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Kovitz 3 INTERNET-DRAFT Caltech 4 Category: Informational 24 November 2003 5 Title: draft-sbml-media-type-02.txt 7 MIME Media Type for SBML, the Systems Biology Markup Language 9 Status of this Memo 11 This document is an Internet-Draft and is subject to all provisions 12 of Section 10 of RFC2026. 14 Internet-Drafts are working documents of the Internet Engineering 15 Task Force (IETF), its areas, and its working groups. Note that 16 other groups may also distribute working documents as Internet- 17 Drafts. 19 Internet-Drafts are draft documents valid for a maximum of six months 20 and may be updated, replaced, or obsoleted by other documents at any 21 time. It is inappropriate to use Internet-Drafts as reference 22 material or to cite them other than as "work in progress." 24 The list of current Internet-Drafts can be accessed at 25 http://www.ietf.org/1id-abstracts.html 27 The list of Internet-Draft Shadow Directories can be accessed at 28 http://www.ietf.org/shadow.html 30 Copyright Notice 32 Copyright (C) The Internet Society (2003). All Rights Reserved. 34 Abstract 36 This document registers the MIME sub-type application/sbml+xml, a 37 media type for SBML, the Systems Biology Markup Language. SBML is 38 defined by The SBML Team at the California Institute of Technology 39 and interested members of the systems biology community. 41 1. Introduction 43 SBML is an XML format for representing and exchanging models of 44 biochemical reaction networks used in systems biology. SBML: 46 o enables researchers in systems biology to use multiple tools, such 47 as simulators, editors, differential-equation solvers, and visual- 48 izers, on a single model without rewriting the model for each tool; 50 Internet-draft-SBML Systems Biology Markup Language 24 November 2003 52 o enables researchers and publishers to make models available on-line 53 to other researchers even if they use a different software environ- 54 ment; 56 o enables models, and the intellectual effort put into them, to sur- 57 vive beyond the lifetime of the software tools used to create them. 59 SBML is the standard model definition language for the DARPA BioSPICE 60 project and the International E. coli Alliance (IECA). 62 Currently, about 30 software applications use SBML, and researchers 63 are using these applications to develop models, mostly in cell biol- 64 ogy. The SBML community hopes that a standardized MIME media type 65 will help researchers share models on a larger scale, drawing more 66 heavily on the capabilities of the world-wide web. 68 A detailed exposition of SBML and its uses within the systems biology 69 community is in [HUCKA2003]. 71 2. IANA Registration 73 This section registers application/sbml+xml as a MIME media type 74 according to the parameters set forth in [RFC2048]. 76 MIME media type name: application 78 MIME subtype name: sbml+xml 80 Required parameters: none. 82 Optional parameters: none. 84 There is no charset parameter. Character handling has identical 85 semantics to the case where the charset parameter of the "applica- 86 tion/xml" media type is omitted, as described in section 3.2 of 87 [RFC3023]. Note that SBML level 2 is defined to have UTF-8 encod- 88 ing [SBML2-1, section 4.1]. 90 Encoding considerations: 92 Same as described in section 3.2 of [RFC3023]. 94 Internet-draft-SBML Systems Biology Markup Language 24 November 2003 96 Security considerations: 98 The security considerations described in section 7 of [RFC3470] all 99 potentially apply to sbml+xml documents. In particular, sbml+xml 100 documents might contain the results of proprietary biological 101 research that their owner may wish to keep private. 103 The XML schema for sbml+xml provides for no active or executable 104 content. 106 Interoperability considerations: 108 The information in an sbml+xml document describes an abstract model 109 of biochemical reactions. It is not tied to any particular soft- 110 ware application, and indeed the primary purpose of SBML is to make 111 these models readable and writable by many different software 112 applications. 114 This might seem to make sbml+xml more appropriate for the "Model" 115 primary content type [RFC2077], but SBML models are not guaranteed 116 to have the required three orthogonal dimensions. SBML models, 117 rather, involve interacting entities that exist within compart- 118 ments. However, ideally, browsers and other software that reads 119 sbml+xml would give a human reader multiple choices of how to view 120 the document: in a data-visualization tool, in a model editor, in a 121 differential-equation analyzer, etc. 123 The systems biology community has and will continue to release new 124 levels and versions of the SBML schema and semantics. New versions 125 attempt to be backward compatible with old versions, but sometimes 126 small incompatibilities are introduced. Every sbml+xml document 127 contains its level and version; programs that read sbml+xml should 128 read this information to be sure they correctly interpret the 129 remainder of the document. 131 Published specification: 133 A list of all current SBML specifications and related documents is 134 maintained at: 136 http://sbml.org/documents 138 Internet-draft-SBML Systems Biology Markup Language 24 November 2003 140 Current specifications are: 142 SBML level 2, version 1 143 http://sbml.org/specifications/sbml-level-2-v1.ps 144 http://sbml.org/specifications/sbml-level-2-v1.pdf 146 SBML level 1, version 2 147 http://sbml.org/specifications/sbml-level-1-v2.ps 148 http://sbml.org/specifications/sbml-level-1-v2.pdf 150 SBML level 1, version 1 151 http://sbml.org/specifications/sbml-level-1-v1.ps 152 http://sbml.org/specifications/sbml-level-1-v1.pdf 154 All specifications are authored by and available in hardcopy form 155 from The SBML Team (see below for mailing information). 157 Applications which use this media type: 159 The following application and database projects read and/or write 160 models in sbml+xml format. Currently, most do not encode or decode 161 MIME-format messages. Hopefully the registration of sbml+xml will 162 make it easier for these projects to connect through a broader 163 infrastructure, such as the creation of repositories of models on 164 the world-wide web. 166 BASIS 167 Bio Sketch Pad 168 BioSpreadsheet 169 BioUML 170 BSTLab 171 CADLIVE 172 CellDesigner 173 Cellerator 174 Cellware 175 Cytoscape 176 Dizzy 177 ESS 178 Gepasi 179 Jarnac 180 JDesigner 181 JigCell 182 JSIM 183 libSBML 184 MathSBML 185 MicroCore 186 MOMA 187 Monod 189 Internet-draft-SBML Systems Biology Markup Language 24 November 2003 191 NetBuilder 192 PathArt 193 PathScout 194 SigPath 195 StochSim 196 TeraSim (planned) 197 Trelis 198 Virtual Cell 199 WinSCAMP 201 A list of SBML-enabled applications, along with URLs for more 202 information about them, is maintained at http://sbml.org. 204 Additional information: 206 For further information, contact: 208 Michael Hucka 209 mhucka@caltech.edu 211 Andrew Finney 212 afinney@cds.caltech.edu 214 The SBML Team 215 http://sbml.org 216 sbml-team@caltech.edu 217 Control and Dynamical Systems, MC 107-81 218 California Institute of Technology 219 Pasadena, CA 91125 220 USA 222 Intended usage: LIMITED USE 224 Author/Change Controller: 226 The SBML specification is a free, open, community effort organized 227 and edited by The SBML Team. The SBML Team has change control over 228 the specification. 230 The SBML Team and interested members of the systems biology commu- 231 nity meet biannually at the "Workshops on Software Platforms for 232 Systems Biology". Information about past and planned workshops is 233 maintained at: 235 http://sbml.org/workshops 237 Internet-draft-SBML Systems Biology Markup Language 24 November 2003 239 3. Author's Address 241 Please direct questions about this memo to: 243 Ben Kovitz 244 Control and Dynamical Systems, MC 107-81 245 California Institute of Technology 246 Pasadena, CA 91125 247 USA 249 Phone: +1 626 395-6911 251 Email: bkovitz@caltech.edu 253 4. Security Considerations 255 Security considerations for sbml+xml are discussed in the "Security 256 Considerations" heading in the IANA registration in section 2. 258 5. References 260 Normative references: 262 [SBML2-1] A. Finney, M. Hucka, "Systems Biology Markup Language 263 (SBML) Level 2: Structures and Facilities for Model 264 Definitions", June 28, 2003. Available from The 265 SBML Team at: 266 http://sbml.org/specifications/sbml-level-2-v1.pdf 268 Informative references: 270 [HUCKA2003] M. Hucka, A. Finney, H.M. Sauro, H. Bolouri, J.C. 271 Doyle, H. Kitano, A.P. Arkin, B.J. Bornstein, D. 272 Bray, A. Cornish-Bowden, A.A. Cuellar, S. Dronov, 273 E.D. Gilles, M. Ginkel, V. Gor, I.I. Goryanin, 274 W.J. Hedley, T.C. Hodgman, J.-H. Hofmeyr, P.J. 275 Hunter, N.S. Juty, J.L. Kasberger, A. Kremling, U. 276 Kummer, N. Le Novere, L.M. Loew, D. Lucio, P. 277 Mendes, E. Minch, E.D. Mjolsness, Y. Nakayama, M.R. 278 Nelson, P.F. Nielsen, T. Sakurada, J.C. Schaff, 279 B.E. Shapiro, T.S. Shimizu, H.D. Spence, J. 280 Stelling, K. Takahashi, M. Tomita, J. Wagner, J. 281 Wang., "The Systems Biology Markup Language (SBML): 282 a Medium for Representation and Exchange of 283 Biochemical Network Models", Bioinformatics 284 19(4):524-531, 2003. 286 Internet-draft-SBML Systems Biology Markup Language 24 November 2003 288 [RFC2048] N. Freed, J. Klensin, and J. Postel, "Multipurpose 289 Internet Mail Extensions (MIME) Part Four: 290 Registration Procedures", RFC 2048, November 1996 292 [RFC2077] S. Nelson and C. Parks, "The Model Primary Content 293 Type for Multipurpose Internet Mail Extensions", 294 RFC 2077, January 1997. 296 [RFC3023] M. Murata, S. St. Laurent, and D. Kohn, "XML Media 297 Types", RFC 3023, January 2001. 299 [RFC3470] S. Hollenbeck, M. Rose, and L. Masinter, "Guidelines 300 for the Use of Extensible Markup Language (XML) 301 within IETF Protocols", RFC 3470, January 2003. 303 Internet-draft-SBML Systems Biology Markup Language 24 November 2003 305 Full Copyright Statement 307 Copyright (C) The Internet Society (date). All Rights Reserved. 309 This document and translations of it may be copied and 310 furnished to others, and derivative works that comment on or 311 otherwise explain it or assist in its implmentation may be 312 prepared, copied, published and distributed, in whole or in 313 part, without restriction of any kind, provided that the above 314 copyright notice and this paragraph are included on all such 315 copies and derivative works. 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