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Published on: February 8, 2017
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The systems biology format converter
Nicolas Rodriguez1,2, Jean-Baptiste Pettit1, Piero Dalle Pezze2
1EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Cambridge, Hinxton, UK.
BMC Bioinformatics
|April 6, 2016
Summary
The System Biology Format Converter (SBFC) offers a unified framework for converting computational models between various formats, addressing interoperability challenges in systems biology research. This Java-based tool enhances model accessibility for researchers and developers.
Area of Science:
- Systems Biology
- Computational Biology
- Bioinformatics
Background:
- Interoperability issues hinder progress in systems biology research due to diverse computational model formats.
- Existing model conversion tools are often developed independently, leading to duplicated efforts and limited synergy.
Purpose of the Study:
- To present a generic, extensible framework for converting computational models between different formats.
- To address the need for a unified solution for systems biology model interoperability.
Main Methods:
- Developed the System Biology Format Converter (SBFC) as a Java-based software.
- Implemented a framework supporting multiple format conversions, including SBML, BioPAX, and Matlab.
- Designed SBFC for use as a standalone executable or a web service.
Main Results:
- SBFC provides a generic framework capable of converting between numerous systems biology model formats.
- The framework currently supports conversions for SBML, BioPAX, SBGN-ML, Matlab, Octave, XPP, GPML, Dot, MDL, and APM.
- The software is implemented in Java and offers flexible deployment options.
Conclusions:
- SBFC is an evolving software project designed to be easily extended with new converters.
- The framework benefits both systems biology modelers and software developers by improving accessibility and reducing redundancy.
- Source code and documentation are freely available, promoting collaborative development and adoption.
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