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
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of Section 10 of RFC2026.
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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;
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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.
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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).
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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/
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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
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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
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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.
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