Systems Biology Markup Language

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The Systems Biology Markup Language (Engl. For systems biology modeling language ), short SBML is a machine-readable to XML -based data exchange format for representing biochemical models. Biochemical models that can be represented are, for example, metabolic networks, signal transduction pathways and gene regulatory networks.

background

Since the beginning of the 3rd millennium, the life sciences have experienced a shift in what knowledge is pursued. In summary, this holistic approach can be referred to as systems biology , the development of which in the context of -omics is largely based on the acquisition of enormous amounts of data using so-called high-throughput technologies .

While the data volumes were organized in classic databases at the beginning , the call for a data exchange format was also pushed forward in order to be able to create and distribute completed models across software and platforms. The SBML meets this call in the field of modeling biochemical networks .

development

The SBML project was initiated by Hamid Bolouri at the "First Workshop on Software Platforms for Systems Biology" in April 2000. Under the chairmanship of John Doyle and Hiroaki Kitano, the first development stage at the Institute for Control and Dynamic Systems (CDS) took place on California Institute of Technology (Caltech). The development was primarily carried out by Michael Hucka, Herbert Sauro, Andrew Finney and Hamid Bolouri and was provisionally completed in June 2007 in Specification Level 2 Version 3. The financial basis for the development work was provided by the Japan Science And Technology Corporation's Exploratory Research for Advanced Technology program (JST ERATO) provided.

In the meantime, the focus of further developments has been directed entirely towards expansion packages in the SBML Level 3 standard.

Specifications

SBML is defined within an XML schema . The various specifications are referred to as levels, which are further graded by the version . The specification level 3 version 1 defines the current standard. It should be noted that previous specifications, e.g. B. l1v1, l2v1 or l2v4 has been classified as deprecated (out of date and no longer supported) by the developers.

Although Level 3 is largely a superset of Levels 1 and 2, the developers put emphasis on the fact that all specifications are coexistent. Level 2 is an extension in that some structural inconsistencies have been removed. Furthermore, through the integration of the MathML namespace, a standard is now used to describe non-linear mathematical relationships.

Implementations

Since the first definition, the C library libSBML has been a powerful software solution for reading SBML files, changing their content in memory and being able to write them again. libSBML is characterized by the fact that it provides numerous wrappers for other programming languages ​​( C ++ , C-Sharp , Java , Matlab , Octave , Python , Perl and Ruby ). In the case of cross-platform programming languages, however, the dependency on an internal C library can be problematic. Therefore, the special library JSBML has been developed since 2009 to support SBML in Java , of which stable versions are now available.

literature

  • M. Hucka et al .: The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models. In: Bioinformatics. Vol. 19, no. 4, 2003, pp. 524-531.
  • A. Finney and M. Hucka: Systems biology markup language: Level 2 and beyond. In: Biochem. Soc. Trans. 31. 2003, pp. 1472-1473.

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