[4] 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.
[5] 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.
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.
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.
The inevitable discovery of limitations and errors led to the development of SBML Level 2 Version 2, issued in September 2006.
Version 4 was finalized after the SBML Forum meeting held in Gothenburg, Sweden, as a satellite workshop of ICSB 2008 in the fall of 2008.
It contains numerous significant changes in syntax and constructs from Level 2 Version 4, but also represents a new modular base for continued expansion of SBML's features and capabilities going into the future.
This revision included a number of textual (but not structural) changes in response to user feedback, thereby addressing the list of errata collected over many years for the SBML Level 2 Version 4 specification.
SBML is sometimes incorrectly assumed to be limited in scope only to biochemical network models because the original publications and early software focused on this domain.
SBML's purpose is to serve as a lingua franca—an exchange format used by different present-day software tools to communicate the essential aspects of a computational model.
Or, alternatively, a package might construct a discrete stochastic representation of the model and use a Monte Carlo simulation method such as the Gillespie algorithm.
The "fbc" package provides support for constraint-based modeling,[16] frequently used to analyze and study biological networks on both a small and large scale.
This package supports the representation of models where an in-depth knowledge of the biochemical reactions and their kinetics is missing and a qualitative approach must be used.
For example, qualitative models typically associate discrete levels of activities with entity pools; consequently, the processes involving them cannot be described as reactions per se, but rather as transitions between states.
The SBML Level 3 Layout package provides a specification for how to represent a reaction network in a graphical form.
The SBML Level 3 package only deals with the information necessary to define the position and other aspects of a graph's layout; the additional details necessary to complete the graph—namely, how the visual aspects are meant to be rendered— are the purview of the separate SBML Level 3 package called Rendering (nicknamed "render").
[25] That, in turn, was based on the SCAMP modeling application[26] which ultimately drew inspiration from the DSL language developed by David Garfinkel for the BIOSIM simulator.
Antimony also supports the following SBML packages: Hierarchical Model Composition, Flux Balance Constraints, and Distributions.
The following example illustrates Antimony being used to describe a simple enzyme-kinetics model: As of February 2020, nearly 300 software systems advertise support for SBML.
SBML has been and continues to be developed by the community of people making software platforms for systems biology, through active email discussion lists and biannual workshops.