cellml_2_0_quick.md

CellML 2.0 Quick Reference

These things exist in CellML 2.0:

Elements are shown with their attributes in brackets. Required elements/attributes are indicated in italics.

• model(name)
  • units(name)
    • unit(units, prefix, multiplier, exponent)
  • component(name)
    • variable(name, units, interface, initial_value)
    • reset(variable, test_variable, order)
      • test_value
        • mathml:math
      • reset_value
        • mathml:math
    • mathml:math
      • All mathml:cn elements must have a cellml:units attribute
  • encapsulation
    • component_ref(component)
      • component_ref(component)
        • ...
  • connection(component_1, component_2)
    • map_variables(variable_1, variable_2)
  • import(xlink:href)
    • units(name, units_ref)
    • component(name, component_ref)

All CellML 2.0 elements can also contain an unnamespaced id attribute.

Encapsulation & public/private interfaces

Encapsulation means parent/child relationships, which affect how connections are made.

There are three rules:

1. Only components that have sibling or parent-child relationships can be connected.
2. Connections between siblings are governed by the public interface.
3. In parent-child relationships, the parent uses the private interface and the child uses the public interface.

Identifiers

Identifiers must start with at least one letter, and only contain letters, numbers, and underscores.

Lists

Elements

• component
• component_ref
• connection
• encapsulation
• import
• model
• reset
• reset_value
• test_value
• unit
• units
• variable
• variable_1
• variable_2

Attributes

• component
• component_1
• component_2
• component_ref
• exponent
• initial_value
• interface
• map_variables
• multiplier
• name
• order
• prefix
• test_variable
• units
• units_ref
• variable

Namespaces

cellml="http://www.cellml.org/cellml/2.0#"
mathml="http://www.w3.org/1998/Math/MathML"

Predefined units

• ampere
• becquerel
• candela
• coulomb
• dimensionless
• farad
• gram
• gray
• henry
• hertz
• joule
• katal
• kelvin
• kilogram
• litre
• lumen
• lux
• metre
• mole
• newton
• ohm
• pascal
• radian
• second
• siemens
• sievert
• steradian
• tesla
• volt
• watt
• weber

Unit prefixes

• yotta
• zetta
• exa
• peta
• tera
• giga
• mega
• kilo
• hecta
• deca
• deci
• centi
• milli
• micro
• nano
• pico
• femto
• atto
• zepto
• yocto

Interface types

• public
• private
• public_and_private
• none (default)

MathML subset

CellML 2.0 documents can use MathML, but must only elements from the Supported MathML Elements set.

MathML basics

• <cn>, <ci>, <apply>, <eq>, <sep />
• Every <cn> must have a cellml:units attribute
• The type of a <cn> must be either real or e-notation
• Every <ci> must refer to a variable from the same component

Arithmetic

• Basic 1: <plus>, <minus>, <times>, <divide>
• Basic 2: <power>, <root>, <exp>, <ln>, <log>, <logbase>
• Non-smooth: <abs>, <floor>, <ceiling>, <rem>
• N-ary comparison: <max>, <min>

Calculus

• First order: <diff>, <bvar>
• Higher order: <degree>

Trig functions

• Basic: <sin>, <cos>, <tan>, <arcsin>, <arccos>, <arctan>
• Hyperbolic: <sinh>, <cosh>, <tanh>, <arcsinh>, <arccosh>, <arctanh>
• Redundant <sec>, <csc>, <cot>, <arcsec>, <arccsc>, <arccot>
• Hyperbolic redundant: <sech>, <csch>, <coth>, <arcsech>, <arccsch>, <arccoth>

Logic and Piecewise

• Piecewise: <piecewise>, <piece>, <otherwise>
• Relations: <eq>, <neq>, <gt>, <lt>, <geq>, <leq>
• Logical operators: <and>, <or>, <xor>, <not>
• Logical constants: <true>, <false>

Note 1: <eq> is a relation in CellML, so the statement x = 5 is treated as fact about x, not an assignment.

Note 2: The <otherwise> element is not required. This means that you can write a statement like x = (y > 0) ? 1 : undefined. The CellML spec doesn't define what implementations should do for these cases.

Note 3: The initial 2.0 spec doesn't rule out that variables can have the value true or false.

Constants

• <pi>
• <exponentiale>
• <notanumber>
• <infinity>