title: CellExcite: an efficient simulation environment for excitable cells.
abstract: BACKGROUND
  Brain, heart and skeletal muscle share similar properties of excitable tissue, featuring both discrete behavior (all-or-nothing response to electrical activation) and continuous behavior (recovery to rest follows a temporal path, determined by multiple competing ion flows). Classical mathematical models of excitable cells involve complex systems of nonlinear differential equations. Such models not only impair formal analysis but also impose high computational demands on simulations, especially in large-scale 2-D and 3-D cell networks. In this paper, we show that by choosing Hybrid Automata as the modeling formalism, it is possible to construct a more abstract model of excitable cells that preserves the properties of interest while reducing the computational effort, thereby admitting the possibility of formal analysis and efficient simulation.
  
  
  RESULTS
  We have developed CellExcite, a sophisticated simulation environment for excitable-cell networks. CellExcite allows the user to sketch a tissue of excitable cells, plan the stimuli to be applied during simulation, and customize the diffusion model. CellExcite adopts Hybrid Automata (HA) as the computational model in order to efficiently capture both discrete and continuous excitable-cell behavior.
  
  
  CONCLUSIONS
  The CellExcite simulation framework for multicellular HA arrays exhibits significantly improved computational efficiency in large-scale simulations, thus opening the possibility for formal analysis based on HA theory. A demo of CellExcite is available at http://www.cs.sunysb.edu/~eha/.
authors.affiliation: Dipartimento di Matematica e Informatica, Università di Camerino, Via Madonna delle Carceri n,9, Camerino, Italy. ezio.bartocci@unicam.it
authors.forename: Ezio
authors.initials: E
authors.lastname: Bartocci
authors.forename: Flavio
authors.initials: F
authors.lastname: Corradini
authors.forename: Emilia
authors.initials: E
authors.lastname: Entcheva
authors.forename: Radu
authors.initials: R
authors.lastname: Grosu
authors.forename: Scott A
authors.initials: SA
authors.lastname: Smolka
mesh_terms: D000200:Action Potentials / Q000502:physiology*; D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D006329:Heart Conduction System / Q000502:physiology*; D006801:Humans; D008954:Models, Biological; D032383:Myocytes, Cardiac / Q000502:physiology*; D009415:Nerve Net / Q000502:physiology*; D009474:Neurons / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface