The core of BioUML is a meta-model. It provides an abstract layer (compartmentalized attributed graph) for comprehensive formal description of wide range of biological and other complex systems. Content of databases on biological pathways, SBML ( Hucka M. et al., 2003) and CellML( Lloyd C.M. et al., 2004) models, as well as biological pathways in BioPAX format can be expressed in terms of the meta model and used by BioUML workbench.
This formal description can be used both for visual depiction and editing of biological system structure and for automated code generation to simulate a model behavior.
Meta-model is problem domain neutral and splits the system description into 3 interconnected levels:
| 1. | graph structure - the system structure is described as compartmentalized graph; |
| 2. | database level - each graph element can contain reference to some database object; |
| 3. |
mathematical model - any graph element can be element of mathematical model.
BioUML supports following mathematical elements: variable, formula, equation, event, state and transition. |
Figure 1.3 demonstrates how this approach is applied for modeling system consisting from two consecutive chemical reactions. Here graph nodes representing chemical substances are considered as variables and corresponding graph edges contain right parts of corresponding differential equations. Using this information BioUML workbench can generate MATLAB or Java code for model simulation.
Figure 1.3
. System from two consecutive chemical reactions (a), its formal description using three meta model levels (b), and corresponding mathematical model (c), that can be generated automatically for system simulations.
Special BioUML diagrams markup language (DML) is developed to
store BioUML meta model instance in XML format. Diagram description is divided into two parts:
| 1) | graph structure - it describes location of diagram elements and contains references to associated with them database objects; |
| 2) | executable model - stores mathematical model associated with graph. |
D etailed description of DML format is available at http://www.biouml.org/dml.shtml