Y involve temperature). Consequently, the SBML unit system has been consciously
Y involve temperature). Consequently, the SBML unit system has been consciously developed inside a way that attempts to simplify implementation of unit help for essentially the most prevalent situations in systems biology, in the expense of requiring units with offsets to be handled explicitly by the modeler. 4.four. UnitDefinitionA unit definition in SBML consists of an instance of a UnitDefinition object, shown in Figure two. The id and name attributes: The expected attribute id and optional attribute name have data types UnitSId and string, respectively. The id attribute is utilised to offer the defined unit a exclusive identifier by which other components of an SBML model definition can refer to it. The name attribute is intended to become used for providing the unit definition an optional humanreadable name; see Section three.3.2 for a lot more recommendations concerning the use of names. There are two essential restrictions and suggestions concerning the use of unit definition id values:J Integr Bioinform. Author manuscript; available in PMC 207 June 02.Hucka et al.Page.The id of a UnitDefinition need to not include a value from Table , the list of reserved base unit names. This constraint basically prevents the redefinition of base units. There is a set of reserved identifiers for the predefined units in SBML; these identifiers are ” substance”, ” volume”, ” area”, ” length”, and ” time”. Applying among these values for id inside a UnitDefinition has the effect of redefining the modelwide default units for the corresponding quantities. We go over this in far more detail in Section 4.four.three.Author Manuscript Author Manuscript Author Manuscript Author Manuscript2.The list of Units: A UnitDefinition object have to include 1 or more Unit objects inside a ListOfUnits container. Section four.four.2 explains the meaning and use of Unit. Example: The following skeleton of a unit definition illustrates an example use of UnitDefinition:4.4.two UnitA Unit object represents a (possibly transformed) reference to a base unit selected in the list in Table . The attribute type indicates the selected base unit, whereas the attributes exponent, scale, and multiplier define how the base unit is getting transformed. These various attributes are described in detail beneath. In SBML Level 2 Version , Unit had an additional attribute called offset. This attribute has been removed entirely in Level 2 Versions two. Modelers and software authors are instead directed to use other strategies of encoding units requiring offsets. The factors for this transform, and some ideas for ways to attain equivalent effects of unit offsets, are discussed in much more detail below. One more adjust in Version three could be the removal of your enumeration UnitKind as well as the redefinition of UnitSId to contain the earlier UnitKind values as reserved symbols. This change has no net effect on permissible Eptapirone free base biological activity models or their representation.J Integr Bioinform. Author manuscript; obtainable in PMC 207 June 02.Hucka et al.PageThe sort attribute: The Unit object class has one particular expected attribute, sort, whose value should be taken from the list PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23814047 of reserved words provided in Table . These reserved symbols are within the worth space of UnitSId (Section 3..eight). Note that the set of acceptable values for the attribute sort will not consist of units defined by UnitDefinition object. This implies that the units definition technique in SBML is just not hierarchical: userdefined units cannot be constructed on leading of other userdefined units, only on leading of base units. SBML differs from CellML (Hedley et al 200) within this respect; CellML enables the constr.
