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.

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.

Input Arguments

File

Character vector or string specifying either of the following:

File name or path and file name supported by your operating system
URL

Examples

collapse all

Get Adjacency Matrix of SimBiology Model

Open Live Script

Load the lotka model.

m1 = sbmlimport("lotka.xml");

Get the adjacency matrix of the model.

[M,Headings] = getadjacencymatrix(m1)

M = 
   (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'}

References

Finney, A., Hucka, M., (2003). Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions.

Version History

Introduced before R2006a

expand all

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.