SBFC

SBFC, the Systems Biology Format Converter, is a Java framework and online service for translating between the file formats used in computational systems biology. It was created by Nicolas Rodriguez as a collaborative, community-driven project, and was described in a 2016 BMC Bioinformatics paper. A hosted web application has long been deployed at the EMBL-EBI BioModels team, offering conversion through file upload, URL reference, or copy-paste, with jobs and results retained for at most 72 hours for privacy. It is free software distributed under the GNU LGPL and supported by the BBSRC, EMBL-EBI, and the US NIH.

Architecturally, SBFC is built around two abstractions: a GeneralModel interface, which defines how a given format is read from and written to a file or string, and a GeneralConverter abstract class, which implements a generic conversion algorithm. Rather than a single universal intermediate representation, converters are pairwise transformations that can be chained by composition — a new A-to-C converter can reuse existing A-to-B and B-to-C steps by invoking their convert() methods. The framework is implemented in Java SE and leans on established libraries, using JSBML (or libSBML) to parse SBML and Paxtools (Paxtools) to emit BioPAX, so it does not reimplement these standards itself.

Most conversion paths originate from SBML, reflecting its role as the central exchange language for kinetic and constraint-based models. Bundled converters export SBML to executable simulation code (MATLAB, Octave, and XPP), to the graphical process-description standard SBGN-ML, to BioPAX, and to visualization formats including GraphViz DOT and the CellDesigner-adjacent APM. Community modules add other paths such as GPML-to-BioPAX and MDL-to-SBML, connecting pathway resources like GPML into the SBML/BioPAX ecosystem. This makes SBFC a bridge between the modeling world and both graph-visualization and pathway-database formats, complementing tools like Paxtools and viewers such as Cytoscape.

Its strengths are a clean, extensible converter model, multiple deployment modes (command line, GUI, REST-like web services with a Java client, and the EBI web app), and reuse of mature parsers. Limitations follow from its scope: conversions are largely SBML-centric and often lossy, since target formats like Dot or executable code capture only part of a model's semantics; integrating non-Java external converters via Runtime exec() reintroduces platform dependence; and the project has seen limited active development in recent years, so format coverage lags newer standards.