Reconstruction of complex biological systems from a huge amount of experimental data requires a formal language that can be easily understood both by human and computer.
It is known that graphical depiction of complex system is the most suitable way of understanding of its structure by human. Graphical notation allows human to completely and formally specify model so computer programs can analyze the model and simulate its behavior (Lee, 2001).
This approach is widely used in engineering and computer science. Some e xamples are:
| · | MATLAB/Simulink ( http://www.mathworks.com ) |
| · | AnyLogic ( http://www.xjtek.com ) - muli-method simulation software |
| · |
UML (
http://www.omg.org/uml/
) - t
he most known graphical language for computer science.
BioUML workbench adopts visual modeling approach for formal description and simulation of complex biological systems (Figure 1.2). Another distinctive feature of BioUML workbench is tight integration with databases on biological pathways, query engine allows user to find interacting components of the system and show results as an editable graph. |
Figure 1.2 . Data flow in BioUML workbench.