A short introduction to CellML. CellML is an XML-based language designed to facilitate the exchange of biological models across the World Wide Web. Processing applications are able to appropriately render models based on the definition of model structure given in a CellML document, and run simulations based on the definition of the underlying mathematics. CellML is designed to be a general framework upon which a wide variety of models may be built. The basic constituents and structure are simple, providing a common basis for describing models and facilitating the creation of complex models from simpler ones by combining models and/or adding detail to existing models.CellML models are represented as a collection of discrete components linked by connections to form a network. A component is a functional unit that may correspond to a physical compartment, a collection of entities engaged in similar tasks, or a convenient modelling abstraction. Components may contain variables, mathematical relationships that specify the interactions between those variables, and metadata. Variables may be local to a component, or made visible to other components via interface attributes. All interactions between variables within a component are described using MathML content markup. The interface attributes describe the external view of the component, specifying those variables visible to other components. A connection is a directed mapping from externally visible variables in one component to those of another. Every variable has a set of units associated with it, making it possible to connect together components with variables defined using different units. CellML offers additional facilities, such as metadata, for adding context information to a model, and component grouping. These assist in the creation and maintenance of models but do not alter the mathematics of the model. All models described using CellML can be reduced to the canonical form: a set of connected components. (Source: http://freecode.com/)

References in zbMATH (referenced in 15 articles , 1 standard article )

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  1. Mirshekari, Elham; Spiteri, Raymond J.: Extending BACOLI to solve the monodomain model (2016)
  2. Spiteri, Raymond J.; Torabi Ziaratgahi, Saeed: Operator splitting for the bidomain model revisited (2016)
  3. De Matteis, Giovanni; Graudenzi, Alex; Antoniotti, Marco: A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development (2013)
  4. Heidlauf, Thomas; Röhrle, Oliver: Modeling the chemoelectromechanical behavior of skeletal muscle using the parallel open-source software library OpenCMISS (2013)
  5. Kannon, Takayuki; Inagaki, Keiichiro; Kamiji, Nilton L.; Makimura, Kouji; Usui, Shiro: PLATO: data-oriented approach to collaborative large-scale brain system modeling (2011) ioport
  6. Tveito, Aslak; Lines, Glenn; Artebrant, Robert; Skavhaug, Ola; Maleckar, Mary M.: Existence of excitation waves for a collection of cardiomyocytes electrically coupled to fibroblasts (2011)
  7. Waltemath, Dagmar; Henkel, Ron; Meyer, Holger; Heuer, Andreas: Das sombi-framework zum ermitteln geeigneter suchfunktionen für biologische modelldatenbasen (2011) ioport
  8. Cooper, Jonathan; Whiteley, Jonathan P.; Gavaghan, David J.: A posteriori error analysis for the use of lookup tables in cardiac electrophysiology simulations (2010)
  9. Bernabeu, Miguel O.; Bordas, Rafel; Pathmanathan, Pras; Pitt-Francis, Joe; Cooper, Jonathan; Garny, Alan; Gavaghan, David J.; Rodriguez, Blanca; Southern, James A.; Whiteley, Jonathan P.: Chaste: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library (2009)
  10. Pitt-Francis, Joe; Pathmanathan, Pras; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Fletcher, Alexander G.; Mirams, Gary R.; Murray, Philip; Osborne, James M.; Walter, Alex; Chapman, S.Jon; Garny, Alan; Van Leeuwen, Ingeborg M.M.; Maini, Philip K.; Rodríguez, Blanca; Waters, Sarah L.; Whiteley, Jonathan P.; Byrne, Helen M.; Gavaghan, David J.: Chaste: A test-driven approach to software development for biological modelling (2009)
  11. González, M.; González, F.; Luaces, A.; Cuadrado, J.: Interoperability and neutral data formats in multibody system simulation (2007)
  12. Webb, Ken; White, Tony: Cell modeling with reusable agent-based formalisms (2006) ioport
  13. Cuellar, Autumn A.; Lloyd, Catherine M.; Nielsen, Poul F.; Bullivant, David P.; Nickerson, David P.; Hunter, Peter J.: An overview of CellML 1.1, a biological model description language (2003) ioport
  14. Garny, A.; Kohl, P.; Noble, D.: Cellular open resource (COR): a public CellML based environment for modeling biological function (2003)
  15. Hedley, Warren J.; Nelson, Melanie R.; Bullivant, David P.; Nielsen, Poul F.: A short introduction to CellML (2001)