SBML export interface for the systems biology toolbox for MATLAB | Zendy

Hening Schmidt | Zendy; Gunnar Drews | Zendy; Julio Vera | Zendy; Olaf Wolkenhauer | Zendy

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SBML export interface for the systems biology toolbox for MATLAB

Author(s) -

Hening Schmidt,

Gunnar Drews,

Julio Vera,

Olaf Wolkenhauer

Publication year - 2007

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btm105

Subject(s) - sbml , toolbox , computer science , interface (matter) , markup language , graphical user interface , programming language , matlab , documentation , user interface , operating system , xml , maximum bubble pressure method , bubble

In this application note, we present an Systems biology markup language (SBML) export interface for the Systems Biology Toolbox for MATLAB. This interface allows modelers to automatically convert models, represented in the toolbox's own format (SBmodels) to SBML files. Since SBmodels do not explicitly contain all the information that is required to generate SBML, the necessary information is gathered by parsing SBmodels. The export can be done in two different ways. First, it is possible to call the export from the command line, thereby directly converting a model to an SBML file. The second option is to inspect and edit the conversion results with the help of a graphical user interface and to subsequently export the model to SBML.

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