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The System Biology Format Converter

The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules.SBFC allows anyone to easily add new converters and to integrate existing converters with a minimum of changes. We will also allow to combine several existing converters.

The SBFC framework currently supports conversion from SBML to BioPAX Level 2 and Level3, XPP, Octave and Dot.

Several others converters are in development:

  • SBGN related:
    • SBML to SBGN-ML
    • SBGN-ML to an SBGN enriched graphical representation designed for use in a web browser

The main Sourceforge page for the SBFC project is http://sourceforge.net/projects/sbfc/

Converters

Here is a small description of all the conversions currently supported. You can access to a more detailed page by clicking on a converter name.

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 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 Dot

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 and you have the possibility to convert them to PNG, SVG, ..)

Download

You can download all those converters from the SBFC project on SourceForge.

There is not yet any official release, so you would have to download the sources from the Subversion repository:

svn co https://sbfc.svn.sourceforge.net/svnroot/sbfc/trunk sbfc

### The compiled java classes are included and some helper scripts are also there
### but if you make any changes to the code you need to compile the project

### To do so, you just need to have [http://ant.apache.org/ Ant] installed.
### At the root of the project, just type :
ant jar

### Your changes should be integrated in the sbfc jar file now.


Online converters service

We are testing a new service that allow anybody to convert models online.

Access to this service can be done via: http://www.ebi.ac.uk/compneur-srv/converters/ or web services [BETA]. It uses the System Biology Format Converter (SBFC) in the background so only the converters already integrated in SBFC are available. It is in a beta stage and is only tested on the latest versions of Firefox at the moment (known to not work properly in IE8, other browsers apart from IE should be fine).


Development

  • How to set up the Systems Biology Format Converter framework in Eclipse (documentation for the new OSGi version of SBFC).

Getting Help and Support

We are developing the user guide and developer documentations but at the moment the documentation is very limited, so do not hesitate to send us an email.


If you wish to contact the team in charge of the development and maintenance of this framework, please use the following email address:

biomodels-net-support [at] lists.sourceforge.net

We welcome new contributors!

There are several dedicated trackers: bug reports or feature requests.

Other Converters

Here is a list of converters that are not yet integrated with SBFC, either because they are still in early stages or not maintained any more or we just didn't had the time to integrate/update them.

You can access to a more detailed page by clicking on a converter name.