History of SBML
In the year 2000, with funding from the Japan Science and Technology Agency (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. Their initial work focused on a system to allow a subset of existing simulation software packages to communicate. This subset consisted of DBSolve, E-Cell, Gepasi, Jarnac, StochSim and The Virtual Cell. The groups developing these tools met on April 28-29, 2000 at the ERATO Software Platforms for Molecular Biology workshop, held at the California Institute of Technology. It became clear during the workshop that a common model representation format was needed to enable exchanging models between software tools. The workshop attendees decided the format should be encoded in XML. The Caltech ERATO team developed a proposal for a format and circulated the draft definition to the meeting attendees in August, 2000. This draft underwent extensive discussion over mailing lists and during the Second 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 and discussions, 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.
The next iteration of SBML took two years in part because software developers requested time to absorb and understand the larger and more complex SBML Level 2. The inevitable discovery of limitations and errors lead to the development of SBML Level 2 Version 2, issued in September 2006. By this time, the team of SBML Editors (who reconcile proposals for changes and write a coherent final specification document) had changed and now consisted of Andrew Finney, Michael Hucka and Nicolas Le Novère.
2007 saw the addition of two more SBML Editors (Sarah Keating and Stefan Hoops) and the development of SBML Level 2 Version 3 after countless contributions by and discussions with the SBML community.