Modular Modeling of Biological Systems

Motivation: Modeling of complex biological systems such as cells, organs or even whole organisms is not a trivial task because of their intricate structure. Although modern computers allow simulation for quite complex models, such models are difficult to support and work with. Modular approach facilitates the creation of complex models by representing them as combinations of submodels. On the other hand, there are a large number of models describing particular subsystems created by different authors using different formalisms and scales.  These models may be reused as “bricks” in the creation of comprehensive overall models. Results: We have developed a modular approach to the modeling of complex biological systems. It includes a formal definition of graphical notation for modular models, an algorithm for the transformation of a modular model into a non-modular model which is appropriate for simulation using standard methods for solving ordinary differential equations  (ODE), and an algorithm for simulating modular model based on the agent-model principles. The approach was implemented in software plug-in for BioUML platform. Availability: The developed software and the source code are freely available as a part of BioUML in both standalone and web versions at www.biouml.org .