Term information
The Systems Biology Markup Language (Level 1) is a format for the representation of biochemical reaction networks and models in various areas of computational biology [Hucka et al., 2003]. [Hucka et al., 2003] state that a model in SBML is defined by the following components: - Compartment: A container of finite volume for wellstirred substances where reactions take place. - Species: A chemical substance or entity that takes part in a reaction. Some example species are ions such as calcium ions and molecules such as ATP. - Reaction: A statement describing some transformation, transport or binding process that can change one or more species. Reactions have associated rate laws describing the manner in which they take place. - Parameter: A quantity that has a symbolic name. SBML provides the ability to define parameters that are global to a model, as well as parameters that are local to a single reaction. - Unit definition: A name for a unit used in the expression of quantities in a model. This is a facility for both setting default units and for allowing combinations of units to be given abbreviated names. - Rule: A mathematical expression that is added to the model equations constructed from the set of reactions. Rules can be used to set parameter values, establish constraints between quantities, etc.