    Network Working Group                                          B. Kovitz
    Request for Comments: 3823                                       Caltech
    Category: Informational                                        June 2004

         MIME Media Type for the Systems Biology Markup Language (SBML)

    Status of this Memo

       This memo provides information for the Internet community.  It does
       not specify an Internet standard of any kind.  Distribution of this
       memo is unlimited.

    Copyright Notice

       Copyright (C) The Internet Society (2004).

    Abstract

       This document registers the MIME sub-type application/sbml+xml, a
       media type for SBML, the Systems Biology Markup Language.  SBML is
       defined by The SBML Team at the California Institute of Technology
       and interested members of the systems biology community.

    1.  Introduction

       SBML is an XML format for representing and exchanging models of
       biochemical reaction networks used in systems biology.  SBML:

       o  enables researchers in systems biology to use multiple tools, such
          as simulators, editors, differential-equation solvers, and
          visualizers, on a single model without rewriting the model for
          each tool;

       o  enables researchers and publishers to make models available on-
          line to other researchers even if they use a different software
          environment;

       o  enables models, and the intellectual effort put into them, to
          survive beyond the lifetime of the software tools used to create
          them.

       Currently, about 60 software applications use SBML, and researchers
       are using these applications to develop quantitative and qualitative
       computational models, mostly in cell biology.  In addition, several
       consortia and alliances have standardized SBML as their model

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    RFC 3823         Systems Biology Markup Language (SBML)        June 2004

       definition language.  The SBML community hopes that a standardized
       MIME media type will help researchers share models on a larger scale,
       drawing more heavily on the capabilities of the world-wide web.

       A detailed exposition of SBML and its uses within the systems biology
       community is available in references [HUCKA2003], [FINNEY2003], and
       [HUCKA2004].

    2.  IANA Registration

       This section registers application/sbml+xml as a MIME media type
       according to the parameters set forth in [RFC2048].

       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.

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    RFC 3823         Systems Biology Markup Language (SBML)        June 2004

          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

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    RFC 3823         Systems Biology Markup Language (SBML)        June 2004

          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

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    RFC 3823         Systems Biology Markup Language (SBML)        June 2004

             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

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    RFC 3823         Systems Biology Markup Language (SBML)        June 2004

    3. Security Considerations

       Security considerations for sbml+xml are discussed in the "Security
       Considerations" heading in the IANA registration in section 2.

    4.  Contributors

       The following people contributed to the content of this document:
       Michael Hucka (Caltech), Andrew Finney (University of Hertfordshire).

    5. References

    5.1.  Normative References

       [SBML2-1]    Finney, A. and Hucka, M., "Systems Biology Markup
                    Language (SBML) Level 2: Structures and Facilities for
                    Model Definitions", June 28, 2003.  Available from The
                    SBML Team at: http://sbml.org/specifications/sbml-
                    level-2-v1.pdf

       [SBML1-2]    Hucka, M., Finney, A., Sauro, H. and Bolouri, H.,
                    "Systems Biology Markup Language (SBML) Level 1:
                    Structures and Facilities for Basic Model Definitions",
                    August 28, 2003.  Available from The SBML Team at:
                    http://sbml.org/specifications/sbml-level-1-v2.pdf

    5.2.  Informative References

       [FINNEY2003] Finney, A. and Hucka, M., "Systems Biology Markup
                    Language: Level 2 and Beyond", Biochemical Society
                    Transactions 31:1472-1473, December, 2003.

       [HUCKA2003]  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 Novere, N., Loew, L.M., Lucio, D., Mendes, P.,
                    Minch, E., Mjolsness, E.D., Nakayama, Y., Nelson, M.R.,
                    Nielsen, P.F., Sakurada, T., Schaff, J.C., Shapiro,
                    B.E., Shimizu, T.S., Spence, H.D., Stelling, J.,
                    Takahashi, K., Tomita, M., Wagner, J., Wang, J., "The
                    Systems Biology Markup Language (SBML): a Medium for
                    Representation and Exchange of Biochemical Network
                    Models", Bioinformatics 19(4):524-531, 2003.

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    RFC 3823         Systems Biology Markup Language (SBML)        June 2004

       [HUCKA2004]  Hucka, M., Finney, A., Bornstein, B. J., Keating, S. M.,
                    Shapiro, B. E., Matthews, M., Kovitz, B. L., Schilstra,
                    M. J., Funahashi, A., Doyle, J. C., and Kitano, H.,
                    "Evolving a Lingua Franca and Associated Software
                    Infrastructure for Computational Systems Biology: The
                    Systems Biology Markup Language (SBML) Project", Systems
                    Biology, Vol. 1, 2004.

       [RFC2048]    Freed, N., Klensin, J. and J. Postel, "Multipurpose
                    Internet Mail Extensions (MIME) Part Four: Registration
                    Procedures", BCP 13, RFC 2048, November 1996.

       [RFC2077]    Nelson, S. and C. Parks, "The Model Primary Content Type
                    for Multipurpose Internet Mail Extensions", RFC 2077,
                    January 1997.

       [RFC3023]    Murata, M., St. Laurent, S. and D. Kohn, "XML Media
                    Types", RFC 3023, January 2001.

       [RFC3470]    Hollenbeck, S., Rose, M. and L. Masinter, "Guidelines
                    for the Use of Extensible Markup Language (XML) within
                    IETF Protocols", BCP 70, RFC 3470, January 2003.

    6.  Author's Address

       Ben Kovitz
       Control and Dynamical Systems, MC 107-81
       California Institute of Technology
       Pasadena, CA  91125
       USA

       Phone: +1 626 395-6911
       EMail: bkovitz@caltech.edu

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    RFC 3823         Systems Biology Markup Language (SBML)        June 2004

    7.  Full Copyright Statement

       Copyright (C) The Internet Society (2004).  This document is subject
       to the rights, licenses and restrictions contained in BCP 78, and
       except as set forth therein, the authors retain all their rights.

       This document and the information contained herein are provided on an
       "AS IS" basis and THE CONTRIBUTOR, THE ORGANIZATION HE/SHE REPRESENTS
       OR IS SPONSORED BY (IF ANY), THE INTERNET SOCIETY AND THE INTERNET
       ENGINEERING TASK FORCE DISCLAIM ALL WARRANTIES, EXPRESS OR IMPLIED,
       INCLUDING BUT NOT LIMITED TO ANY WARRANTY THAT THE USE OF THE
       INFORMATION HEREIN WILL NOT INFRINGE ANY RIGHTS OR ANY IMPLIED
       WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

    Intellectual Property

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       Intellectual Property Rights or other rights that might be claimed to
       pertain to the implementation or use of the technology described in
       this document or the extent to which any license under such rights
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       made any independent effort to identify any such rights.  Information
       on the procedures with respect to rights in RFC documents can be
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       specification can be obtained from the IETF on-line IPR repository at
       http://www.ietf.org/ipr.

       The IETF invites any interested party to bring to its attention any
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       this standard.  Please address the information to the IETF at ietf-
       ipr@ietf.org.

    Acknowledgement

       Funding for the RFC Editor function is currently provided by the
       Internet Society.

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