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Conversion issues

The remaining issues of the conversion, i.e., what the current version does not convert or converts with a loss. The failure reasons of the SBML test suite measure them against the semantic test cases; what is converted is listed in What is converted and CellML to SBML.

SBML to CellML

  • Units of an incomplete annotation. The units of the variables are converted when every variable has units in the SBML model, see Units; with a single compartment, species or parameter without units every variable stays dimensionless. A number without units in a formula is always dimensionless, CellML requires units on every number and SBML has none to give.
  • Unit warnings of libcellml. The CellML specification applies the exponent of a unit to its prefix but not to its multiplier, which libcellml.Units.scalingFactor follows and the converter writes. The unit check of the libcellml 0.7.1 analyser applies the exponent to the multiplier as well, so it warns about equations with units such as per_min ((60 second)^-1 in SBML, 1/60 second^-1 in CellML) which are consistent (cellml/libcellml#1463). The warnings do not make a model invalid.
  • Initial assignments are evaluated to initial values (libsbml's expandInitialAssignments), so the CellML model has the value but not the formula. An assignment which libsbml cannot evaluate (a call of a recursive function definition, a rateOf with a local parameter, a delay, or the value of such an assignment) stays unconverted with a warning. libsbml takes only 1 as true when it evaluates a number as a condition (piecewise(0, 5, 1) gives 1, test case 01282).
  • An infinite or NaN initial value of a state cannot be expressed: CellML initial values are real numbers (a constant gets the equation x = INF instead).
  • Metadata without a CellML element: the names, notes and annotations of rules, function definitions, initial assignments, constraints and events are not converted, neither are annotations which are not RDF (e.g., of COPASI or layout tools). Everything else goes into the RDF file next to the CellML model, see Metadata.
  • Events are skipped with a warning. CellML 2.0 has no events; a subset could be expressed with resets.
  • Coupled algebraic rules, which determine their variables only together (x + y = 4, x - y = 2), cannot be analysed by libcellml; an algebraic rule which determines no variable is skipped with a warning.
  • stoichiometryMath of level 2 species references is not converted, the stoichiometry attribute is used.
  • N-ary relations such as a > b > c are not split into binary ones; CellML only has binary relations.
  • Time without differential equations. CellML knows the variable of integration only from a differential equation: a model without one has no time variable, and a formula using time in such a model cannot be converted.
  • An SBML id time collides with the variable of integration time of the CellML model and with the time column of the simulation results.
  • The delay symbol is not converted, CellML has no delays.
  • rateOf of a variable whose rate depends on itself, or which an assignment rule sets, is not converted; in an initial assignment neither when the rate has a local parameter. The rate of a concentration in a compartment which changes needs the rate of the compartment, so it is converted when a rate rule changes the compartment and not when an assignment or algebraic rule does.
  • Unset initial values of variables which no assignment rule or initial assignment sets are 1.0, with a warning.

CellML to SBML

  • External variables are not supported and raise CellML2SBMLConversionError; a system of coupled implicit equations cannot be analysed by libcellml.
  • New base units (units without a unit) have no SBML counterpart and are dimensionless in SBML, with a warning; only new base units named item become the SBML unit kind.
  • Resets trigger on the equality of the test variable and the test value; a continuous simulator may not fire this trigger, see the limitations.