SBML development has been and continues to be motivated and directed by the systems biology community. The process is managed by the SBML Editors (see next question), but they do so under the control of the community. The editors collect proposals for changes to SBML from the SBML Working Groups and from other groups and individuals, and then seek to establish a consensus in the community about how to proceed with the proposals.

All together, the various efforts of the SBML Team have been supported by the following organizations: the National Institutes of Health (USA); the International Joint Research Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the Japanese Ministry of Agriculture; the Japanese Ministry of Education, Culture, Sports, Science and Technology; the BBSRC e-Science Initiative (UK); the DARPA IPTO Bio-Computation Program (USA); the Army Research Office's Institute for Collaborative Biotechn.

All the groups that have produced the software listed in Question 2 are involved to some extent in the development of SBML.

The Systems Biology Markup Language (SBML) is a machine-readable format for describing qualitative and quantitative models of biochemical networks. It can also be used to express the interactions of biochemical networks with other phenomena. By a ''biochemical network'', we mean a system consisting of biochemical entities linked by chemical reactions that alter, transport and/or transform the entities.

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SBML is designed to enable the exchange of biochemical network models between different software packages. The aim is to (1) enable the enable the exchange of models between software tools with little or no human intervention, thus allowing the tools to be properly integrated; and (2) enable these models to be published in electronic form alongside, for example, peer-reviewed journal articles. The emphasis in SBML is on supporting quantitative models.

SBML model consists of a set of chemical entities linked by reactions that can transform one entity into another or transport entities between compartments. A compartment in SBML is a location having a defined size or extent (which may be in terms of volume, area, or length). Every chemical species in an SBML model must be located in a compartment. SBML can represent not only biochemical networks, but also quantitative models of interaction between these networks and other phenomena.

SBML originated out of a workshop on software platforms for systems biology held in the year 2000 with funding by the Japan Science and Technology Corporation (JST). The original authors were Michael Hucka, Andrew Finney, Herbert Sauro and Hamid Bolouri, but SBML is now very much a community effort. Please see Section 8 for more details about the history of SBML. See Section 7 about how you can participate in SBML's evolution.

The Systems Biology Markup Language is formally defined in specification documents (see Question 4.2).

SBML is being developed in a series of levels, where each level adds new features and fixes problems with the previous level. The lowest-numbered levels provide fundamental features that are common to all biochemical network models. Higher-numbered levels add more features that are specific to particular classes of tools. Any level can be used as a standard for interchanging models.

The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A. , Cuellar, A. A., Dronov, S., Gilles, E. D., Ginkel, M., Gor, V., Goryanin, I. I., Hedley, W. J., Hodgman, T. C., Hofmeyr, J.-H., Hunter, P. J., Juty, N. S., Kasberger, J. L., Kremling, A., Kummer, U., Le Novère, N., Loew, L. M., Lucio, D.

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Not specifically. There is no reason why SBML models could not be stored in a database, nor is there any reason why you could not use SBML as a schema. However, this was not the motivation for creating SBML. An SBML model is meant to encode a consistent view of knowledge of a biological system. SBML is not meant to encode a large set of potentially conflicting knowledge about such a system.

The registration pages for the mailing list and the web forum are accessible from http://sbml.org/forums.

The list of tools supporting SBML has grown to over 100 at the time of this writing, and it is no longer feasible to maintain a list in this FAQ. Instead, we refer readers to the front page of the web site http://sbml.org, which gives a list of software and provides links to more information about them.

The BioModels Database provides a database of many dozens of models that have been published in the literature. The models in the database have been checked by humans to correspond to the publication and have been annotated with links to other data resources to make searching easier.

SBML Level 2 Version 1 was finalized in June 2003. SBML Level 2 Version 2 is in final draft stage and expected to be finalized in 2006. New development is oriented towards SBML Level 3.

The idea is that the units associated with every math entity in a model should be precisely defined, while at the same time allowing for reasonable default unit definitions. The set of math entities important in this regard includes variables, parameters and the result of equations.

We recommend SBML Level 2, despite the fact that at the moment more tools support Level 1, because Level 2 fixes known problems with Level 1 and we anticipate that Level 2 will be forward-compatible with Level 3.

Don't Panic. Few if any packages support all aspects of SBML. Depending on what you wish do with a model you can either ignore features that are not relevant to your tool or report errors when certain features are used. In most cases a simulator will simply report an error if it encounters a feature that it is unable to support.