Repository

Navigation
To browse the projects in the ontology view use either the graphical scheme below or the navigation panel on the left. The root level is displayed after clicking on the Projects button in the main menu bar at the top of the screen. For switching to model view, click on the project name in the navigation tree.

The central feature of the ontology view is the graphical scheme representing the projection of the project to respective biological structures. The graphical scheme is active, the individual model parts implemented in the project are emphasized yellow when moving the mouse over them. After clicking on any implemented part, the scheme is zoomed in. The description panel at the bottom contains all the detailed information relevant for the currently focused project level.

Annotations Tab
All the annotation terms relevant for the currently focused level of the project are displayed on the Annotation Tab below the scheme. Individual annotation data can be unfolded by clicking on the requested annotation item header.

Components Tab
The Components Tab displays all the model species (state variables) relevant for the currently focused project level. Annotation data for particular components are accessible after clicking on the requested component header.

Reactions Tab
Reactions Tab contains information regarding the modeled reactions. After clicking on the particular reaction header, the reacting components and relevant kinetic parameters are displayed.

Parameters Tab
All quantitative parameters are managed under Parameters Tab. Constants are separated from algebraically evaluated parameters.

Simulation Tab
Simulation and SBML export are available by clicking on appropriate buttons at the bottom of the tab. All relevant settings of parameters and initial conditions is listed in respective folders. Folder Options contains parameters of the simulation algorithm.