SBML API

In addition to the SBML importer, Myokit contains an API to represent SBML models, along with methods to read SBML documents. These methods are used under the hood by the importer.

In most cases, it’s easier to avoid these methods and use the SBML Importer instead.

SBML Model API

class myokit.formats.sbml.Compartment(model, sid)

Represents a compartment in SBML; to create a compartment use model.add_compartment().

A compartment acts as a Quantity, where the value represents the compartment’s size.

Arguments:

model
The myokit.formats.sbml.Model this compartment is in.
sid
This compartment’s SId.
initial_value()
Returns a myokit.Expression for this quantity’s initial value,
or None if not set.
is_rate()

Returns True if this quantity’s value is defined through a rate, else False.

set_initial_value(value)

Sets a myokit.Expression for this quantity’s initial value.

set_size_units(units)

Sets the myokit.Unit for this compartment’s size.

set_spatial_dimensions(dimensions)

Sets the dimensionality of this compartment’s size (usually 1, 2, or 3); this is used to determine the units for the compartment size in the case that they are not explicitly set.

set_value(value, is_rate=False)

Sets a myokit.Expression for this quantity’s value.

Arguments:

value
An expression
rate
Set to True if the expression gives the rate of change of this variable.
sid()

Returns this compartment’s sid.

size_units()

Returns the units of this compartment’s size.

If not set explicitly, the units will be retrieved from the model. If not set there either, units of dimensionless are returned.

spatial_dimensions()

Returns this compartment’s spatial dimensions, or None if not set.

value()

Returns a myokit.Expression for this quantity’s value, or None if not set.

class myokit.formats.sbml.Model(name=None)

Represents a model in SBML.

Arguments:

name
A user-friendly name for this model.
add_compartment(sid)

Adds a myokit.formats.sbml.Compartment to this model.

add_parameter(sid)

Adds a myokit.formats.sbml.Parameter to this model.

add_reaction(sid)

Adds a myokit.formats.sbml.Reaction to this model.

add_species(compartment, sid, is_amount=False, is_constant=False, is_boundary=False)

Adds a myokit.formats.sbml.Species to this model (located in the given compartment).

add_unit(unitsid, unit)

Adds a user unit with the given unitsid and myokit unit.

area_units()

Returns the default compartment size units for 2-dimensional compartments, or dimensionless if not set.

assignable(sid)

Returns the Compartment, Species, SpeciesReference, or Parameter referenced by the given SId.

base_unit(unitsid)

Returns an SBML base unit, raises an SBMLError if not supported.

compartment(sid)

Returns the compartment with the given sid.

conversion_factor()

Returns the Parameter acting as global species conversion factor, or None if not set, see Species.conversion_factor().

extent_units()

Returns the default extent units in this model, or dimensionless if not set.

length_units()

Returns the default compartment size units for 1-dimensional compartments, or dimensionless if not set.

myokit_model()

Converts this SBML model to a myokit.Model.

SBML IDs are used for naming components and variables. If an ID starts with an underscore, the myokit name will be converted to underscore<name>.

Compartments defined by the SBML file are mapped to Myokit Components.

name()

Returns this model’s name.

notes()

Returns a string of notes (if set), or None.

parameter(sid)

Returns the Parameter with the given id.

reaction(sid)

Returns the Reaction with the given id.

set_area_units(units)

Sets the default compartment size units for 2-dimensional compartments.

set_conversion_factor(factor)

Sets a Parameter as global conversion factor for species, see Species.conversion_factor().

set_extent_units(units)

Sets the default units for “reaction extent”, i.e. for the kinetic law equations in reactions.

set_length_units(units)

Sets the default compartment size units for 1-dimensional compartments.

set_notes(notes=None)

Sets an optional notes string for this model.

set_substance_units(units)

Sets the default units for reaction amounts (not concentrations).

set_time_units(units)

Sets the time units used throughout the model.

set_volume_units(units)

Sets the default compartment size units for 3-dimensional compartments.

species(sid)

Returns the species with the given id.

substance_units()

Returns the default units for reaction amounts (not concentrations), or dimensionless if not set.

time_units()

Returns the default units for time, or dimensionless if not set.

unit(unitsid)

Returns a user-defined or predefined unit.

volume_units()

Returns the default compartment size units for 3-dimensional compartments, or dimensionless if not set.

class myokit.formats.sbml.ModifierSpeciesReference(species, sid=None)

Represents a reference to a modifier species in an SBML reaction.

sid()

Returns this species reference’s SId, or None if not set.

species()

Returns the species this object refers to.

class myokit.formats.sbml.Parameter(model, sid)

Represents a parameter in SBML; to create a parameter use model.add_parameter().

Arguments:

model
The model this parameter is in.
sid
This parameter’s SId.
initial_value()
Returns a myokit.Expression for this quantity’s initial value,
or None if not set.
is_rate()

Returns True if this quantity’s value is defined through a rate, else False.

set_initial_value(value)

Sets a myokit.Expression for this quantity’s initial value.

set_units(units)

Sets this parameters units to the given Units.

set_value(value, is_rate=False)

Sets a myokit.Expression for this quantity’s value.

Arguments:

value
An expression
rate
Set to True if the expression gives the rate of change of this variable.
sid()

Returns this parameter’s sid.

units()

Returns the units this parameter is in, or None if not set.

value()

Returns a myokit.Expression for this quantity’s value, or None if not set.

class myokit.formats.sbml.Quantity

Base class for anything that has a numerical value in an SBML model, and can be set by rules, reactions, or initial assignments.

initial_value()
Returns a myokit.Expression for this quantity’s initial value,
or None if not set.
is_rate()

Returns True if this quantity’s value is defined through a rate, else False.

set_initial_value(value)

Sets a myokit.Expression for this quantity’s initial value.

set_value(value, is_rate=False)

Sets a myokit.Expression for this quantity’s value.

Arguments:

value
An expression
rate
Set to True if the expression gives the rate of change of this variable.
value()

Returns a myokit.Expression for this quantity’s value, or None if not set.

class myokit.formats.sbml.Reaction(model, sid)

Represents an SBML reaction; to create a reaction use Model.add_reaction().

Arguments:

model
The model this reaction is in.
sid
This reaction’s SId.
add_modifier(species, sid=None)

Adds a modifier to this reaction and returns the created object.

add_product(species, sid=None)

Adds a reaction product to this reaction and returns the created object.

add_reactant(species, sid=None)

Adds a reactant to this reaction and returns the created object.

kinetic_law()

Returns the kinetic law set for this reaction, or None if not set.

modifiers()

Returns the list of modifiers used by this reaction (as SpeciesReference objects).

products()

Returns the list of products created by this reaction (as SpeciesReference objects).

reactants()

Returns the list of reactions used by this reaction (as SpeciesReference objects).

set_kinetic_law(expression)

Sets this reaction’s kinetic law (as a myokit.Expression).

sid()

Returns this reaction’s sid.

species(sid)

Finds and returns a Species used in this reaction.

class myokit.formats.sbml.SBMLError

Raised if something goes wrong when working with an SBML model.

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class myokit.formats.sbml.Species(compartment, sid, is_amount, is_constant, is_boundary)

Represents an SBML species; to create a species use Compartment.add_species().

Arguments:

compartment
The Compartment that this species is in.
sid
This species’s SId.
is_amount
Whether this species value is represented as an amount (if false, it is represented as a concentration, which depends on the size of the compartment it is in).
is_constant
Whether or not this species is constant.
is_boundary
Whether or not this species is at the boundary of a reaction.
compartment()

Returns the Compartment that this species is in.

conversion_factor()

Returns the Parameter acting as conversion factor for this species, or the model default if not set (and None if that isn’t set either).

When calculating the rate of change of the species, multiplying by this factor converts from the species units to “number of reaction events”.

initial_value()

Returns a myokit.Expression (or None) for this species’ initial value, and a boolean indicating whether initial value is provided in amount (True) or in concentration (False).

is_amount()

Returns True only if this species is defined as an amount (not a concentration).

is_boundary()

Returns True only if this species is at a reaction boundary.

is_constant()

Returns True only if this species is constant.

is_rate()

Returns True if this quantity’s value is defined through a rate, else False.

set_conversion_factor(factor)

Sets a Parameter as conversion factor for this species, see conversion_factor().

set_initial_value(value, in_amount=None)

Sets a myokit.Expression for this species’ initial value.

in_amount is a boolean that indicates whether the initial value is measured in amount (True) or concentration (False). If set to None value is treated to have the same units as the species.

set_substance_units(units)

Sets the units this species amount (not concentration) is in.

set_value(value, is_rate=False)

Sets a myokit.Expression for this quantity’s value.

Arguments:

value
An expression
rate
Set to True if the expression gives the rate of change of this variable.
sid()

Returns this species’s sid.

substance_units()

Returns the units an amount of this species (not a concentration) is in, or the model default if not set.

value()

Returns a myokit.Expression for this quantity’s value, or None if not set.

class myokit.formats.sbml.SpeciesReference(species, sid=None)

Represents a reference to a reactant or product species in an SBML reaction.

A species reference acts as a Quantity, where the value represents the species’ stoichiometry.

initial_value()
Returns a myokit.Expression for this quantity’s initial value,
or None if not set.
is_rate()

Returns True if this quantity’s value is defined through a rate, else False.

set_initial_value(value)

Sets a myokit.Expression for this quantity’s initial value.

set_value(value, is_rate=False)

Sets a myokit.Expression for this quantity’s value.

Arguments:

value
An expression
rate
Set to True if the expression gives the rate of change of this variable.
sid()

Returns this species reference’s SId, or None if not set.

species()

Returns the species this object refers to.

value()

Returns a myokit.Expression for this quantity’s value, or None if not set.

SBML Parsing

class myokit.formats.sbml.SBMLParser

Parses SBML models, creating an SBML Model structure that can be converted to a myokit.Model object.

Support notes:

  • SBML older than Level 2 version 1 is unlikely to work.
  • Algebraic rules are not supported.
  • Constraints are not supported.
  • Events are not supported.
  • Function definitions are not supported.
  • Local parameters in reactions are not supported.
  • Units “celsius” are not supported.
  • Since SBML does not support units in equations, variable units will be set, but RHS units will not.
parse(element)

Parses an SBML document rooted in the given ElementTree element and returns a myokit.Model.

parse_file(path)

Parses the SBML file at path and returns a myokit.Model.

parse_string(text)

Parses the SBML XML in the string text and returns a myokit.Model.

class myokit.formats.sbml.SBMLParsingError(message, element=None)

Thrown if an error occurs when parsing SBML.

The argument element can be used to pass in an element that caused the error.