Comprehensive model for formalized description, visualization and simulation of biological systems

BioUML is integrated extensible workbench for systems biology (http://www.biouml.org). Its core is BioUML meta model that provides a formalism for comprehensive description, visualization and simulation of wide range of biological and other complex systems. The suggested model is problem domain neutral and splits the system description into three interconnected levels: 1) graph structure the system structure is described as compartmentalized graph; 2) database level each graph element can contains reference to database object, additionally arbitrary attributes can be associated with graph element; 3) executable model any graph element can be element of executable (mathematical) model, for example it can be variable or equation. Taking into account problem domain specificity we introduce concept of diagram type, diagram view builder to visualize the graph structure as diagram using problem domain specific visual syntax and semantic controller to provide semantic integrity during the diagram editing. The module concept allows to developer define new diagram types and incorporate other databases on biological pathways into BioUML framework.