title: The systems biology format converter.
abstract: BACKGROUND
  Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However, they have been developed independently, resulting in redundancy of efforts and lack of synergy.
  
  
  RESULTS
  Here we present the System Biology Format Converter (SBFC), which provide a generic framework to potentially convert any format into another. The framework currently includes several converters translating between the following formats: SBML, BioPAX, SBGN-ML, Matlab, Octave, XPP, GPML, Dot, MDL and APM. This software is written in Java and can be used as a standalone executable or web service.
  
  
  CONCLUSIONS
  The SBFC framework is an evolving software project. Existing converters can be used and improved, and new converters can be easily added, making SBFC useful to both modellers and developers. The source code and documentation of the framework are freely available from the project web site.
authors.affiliation: EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK.|The Babraham Institute, Babraham Campus, CB22 3AT, Cambridge, UK.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Rodriguez
authors.affiliation: EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK.
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Pettit
authors.affiliation: The Babraham Institute, Babraham Campus, CB22 3AT, Cambridge, UK.
authors.forename: Piero
authors.initials: P
authors.lastname: Dalle Pezze
authors.affiliation: EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK.|The Babraham Institute, Babraham Campus, CB22 3AT, Cambridge, UK.
authors.forename: Lu
authors.initials: L
authors.lastname: Li
authors.affiliation: EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Henry
authors.affiliation: EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK.
authors.forename: Martijn P
authors.initials: MP
authors.lastname: van Iersel
authors.affiliation: EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK.
authors.forename: Gael
authors.initials: G
authors.lastname: Jalowicki
authors.affiliation: Department of Bioinformatics, BiGCaT, Maastricht University, Maastricht, 6229, The Netherlands.
authors.forename: Martina
authors.initials: M
authors.lastname: Kutmon
authors.affiliation: EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK.
authors.forename: Kedar N
authors.initials: KN
authors.lastname: Natarajan
authors.affiliation: California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, 91125, CA, USA.
authors.forename: David
authors.initials: D
authors.lastname: Tolnay
authors.affiliation: California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, 91125, CA, USA.
authors.forename: Melanie I
authors.initials: MI
authors.lastname: Stefan
authors.affiliation: Department of Bioinformatics, BiGCaT, Maastricht University, Maastricht, 6229, The Netherlands.
authors.forename: Chris T
authors.initials: CT
authors.lastname: Evelo
authors.affiliation: EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK. lenov@babraham.ac.uk.|The Babraham Institute, Babraham Campus, CB22 3AT, Cambridge, UK. lenov@babraham.ac.uk.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Le Novère
mesh_terms: D016208:Databases, Factual; D020407:Internet; D049490:Systems Biology; D014584:User-Computer Interface
keywords: Converter; Format; SBML; Systems biology