Model Construction and Simulation

Biological models are constructed in a text editor window with support for syntax checking and highlighting of BNGL Keywords. Models are comprised of molecular elements and the rules that affect them. Once the models are completed, they can be simulated from the editor menu with either a stochastic or deterministic simulator. Parameter Scanning allows for finding the effects of varrying a model parameter across several simulations.

Model Visualization: Interactive Contact Map

During model construction, visual representations of the molecules and chemical rules are displayed in the visualization window. Interacting with the visualization produces the text representations for the structures, and overlays that display more information about molecule interaction.

Model Visualization: Interactive Influence Graph

Interaction between the rules is also displayed in the visualization window. The context view in the lower left corner allows for easier navigation of the large interaction graph.

Results Analysis

After a simulation, the results viewer window plots concentration values of all measured molecules. All results are saved by the tool, and can be viewed or compared to other results by selecting the file from the browser in the upper left corner of the results viewer.

Species Graph

The lower left panel in the results viewer contains a moleculer species browser that contains all of the molecules produced by a simulation. Clicking on a molecule in this browser will display a graphical representation of it in the visualization window.