From 2009.igem.org

Complicated gene regulatory networks are difficult to visualise. System Biology Graphical Notation provides a way to present the processes In an easily understandable manner. However one of the main challenges while using SBGN is to visualise processes that take place at different times and depend on each other. This year because of the complexity of our project we decided to add the 4th dimension to graphical notation. We prepared a javaFX application that takes into account the dependencies between entities and provide appropriate visual output. Below you can see the recorded output that mimics the desired behaviour of our system.

Genes and cellular proteins are in the left compartment. Species that can be added to control the system are on the right and can be controlled by the user. Species degradation is symbolised by ‘shrinking’. Promoters become activated/repressed basing on the presence of regulators. The initial state of the cell in the application is total repression state. All 3 operons coding for functional genes are repressed. Only regulatory genes that repress those operons are transcribed. Application graphics are based on CellDesigner graphics. Below the standard CellDesigner model.