Import SBML-formatted file
sbmlimport
adds an initial assignment rule when importing SBML models with the following conditions.
If an SBML model has a species s initialized to X using initialAmount
and has the attribute setting hasOnlySubstanceUnits = false
:
SimBiology sets the initial amount of s to X.
If the model does not already have an initial assignment or repeated assignment rule for s, SimBiology adds an initial assignment rule s = X / V
, where V is the compartment volume (capacity). This rule ensures that the initial amount of s is a concentration unit.
If the model already has an initial assignment or repeated assignment rule for s, then SimBiology does not use the value X. Instead, SimBiology evaluates the rule and sets the appropriate initial amount.
If an SBML model has a species s initialized to X using initialConcentration
and has the attribute setting hasOnlySubstanceUnits = true
:
SimBiology sets the initial amount of s to X.
If the model does not already have an initial assignment or repeated assignment rule for s, SimBiology adds an initial assignment rule s = X * V
, where V is the compartment volume (capacity). This rule ensures that the initial amount of s is an amount unit.
If the model already has an initial assignment or repeated assignment rule for s, then SimBiology does not use the value X. Instead, SimBiology evaluates the rule and sets the appropriate initial amount.
If a species s in an SBML model has the attribute setting
hasOnlySubstanceUnits
= true without any units defined,
SimBiology issues a warning and sets the species amount unit to a default unit (mole) to
ensure it is interpreted as an amount, not a concentration. The imported SimBiology
model has the DimensionalAnalysis
property set to false to prevent
dimensional analysis errors.
modelObj = sbmlimport(
File
)
modelObj = sbmlimport(
imports File
)File
,
a Systems Biology Markup Language (SBML)-formatted file, into MATLAB
and creates a model object modelObj
.
File
is a character vector or string specifying a file name or a
path and file name supported by your operating system. File
extensions are .sbml
or
.xml
.File
can also be a URL, if you
have the Java® programming language.
sbmlimport
supports SBML Level 3 Version
1 and earlier.
For functional characteristics and limitations, see SBML Support.
|
Character vector or string specifying either of the following:
|
Import SBML model:
sbmlobj = sbmlimport('oscillator.xml');
Finney, A., Hucka, M., (2003). Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions.
DimensionalAnalysis
| get
| sbiosimulate
| sbmlexport
| set