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Converters

SBML is a lingua franca in systems biology. In order to further facilitate exchange of models, many software tools have been developed to convert between SBML and other formats. For the benefit of the SBML-using community, this page provides a list of conversion tools of which we are aware. Please contact sbml-team@googlegroups.com if we have missed any. These tools are third-party software, and not the product of the SBML Team.

Note that the conversion tools listed here differ in their coverage of SBML—some may be more complete than others. In addition, different tools are in different states of development, maturity and maintenance status.

Conversion to SBML

BioPAX to SBML

The Biological Pathways Exchange format (BioPAX) is a standard language that aims to enable integration, exchange and analysis of biological pathway data. It is expressed in OWL/XML. BioPAX2SBML, developed at the University of Tuebingen, is capable of translating BioPAX (Level 2 and 3) into SBML (Level 3 Version 1 with the qual package) including reactions and relations in one single model.

Qualitative translation of relations from BioPAX to SBML
Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, and Zell A.
Paper published in Bioinformatics, 28: 2648-2653, 2012.
Description of a tool to convert models encoded in BioPAX into SBML with the Qual package.

CellML to SBML

CellML is a language being developed by the Auckland Bioengineering Institute to store and exchange computer-based mathematical models.

Both Antimony and JSim can be used to convert between SBML and CellML, in addition to each program's native model definition languages.

SBML and CellML Translation in Antimony and JSim
Smith L.P., Butterworth E., Bassingthwaighte J., Sauro H.
Paper published in Bioinformatics, 10.1093/bioinformatics/btt641, 2013.
Description of two tools that each convert CellML and SBML models, and the challenges discovered.

An XSLT conversion tool is provided by the BioModels Database group. Only CellML 1.0 is imported. Only SBML Level 2 is exported.

CellML2SBML: Conversion of CellML into SBML
Schilstra M.J., Li L., Matthews J., Finney A., Hucka M., Le Novère N.
Paper published in Bioinformatics, 18: 1018-1020, 2006.
Description of a tool to convert models encoded in CellML into SBML.

KEGG to SBML

KEGG PATHWAY Database is a collection of manually drawn biochemical pathway maps. Due to the widespread use of these maps in systems biology, several software tools have been developed to convert KEGG maps into SBML.

KEGGtranslator

KEGGtranslator is a Java tool developed at the University of Tuebingen which can convert files encoded in KGML format into SBML Level 2 and 3.

Precise generation of systems biology models from KEGG pathways
Wrzodek C., Büchel F., Ruff M., Dräger A., Zell A.
Paper published in BMC Systems Biology, 7:15, 2013.
Description of an updated version of KEGGtranslator.
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
Wrzodek C., Dräger A., Zell A.
Paper published in Bioinformatics, 27: 2314-2315, 2011.
Description of a tool to convert KEGG Pathway files into SBML.

KEGGconverter

KEGGconverter is a tool implemented in Java which can convert Metabolic Pathways encoded in KGML format into fully functional and Kinetic enabled SBML models. The tool seems currently unmaintained.

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database
Moutselos K, Kanaris I, Chatziioannou A, Maglogiannis I, Kolisis F.N.
Paper published in BMC Bioinformatics, 10:324, 2009.
Description of a tool to convert KEGG metabolic maps into SBML.

Conversion from SBML

SBML to BioPAX

The Biological Pathways Exchange format (BioPAX) is a standard language that aims to enable integration, exchange and analysis of biological pathway data. It is expressed in OWL/XML.

SBFC SBML to BioPAX

The Systems Biology Format Converter provides a Java module converting SBML into BioPAX. All Levels and Versions of SBML are imported. BioPAX Level 2 and Level 3 are exported.

XSL SBML to BioPAX

Prior to SBFC, an XSL-based converter from SBML to BioPAX was provided. Only SBML Level 2 is imported. Only BioPAX Level 2 is exported. The converter is currently unmaintained.

SBML to CellML

CellML is a language being developed by the Auckland Bioengineering Institute to store and exchange computer-based mathematical models.

An XSLT conversion tool has been developed by the BioModels Database group. Only SBML Level 2 is imported. Only CellML 1.0 is exported.

Both Antimony and JSim can be used to convert between SBML and CellML, in addition to each program's native model definition languages.

SBML and CellML Translation in Antimony and JSim
Smith L.P., Butterworth E., Bassingthwaighte J., Sauro H.
Paper published in Bioinformatics, 10.1093/bioinformatics/btt641, 2013.
Description of two tools that each convert CellML and SBML models, and the challenges discovered.

SBML to dot

The dot language is the format used by the software Graphviz to describe networks.

SBFC SBML to dot

The Systems Biology Format Converter provides a Java module converting SBML into dot language. All Levels and Versions of SBML are imported.

XSL SBML to dot

Prior to SBFC, the BioModels team provided an XSL-based converter. Only SBML Level 2 is imported. The converter is currently unmaintained.

SBML to GRN

SBML2GRN is a tool developed by the Hans-Knöll-Institute and the University of Tuebingen aiming to ease the encoding of gene regulatory networks (GRN) in SBML. The tool is encoded in Java and provides an interface with R.

SBML to LaTeX

LaTeX is a typesetting system designed for the production of technical and scientific documentation. The Center for Bioinformatics Tübingen developed a software tool using SBML and its annotation to generate a human readable report written in LaTeX.

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports
Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A.
Paper published in Bioinformatics, 25(11):1455-1456, 2009.
Description of a tool to generate text versions of SBML models in the LaTex and PDFformats.

SBML to Octave

GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable. The Systems Biology Format Converter provides a Java module converting SBML into Octave language. All Levels and Versions of SBML are imported.

SBML to Scilab

SciLab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. An XSLT conversion tool has been developed by the BioModels Database group. Only SBML Level 2 is imported.

SBML to XPP

XPP is a tool for studying dynamical systems. Problems and procedures can be encoded in a scripting format.

SBFC SBML to XPP

The Systems Biology Format Converter provides a Java module converting SBML into XPP script. All Levels and Versions of SBML are imported.

XSL SBML to XPP

Prior to SBFC, an XSL-based converter was provided by the BioModels Database group. Only SBML Level 2 is imported. The converter is currently unmaintained.

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This page was last modified 22:40, 22 October 2016.



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