SBML export interface for the systems biology toolbox for MATLAB

Hening Schmidt; Gunnar Drews; Julio Vera; Olaf Wolkenhauer

doi:10.1093/bioinformatics/btm105

SBML export interface for the systems biology toolbox for MATLAB

Hening Schmidt^*, Gunnar Drews, Julio Vera, Olaf Wolkenhauer

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

Summary: 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.

Original language	English
Pages (from-to)	1297-1298
Number of pages	2
Journal	Bioinformatics
Volume	23
Issue number	10
DOIs	https://doi.org/10.1093/bioinformatics/btm105
State	Published - 15 May 2007
Externally published	Yes

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10.1093/bioinformatics/btm105

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title = "SBML export interface for the systems biology toolbox for MATLAB",

abstract = "Summary: 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.",

author = "Hening Schmidt and Gunnar Drews and Julio Vera and Olaf Wolkenhauer",

year = "2007",

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AU - Schmidt, Hening

AU - Drews, Gunnar

AU - Vera, Julio

AU - Wolkenhauer, Olaf

PY - 2007/5/15

Y1 - 2007/5/15

N2 - Summary: 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.

AB - Summary: 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.

UR - https://www.scopus.com/pages/publications/34447303074

U2 - 10.1093/bioinformatics/btm105

DO - 10.1093/bioinformatics/btm105

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SN - 1367-4803

VL - 23

SP - 1297

EP - 1298

JO - Bioinformatics

JF - Bioinformatics

IS - 10

ER -

SBML export interface for the systems biology toolbox for MATLAB

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