Applications Overview

Applications allow users to specify 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
Hybrid Deterministic Stochastic, a stochastic model with at least 1 species specification set to 'Force Continuous' (See Spatial Stochastic or Non-Spatial Stochastic under Species Specifications).
Network-free, a special stochastic network-free application that does not require generating a network to simulate.

Additionally, by defining Geometry, deterministic, stochastic or network-free applications can be made:

Compartmental (1D, 2D or 3D), where the topology and size of compartments are defined, but species are assumed to be well mixed within their compartments. A compartmental application is simulated using either differential equations (for deterministic application), or using stochastic simulation algorithms (for stochastic application).
Spatial (1D, 2D or 3D), where the geometry of compartments is defined, and species diffuse within compartments. A spatial application is simulated using either partial differential equations (for deterministic applications), or using the stochastic agent-based simulation algorithm SmolDyn (for stochastic applications). Presently Network-free applications do not allow spatial geometry (compartmental only).

The Application directory displays the Applications associated with the BioModel. The main window displays the selected application and provides buttons to create new applications or to delete or copy applications. Properties for a selected object (e.g. species, reaction, simulation) are displayed in the Properties Pane below the main window.

Create a new application by selecting "Applications" in the left menu. Right click opens a menu to create either a deterministic or stochastic application. Or, use the New Application button in the main window.

View/Edit application components and properties by double-clicking, or selecting the + icon beside, the 'Applications' tree in the navigation panel to expose the names of applications contained in the BioModel; select one of the Application names to activate the 'view' and 'properties' panels that display all the application detail editors.