RULE-BASED MODELING IN BIOUML
Motivation and Aim: The traditional approach to mathematical modeling of biological systems involves usage of nonlinear systems of ordinary differential equations (ODEs) with given initial conditions. Talking about the modeling, we emphasize the fact that we consider an abstraction and study the mathematical description of some qualitative and quantitative characteristics of biological processes. The level of detail is dependent on the problem and based on the knowledge of the researcher. On the one hand, many meaningful models consist of few non-linear equations. On the other hand, a detailed study of the biochemical networks leads to development of large-scale models consisting of hundreds of variables and, therefore, equations. Moreover, if we incorporate to the model site-specific details of protein-protein interactions, the number of protein modifications increases dramatically, and complexity of the model becomes combinatorial. For example, a protein comprising n amino acids can be potentially found in 2n distinct phosphorylation states.
The principles for creation of the «rule-based» models were implemented in several software resources including KaSim (http://dev.executableknowledge.org/) and BioNetGen (www.bionetgen.org). BioUML supports the BioNetGen language (BNGL) and a special graphical notation created on the basis of SBGN and use it to visualize the «rule-based» models.
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