Network Working Group B. Kovitz INTERNET-DRAFT Caltech Category: Informational 7 October 2003 Title: draft-sbml-media-type-00.txt MIME Media Type for SBML, the Systems Biology Markup Language Status of this Memo This document is an Internet-Draft and is subject to all provisions of Section 10 of RFC2026. Internet-Drafts are working documents of the Internet Engineering Task Force (IETF), its areas, and its working groups. Note that other groups may also distribute working documents as Internet- Drafts. Internet-Drafts are draft documents valid for a maximum of six months and may be updated, replaced, or obsoleted by other documents at any time. It is inappropriate to use Internet- Drafts as reference material or to cite them other than as "work in progress." The list of current Internet-Drafts can be accessed at http://www.ietf.org/1id-abstracts.html The list of Internet-Draft Shadow Directories can be accessed at http://www.ietf.org/shadow.html Copyright Notice Copyright (C) The Internet Society (2003). All Rights Reserved. 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 visual- izers, on a single model without rewriting the model for each tool; Kovitz [Page 1] Internet-draft-SBML Systems Biology Markup Language 7 October 2003 o enables researchers and publishers to make models available on-line to other researchers even if they use a different software environ- ment; o enables models, and the intellectual effort put into them, to sur- vive beyond the lifetime of the software tools used to create them. SBML is the standard model definition language for the DARPA BioSPICE project and the International E. coli Alliance (IECA). Currently, about 30 software applications use SBML, and researchers are using these applications to develop models, mostly in cell biol- ogy. 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 in [HUCKA2003]. 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: charset This parameter has identical semantics to the charset parameter of the "application/xml" media type described in [RFC3023]. 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. Kovitz [Page 2] Internet-draft-SBML Systems Biology Markup Language 7 October 2003 Interoperability considerations: The information in an sbml+xml document describes an abstract model of biochemical reactions. It is not tied to any particular soft- ware 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 compart- ments. 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). Kovitz [Page 5] Internet-draft-SBML Systems Biology Markup Language 7 October 2003 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. BASIS http://www.basis.ncl.ac.uk Bio Sketch Pad http://bio.bbn.com/biospice/biosketchpad/index.html BioSpreadsheet http://biocomp.ece.utk.edu/Subpages/downloads.html BioUML http://www.biouml.org BSTLab mailto:schwacke@musc.edu CADLIVE http://kurata21.bse.kyutech.ac.jp/cadlive/ CellDesigner http://www.systems-biology.org/002/ Cellerator http://www-aig.jpl.nasa.gov/public/mls/cellerator/ Cellware http://www.bii.a-star.edu.sg/sbg/cellware Cytoscape http://www.cytoscape.org/ Dizzy http://labs.systemsbiology.net/bolouri/software/Dizzy ESS http://biocomp.ece.utk.edu/ Gepasi http://www.gepasi.org/ Kovitz [Page 6] Internet-draft-SBML Systems Biology Markup Language 7 October 2003 Jarnac http://www.sys-bio.org/ JDesigner http://www.sys-bio.org/ JigCell http://gnida.cs.vt.edu/~cellcyclepse/ JSIM http://nsr.bioeng.washington.edu/DOC/JSIMDOC/JSim1.5_New_Features libSBML http://www.sbml.org/libsbml.html MathSBML http://www.sbml.org/mathsbml.html MicroCore http://www.ucl.ac.uk/oncology/MicroCore/microcore.htm MOMA http://arep.med.harvard.edu/moma Monod http://monod.molsci.org NetBuilder http://strc.herts.ac.uk/bio/maria/NetBuilder/ PathArt http://jubilantbiosys.com/pd.htm PathScout http://simpath.lionbioscience.com:8080/documentation/pathscout11 SigPath http://www.sigpath.org StochSim http://www.zoo.cam.ac.uk/comp-cell/StochSim.html TeraSim (planned) http://teranode.com/products.htm Trelis http://www.sourceforge.net/projects/trelis Kovitz [Page 7] Internet-draft-SBML Systems Biology Markup Language 7 October 2003 Virtual Cell http://www.nrcam.uchc.edu/vcell_development/vcell_dev.html WinSCAMP http://www.sys-bio.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 commu- nity meet biannually at the "Workshops on Software Platforms for Systems Biology". Information about past and planned workshops is maintained at: http://sbml.org/workshops Kovitz [Page 8] Internet-draft-SBML Systems Biology Markup Language 7 October 2003 3. Author's Address Please direct questions about this memo to: 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 4. References [HUCKA2003] M. Hucka, A. Finney, H.M. Sauro, H. Bolouri, J.C. Doyle, H. Kitano, A.P. Arkin, B.J. Bornstein, D. Bray, A. Cornish-Bowden, A.A. Cuellar, S. Dronov, E.D. Gilles, M. Ginkel, V. Gor, I.I. Goryanin, W.J. Hedley, T.C. Hodgman, J.-H. Hofmeyr, P.J. Hunter, N.S. Juty, J.L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L.M. Loew, D. Lucio, P. Mendes, E. Minch, E.D. Mjolsness, Y. Nakayama, M.R. Nelson, P.F. Nielsen, T. Sakurada, J.C. Schaff, B.E. Shapiro, T.S. Shimizu, H.D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang., "The Systems Biology Markup Language (SBML): a Medium for Representation and Exchange of Biochemical Network Models", Bioinformatics 19(4):524-531, 2003. [RFC2048] N. Freed, J. Klensin, and J. Postel, "Multipurpose Internet Mail Extensions (MIME) Part Four: Registration Procedures", RFC 2048, November 1996 [RFC2077] S. Nelson and C. Parks, "The Model Primary Content Type for Multipurpose Internet Mail Extensions", RFC 2077, January 1997. [RFC3023] M. Murata, S. St. Laurent, and D. Kohn, "XML Media Types", RFC 3023, January 2001. [RFC3470] S. Hollenbeck, M. Rose, and L. Masinter, "Guidelines for the Use of Extensible Markup Language (XML) within IETF Protocols", RFC 3470, January 2003. Kovitz [Page 9] Internet-draft-SBML Systems Biology Markup Language 7 October 2003 Full Copyright Statement Copyright (C) The Internet Society (date). All Rights Reserved. This document and translations of it may be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implmentation may be prepared, copied, published and distributed, in whole or in part, without restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. However, this document itself may not be modified in any way, such as by removing the copyright notice or references to the Internet Society or other Internet organizations, except as needed for the purpose of developing Internet standards in which case the procedures for copyrights defined in the Internet Standards process must be followed, or as required to translate it into languages other than English. 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