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. 2016 Apr 5:17:154.
doi: 10.1186/s12859-016-1000-2.

The systems biology format converter

Nicolas Rodriguez  1   2 , Jean-Baptiste Pettit  1 , Piero Dalle Pezze  2 , Lu Li  1   2 , Arnaud Henry  1 , Martijn P van Iersel  1 , Gael Jalowicki  1 , Martina Kutmon  3 , Kedar N Natarajan  1 , David Tolnay  4 , Melanie I Stefan  4 , Chris T Evelo  3 , Nicolas Le Novère  5   6
Affiliations

The systems biology format converter

Nicolas Rodriguez et al. BMC Bioinformatics. .

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.

Keywords: Converter; Format; SBML; Systems biology.

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Figures

Fig. 1
Fig. 1
SBFC overview. Overview for the software package SBFC. At the SBFC core a general converter translates a general model into another. Instantiations of general model and general converter are easily implemented in SBFC, providing users with a wide range of options for converting between specific model formats. Software libraries for importing or exporting model formats can be reused by different converters. For instance, the converter SBML2BioPAX currently uses the software libraries JSBML to import an SBML model, and PAXTOOLS to export it
Fig. 2
Fig. 2
Creation of complex converters. a In this scenario, three existing formats (A, B, and C) and two converters (A2B and B2C) are considered. Each of the A, B and C classes represents a different format and implements the interface GeneralModel. The converters extend the GeneralConverter class and translate from A to B, and from B to C respectively. b A new converter A2C translating from A to C, can be added effortlessly by invoking the method convert() implemented in the converters A2B and B2C. c Java source code illustrating the implementation of the method convert() for the converter class A2C
Fig. 3
Fig. 3
SBFC standalone graphical user interface. A simple GUI is provided to quickly convert a file. The user can browse and select a file, choose a converter, select a destination for the resulting conversion an launch the job. The result can optionally be displayed in a separate window
Fig. 4
Fig. 4
SBFC online. After selecting the input format, the available output format list is updated accordingly. A short description about the selected model format appears once an item from the combobox is selected. Three methods to submit the files to be converted are offered: file upload, model URL, and copy/paste. Files can be uploaded via a dialog window or by simply dragging and dropping them on the red box. Several files can be loaded before launching the conversion. The result page presents a list of all conversion jobs. Until the job is completed, a red “pending” box is displayed. The box turns to a green “complete” when the resulting files are available
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