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AlgebraicRule

An equation which has to hold at every moment of the simulation.

An algebraic rule states that an expression is zero: 0 = f(W). It constrains the elements of the model without saying which of them it determines, which is why a simulator has to solve it together with the rest of the system. A model must not be overdetermined, so at least one element of the equation has to be free, that is not constant and not determined by another rule or by the reactions.

The report shows the rendered equation and the units it produces; which element it determines follows from the rest of the model.

Attributes

attribute type required meaning specification
math Math optional the expression which has to be zero core 4.9.1

Every element of a model also carries the common attributes of SBase.

math

The math is an arbitrary expression which returns a number, and the rule says that this number is zero at all times.

The report renders the expression in the column "math" and in the inspector.

Default: how the rule behaves mathematically stays undefined.

  • 20907 (error): Every AssignmentRule, RateRule and AlgebraicRule object must contain exactly one MathML <math> element. The <math> element is optional in L3V2 and beyond.

In the report

field type meaning
derived units latex the units of the expression as the report derives them

derived units

The report derives the units of the expression from the units of the quantities it uses. The terms of an equation should all have the same units.

Validation rules

  • 10601 (error): The system of equations created from an SBML model must not be overdetermined.
  • 10705 (warning): The value of the 'sboTerm' attribute on a rule is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a mathematical expression (i.e., terms derived from SBO:0000064, "mathematical expression"). Note: This applies to Algebraic Rules in addition to Rate and Assignment Rules.
  • 20910 (error): An AlgebraicRule object may have the optional attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on an AlgebraicRule object.
  • AssignmentRule: a formula which holds at every moment of the simulation
  • RateRule: a formula which gives the rate of change of an element

Specification

SBML Level 3 Version 2 Core, Section 4.9.2 (Hucka et al. 2019, J Integr Bioinform 16(2):20190021).