Modular modeling

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Modular model notation

Modular approach to modeling of biological systems has been rapidly developing in recent years. It implies system decomposition into subsystems, each of which can be modeled and validated independently. Model of the whole system is given as a combination of the subsystem models (modules). This approach makes the structure of complex hierarchic models more explicit by allocation of functional units and their interconnections.It also allows incorporating models developed by different authors, focusing on different parts of the system and utilizing different scales and even formalisms into complex models.

The BioUML platform provides powerful support for modular modeling of complex biological systems, using different mathematical formalisms. It's main components are:

  • graphic notation - provides rules for graphical presentation of modular models;
  • flattening algorithm - provides transformation of a modular model into a flat model for further simulation. This conversion is possible if all the modules use the same formalism, namely, algebraic-differential equations with discrete events;
  • agent based modeling - is used for simulation modular models when modules use different mathematical formalisms to describe behavior of module components.

We have developed a number of examples demonstrating application of this approach:

All these models are freely available via the web interface provided by the BioUML platform.

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