Architecture of ProMoT. Diagram of the software architecture of ProMoT. Added or extended software components are highlighted in green and bold face. Models can be set up either via the GUI or a text editor using the MDL format. The kernel can read and write model representations to files in MDL format. It can also read SBML models for Systems Biology. Internally models are represented as classes with inheritance and aggregation mechanisms. The user can manipulate and visualize these classes via the GUI. For analysis, a model instance is created and processed by one of the different writers for generating the input of an analysis system.