SBML

The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today. The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today. Late in the year 1999 through early 2000, with funding from the Japan Science and Technology Corporation (JST), Hiroaki Kitano and John C. Doyle assembled a small team of researchers to work on developing better software infrastructure for computational modeling in systems biology. Hamid Bolouri was the leader of the development team, which consisted of Andrew Finney, Herbert Sauro, and Michael Hucka. Bolouri identified the need for a framework to enable interoperability and sharing between the different simulation software systems for biology in existence during the late 1990s, and he organized an informal workshop in December 1999 at the California Institute of Technology to discuss the matter. In attendance at that workshop were the groups responsible for the development of DBSolve, E-Cell, Gepasi, Jarnac, StochSim and The Virtual Cell. Separately, earlier in 1999, some members of these groups also had discussed the creation of a portable file format for metabolic network models in the BioThermoKinetics (BTK) group. The same groups who attended the first Caltech workshop met again on April 28–29, 2000, at the first of a newly created meeting series called Workshop on Software Platforms for Systems Biology. It became clear during the second workshop that a common model representation format was needed to enable the exchange of models between software tools as part of any functioning interoperability framework, and the workshop attendees decided the format should be encoded in XML. The Caltech ERATO team developed a proposal for this XML-based format and circulated the draft definition to the attendees of the 2nd Workshop on Software Platforms for Systems Biology in August, 2000. This draft underwent extensive discussion over mailing lists and during the 2nd Workshop on Software Platforms for Systems Biology, held in Tokyo, Japan, in November 2000 as a satellite workshop of the ICSB 2000 conference. After further revisions, discussions and software implementations, the Caltech team issued a specification for SBML Level 1, Version 1 in March, 2001. SBML Level 2 was conceived at the 5th Workshop on Software Platforms for Systems Biology, held in July 2002, at the University of Hertfordshire, UK. By this time, far more people were involved than the original group of SBML collaborators and the continued evolution of SBML became a larger community effort, with many new tools having been enhanced to support SBML. The workshop participants in 2002 collectively decided to revise the form of SBML in Level 2. The first draft of the Level 2 Version 1 specification was released in August 2002, and the final set of features was finalized in May 2003 at the 7th Workshop on Software Platforms for Systems Biology in Ft. Lauderdale, Florida.