sbmlimport
Import SBML-formatted file
Description
Examples
Get Adjacency Matrix of SimBiology Model
Load the lotka model.
m1 = sbmlimport("lotka.xml");
Get the adjacency matrix of the model.
[M,Headings] = getadjacencymatrix(m1)
M = 7x7 sparse double matrix (9 nonzeros)
(5,1) 1
(5,2) 1
(6,3) 1
(7,4) 1
(1,5) 1
(2,5) 1
(2,6) 1
(3,6) 1
(3,7) 1
Headings = 7x1 cell
{'x' }
{'y1' }
{'y2' }
{'z' }
{'Reaction1'}
{'Reaction2'}
{'Reaction3'}
Input Arguments
File
— Name of SBML file
character vector | string scalar
Name of an SBML file, specified as a character vector or string scalar.
Specify a file name or a path and file name. The acceptable file extensions are
.sbml
or .xml
. You can also specify a
URL.
The function supports SBML Level 3 Version 1 and earlier. For functional characteristics and limitations, see SBML Support.
Data Types: char
| string
References
[1] Finney, A., Hucka, M., (2003). Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions.
Version History
Introduced before R2006aR2022a: Support for URL schemes other than HTTP and HTTPS has been removed
Support for passing in a URL that is not HTTP
and
HTTPS
has been removed in a future release. Download the file locally
first and then use the file name as an input to sbmlimport
instead.
R2017b: sbmlimport
adds initial assignment rule when importing some SBML models
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 settinghasOnlySubstanceUnits = 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 settinghasOnlySubstanceUnits = 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 theDimensionalAnalysis
property set to false to prevent dimensional analysis errors.
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