sbmlimport

Import SBML-formatted file

Syntax

modelObj = sbmlimport(File)

Description

modelObj = sbmlimport(File) imports File, a Systems Biology Markup Language (SBML)-formatted file, into MATLAB and creates a Model object modelObj.

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 = 7×7 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 = 7×1 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 R2006a

R2026a: Support for SBML version 3.2

SimBiology supports SBML level 3 version 2 (L3V2). You can import and export SBML L3V2 formatted files using sbmlimport and sbmlexport, respectively. For details, see SBML Support.

To specify the SBML version, use the Version name-value argument of sbmlexport.

SBML level 3 no longer supports the outside attribute. Therefore, if you want to preserve the compartment ownership (Owner) information from your model, use an earlier SBML version, such as 2.5. Otherwise, if you save your SimBiology model in the 3.2 format and reimport it, you see the following changes in the model:

• No compartments are nested in the model and in the Diagram view of SimBiology Model Builder.

• The compartment properties Compartments and Owner are empty.

Note that the SBML version you use does not affect the model simulation results.

R2022a: 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 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.