(RFC 3823 published June 2004, subtype last updated June 2004) MIME media type name: application MIME subtype name: sbml+xml Required parameters: none. Optional parameters: none. There is no charset parameter. Character handling has identical semantics to the case where the charset parameter of the "application/xml" media type is omitted, as described in section 3.2 of [RFC3023]. Note that SBML level 2 is defined to have UTF-8 encoding [SBML2-1, section 4.1]. Encoding considerations: Same as described in section 3.2 of [RFC3023]. Security considerations: The security considerations described in section 7 of [RFC3470] all potentially apply to sbml+xml documents. In particular, sbml+xml documents might contain the results of proprietary biological research that their owner may wish to keep private. The XML schema for sbml+xml provides for no active or executable content. Interoperability considerations: The information in an sbml+xml document describes an abstract model of biochemical reactions. It is not tied to any particular software application, and indeed the primary purpose of SBML is to make these models readable and writable by many different software applications. This might seem to make sbml+xml more appropriate for the "Model" primary content type [RFC2077], but SBML models are not guaranteed to have the required three orthogonal dimensions. SBML models, rather, involve interacting entities that exist within compartments. However, ideally, browsers and other software that reads sbml+xml would give a human reader multiple choices of how to view the document: in a data-visualization tool, in a model editor, in a differential-equation analyzer, etc. The systems biology community has and will continue to release new levels and versions of the SBML schema and semantics. New versions attempt to be backward compatible with old versions, but sometimes small incompatibilities are introduced. Every sbml+xml document contains its level and version; programs that read sbml+xml should read this information to be sure they correctly interpret the remainder of the document. Published specification: A list of all current SBML specifications and related documents is maintained at: http://sbml.org/documents Current specifications are: SBML level 2, version 1 http://sbml.org/specifications/sbml-level-2-v1.ps http://sbml.org/specifications/sbml-level-2-v1.pdf SBML level 1, version 2 http://sbml.org/specifications/sbml-level-1-v2.ps http://sbml.org/specifications/sbml-level-1-v2.pdf SBML level 1, version 1 http://sbml.org/specifications/sbml-level-1-v1.ps http://sbml.org/specifications/sbml-level-1-v1.pdf All specifications are authored by and available in hardcopy form from The SBML Team (see below for mailing information). Applications which use this media type: The following application and database projects read and/or write models in sbml+xml format. Currently, most do not encode or decode MIME-format messages. Hopefully the registration of sbml+xml will make it easier for these projects to connect through a broader infrastructure, such as the creation of repositories of models on the world-wide web. BALSA BASIS BioCharon biocyc2SBML BioGrid BioNetGen Bio Sketch Pad BioSpreadsheet BioUML BSTLab CADLIVE CellDesigner Cellerator Cellware COPASI Cytoscape DBsolve Dizzy E-CELL ecellJ ESS Gepasi Jarnac JDesigner JigCell JSIM JWS Karyote KEGG2SBML Kinsolver (planned) libSBML MathSBML MMT2 Modesto MOMA (planned) Monod NetBuilder PathArt PathScout PaVESy PathwayBuilder ProcessDB (planned) SBW SCIpath SigPath SigTran Simpathica SimWiz StochSim STOCKS Trelis Virtual Cell VLX Suite WinSCAMP A list of SBML-enabled applications, along with URLs for more information about them, is maintained at http://sbml.org. Additional information: For further information, contact: Michael Hucka mhucka&caltech.edu Andrew Finney afinney&cds.caltech.edu The SBML Team http://sbml.org sbml-team&caltech.edu Control and Dynamical Systems, MC 107-81 California Institute of Technology Pasadena, CA 91125 USA Intended usage: LIMITED USE Author/Change Controller: The SBML specification is a free, open, community effort organized and edited by The SBML Team. The SBML Team has change control over the specification. The SBML Team and interested members of the systems biology community meet regularly at the "Workshops on Software Platforms for Systems Biology". Information about past and planned workshops is maintained at: http://sbml.org/workshops