A short introduction to CellML

CellML (TM) 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 struct ure 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 m odels may be built;. The basic constituents and structure are simple; provi ding a common basis for describing models and facilitating the creation of complex models from simpler ones by combining models and/or adding detail t o 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 ma y correspond to a physical compartment;, a collection of entities engaged i n similar tasks, or a convenient modelling abstraction. Components may cont ain variables, mathematical relationships that specify the interactions bet ween those variables, and metadata. Variables may be local to a component, or made visible to other components via interface attributes. All interacti ons between variables within a component are described using MathML content markup. The interface attributes describe the external view of tile compon ent, specifying those variables visible to other components. A connection i s a directed mapping from externally visible variables in one component to those of another. Every variable has a set of units associated with it, mak ing it possible to connect together components with variables defined using different units. CellML offers additional facilities, such as metadata, for adding context i nformation to a model, and component grouping. These assist in the creation and maintenance of models but do not alter the mathematics of the model. A ll models described using CellML can be reduced to the canonical form: a se t of connected components.