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The System Biology Format Converter

We are developing a new converter framework that will allow us and contributors to add easily new converter. The framework is developed on sourceforge, see the System Biology Format Converter project pages.

It is currently supporting SBML to BioPax 2 and 3, SBML to XPP and SBML to Octave.

Online converters service

We are testing a new online service that would allow you to convert your own models yourself, either via the online converters web page or via webservices.
It is using the System Biology Format Converter (SBFC) in the background so only the converters already integrated in the SBFC are available. It is in a beta stage and is only tested on the latest versions of firefox at the moment.



SBML Converters

Here is a list of all the conversions to and from SBML that we are developing and maintaining.

SBML to Octave

GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.

SBML to XPP

XPP-Aut is a numerical analysis software. It permits to solve differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.

SBML to SciLab

SciLab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications.

SBML to CellML   &  CellML to SBML

CellML is an open standard based on the XML markup language like SBML. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The main difference between CellML and SBML is that the former is based on modules while the latter is based on hierarchical components.

SBML to BioPax

The main objective of the BioPAX initiative is to develop a data exchange format for biological pathways that is flexible, extensible, optionally encapsulated and compatible with other standards and can be widely adopted in a timely manner.

SBML to Graph (SBGN PD like)

The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools.
SBGN Process Description (PD) language shows the temporal courses of biochemical interactions in a network. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram.

GraphViz is an open source graph visualization software. The language used to encode the graphics processed by GraphViz is called DOT. Note that a "dot" file can be used with other graphical software.

Scalable Vector Graphics (SVG) is a language for describing two-dimensional graphics and graphical applications in XML. It is an open standard created by the World Wide Web Consortium.

Download

You can download all these converters from the BioModels Database project on SourceForge.

Getting Help and Support

Please send any help requests or bug reports to :


biomodels-net-support at lists.sourceforge.net
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