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.
Several others converters are in development:
- SBGN related:
- SBML to SBGN-ML [SEE BELOW]
- 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/
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.
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.
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.
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.
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, ..)
The mission of the SBGN-ML project is to develop high quality, standard graphical languages for representing biological processes and interactions. [IN PROGRESS]
A list of scripts for converting between SBML levels and versions. Scripts for converting SBML model annotation from Miriam (urn) to identifiers.org (url) and viceversa are also provided. [IN PROGRESS]
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).
- How to set up the Systems Biology Format Converter framework in Eclipse.
- How to set up the Systems Biology Format Converter framework in Eclipse (documentation for the new OSGi version of SBFC) [IN PROGRESS]
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!
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.
- MDL to SBML: this converter is depending on the SBML L3 spatial package and it is still in development.
- SBML to XPP (outdated XSL version)
- SBML to Dot (outdated XSL version)
- SBML to BioPax (outdated XSL version)
- SBML to Scilab (outdated XSL version)
- SBML to CellML (outdated XSL version)
- CellML to SBML (outdated XSL version)