Glossary¶

CellML environment CellML Environment: The CellML Environment is the primary object in the OpenCMISS API which manages the use of CellML models in Iron. A single instance of a CellML environment is able to manage multiple CellML models (and multiple instances of the same model, if required).
CellML intermediate field: The OpenCMISS field which is used to contain the intermediate variables for the CellML models for a given CellML environment, these are wanted variables which are not state variables in the CellML model(s).
CellML models field: The field which associates CellML models within a given CellML environment to finite element models in OpenCMISS.
CellML parameters field: The OpenCMISS field which is used to define spatially varying known parameters in the CellML models for a given CellML environment.
CellML variable ID CellML variable name: In order to uniquely identify variables from CellML models using a text string, OpenCMISS methods use identifiers of the form: component_name/variable_name. Where component_name is the value of the name attribute of the component in which the desired variable is located and the variable_name is the value of that variable’s name attribute. Variables in the CellML model which are connected can be addressed by any of the relevant CellML variable ID’s.
known Known variables: CellML models used in OpenCMISS are required to be mathematically complete and suitably constrained. Often for such models to be useful in simulations, the definition of specific variables from the model(s) must be overridden in order to allow their value to be controlled during the simulation by OpenCMISS fields. Such variables are said to be known. When addressing variables from CellML models in the OpenCMISS API we use the standard CellML variable ID.
wanted Wanted variables: In order for OpenCMISS to have access to retrive the value of variables from CellML models, those variables must be flagged to OpenCMISS. Such variables are said to be wanted. When addressing variables from CellML models in the OpenCMISS API we use the standard CellML variable ID.