SBML

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

Background

Since the beginning of the third millennium, the life sciences experienced a shift in its which knowledge is pursued. In summary, this holistic approach under the concept of systems biology, based their development in the context of - omiks largely due to the acquisition of enormous amounts of data by means of so-called high -throughput technologies.

The data sets were organized at the beginning in classical databases so parallel got the call for a data exchange format feed in order to create and distribute software and completed models across platforms can. The SBML counters this reputation in the field of modeling of biochemical networks.

Development

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

Meanwhile, the focus of further developments is entirely focused on Level 3 expansion packs in the standard SBML.

Specifications

Defines SBML is within an XML schema. The various specifications are referred to as level, the experience with the version still a gradation. The specification Level 3 Version 1 defines the current standard. It should be noted that previous specifications, for example l1v1, l2v1 l2v4 or by the developers as deprecated ( outdated and no longer supported) was classified.

Although Level 3 is largely a superset of Level 1 and 2, the developers value the emphasis that all specifications are coexistent. Level 2 is an extension to the effect that some structural inconsistencies were canceled. Furthermore, a standard is now being used to describe non-linear mathematical relationships by integrating the MathML namespace.

Implementations

Since the first definition is consistent with the C library libSBML a powerful software solution available to read SBML files, change their content in memory and to be able to write again. libSBML is characterized by numerous wrappers for other programming languages ​​( C , C Sharp, Java, Matlab, Octave, Python, Perl and Ruby ) provide. In the case of cross-platform programming languages ​​, however, the function of an internal C library can be problematic. Therefore, since 2009, the special library JSBML is developed to support SBML in Java, of which stable versions are available now.

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