Dynamic computer simulations are essential for quantitative understanding of integrated mechanisms underlying various cell functions and can provide a powerful tool to create and test working hypotheses. We have been developing mathematical models of cell functions and biodynamics by integrating experimental data and implemented cardiac cell (Kyoto model from Matsuoka
et al., 2003 and 2004, LRd model from Faber and Rudy, 2000, Noble
et al., 1998), an epithelial cell (Strieter
et al., 1990) and a pancreatic β cell model (Magnus and Keizer, 1998) using a common biological simulation tool called
simBio, which is written in
Java
, uses XML and solves ordinary differential equations. In analogy to biological functional structures, a cell model in
simBio is composed of independent functional modules called
Reactors such as ion channels and sarcoplasmic reticulum, and dynamic variables called
Nodes such as ion concentrations. Interactions between
Reactors and
Nodes are described by the graph theory and the resulting graph represents a blueprint of an intricate cellular system. Each
Reactor can be composed or improved independently and can easily be reused for different models. We have designed
simBio as a tool for a simple conversion of a biological system into machine code, for an easy model expansion, and for a reuse of models as a whole or in part as sub-models in different contexts. Thus, the development of a large variety of biological models will be enhanced. The
simBio package is freely available from http://www.sim-bio.org/.
[Jpn J Physiol 55 Suppl:S97 (2005)]
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