overview

Applications allow users to define the quantitative conditions needed to define, run and visualize a Virtual Experiment, i.e. a numerical simulation of the BioModel with specific initial conditions, within a given geometry, and with a selected type of simulation method. In the Application,

• the mapping between the model and the geometry is established in the Geometry tab
• Specifications for species, reactions and network (for rule-based application) are defined,
• specific Protocols (events, electric stimulation) can be included,
• for each application, multiple Simulations can be created that can include different initial conditions.
• Parameter Estimation can be performed

Applications can be

• Deterministic
• Stochastic
• Network-free, a special single-compartment stochastic network-free application

Additionally, by defining Geometry deterministic or stochastic applications can be made into

• Compartmental (1D, 2D or 3D), where topology and size of compartments are defined, but species are assumed to be well mixed within their compartments. Such application is simulated using either differential equations (for deterministic application), or using stochastic simulation algorithms (for stochastic application).
• Spatial (2D or 3D), where geometry of compartments is defined, and species are not well mixed but diffuse within compartments. Such application is simulated using either partial differential equations (for deterministic application), or using stochastic agent-based simulation algorithms SmolDyn (for stochastic application).

Create a new application by clicking on "Applications" in the left menu. Right click brings a menu to create either a deterministic or stochastic application. Or, use the Add New button in the main window.

Click on an application to view the application expand the tree and to display the different components of the application.