24:
218:
Level 1 Version 1 of SED-ML officially appeared in March 2011, but SED-ML was presented, discussed and further specified during several community meetings in the years in between, including the combined "CellML-SBGN-SBO-BioPAX-MIASE workshop" in 2009, or the "2010 SBML-BioModels.net
Hackathon".
209:
The SED-ML project was first discussed publicly at the 12th SBML Forum
Meeting in 2007, in Long Beach (US). The first version of SED-ML was then presented at the "Super-hackathon "standards and ontologies for Systems Biology"" in Okinawa in 2008. Back then, the language was called MIASE-ML (in
214:
guidelines). In
Okinawa, many researchers showed a high interest in the format, and discussions were vital. MIASE became the Minimum Information guideline for simulation experiments. MIASE-ML was renamed into "Simulation Experiment Description Markup Language" (SED-ML).
176:
The
Simulation entity contains all information about the simulation settings and the steps taken during simulation, e.g., the particular type of simulation and the algorithm used for the execution of the simulation. The simulation algorithm is specified with a
160:
The Model entity is used to reference the models used in the simulation experiment and to define pre-processing procedures on these models before simulation. Models must be in standard representation formats (e.g.,
173:). Examples for pre-processing are, e.g., changing the value of an observable, computing the change of a value using mathematics, or general changes on any XML element of the model representation.
206:(EMBL-EBI). In 2007, Dagmar Waltemath and Nicolas Le Novère started to draft such a format during Dagmar's Marie-Curie funded internship in the Computational Neuroscience group at EMBL-EBI.
492:
528:
187:
The DataGenerator entity encodes post-processing procedures which need to be applied to the simulation result before output, e.g., normalisation of data.
226:. Besides dedicated sessions at various meetings, the development of SED-ML benefits from community interactions on the SED-ML-discuss mailing list.
533:
280:
D. Waltemath; F. T. Bergmann; R. Adams; N. Le Novère (2011). "Simulation
Experiment Description Markup Language (SED-ML): Level 1 Version 1".
303:
D. Waltemath; R. Adams; F.T. Bergmann; M. Hucka; F. Kolpakov; A.K. Miller; I.I. Moraru; D. Nickerson; J.L. Snoep; N. Le Novère (2011).
461:
433:
203:
222:
Since then SED-ML has been developed in collaboration with the communities forming the "computational modeling in biology network"
238:. Format development is coordinated by an editorial board elected by the community. Discussions take place at SED-ML-discuss.
543:
305:"Reproducible computational biology experiments with SED-ML – The Simulation Experiment Description Markup Language"
61:
148:
SED-ML Level 1 Version 1, the first version of SED-ML, enables descriptions of time course simulation experiments.
538:
497:
194:
More information on the SED-ML structure is available from the SED-ML home page and the reference publication.
331:
426:
142:
184:
The Task entity applies one of the defined simulations with one of the referenced models at a time.
31:
419:
326:
316:
285:
202:
The idea of developing a standard format for simulation experiment encoding was born at the
106:
23:
190:
The Output entity specifies the simulation output, e.g., the particular plots to be shown.
88:
371:
522:
507:
289:
321:
304:
145:
of biological systems. It is a free and open community development project.
442:
235:
223:
170:
476:
456:
346:
166:
502:
211:
178:
466:
162:
415:
393:
141:, for the encoding and exchange of simulation descriptions on
138:
98:
411:
135:
Simulation
Experiment Description Markup Language (SED-ML)
122:
258:
485:
449:
259:"Simulation Experiment Description Markup Language"
236:
COmputational
Modeling in Biology Network (COMBINE)
117:
104:
94:
84:
60:
42:
30:
332:20.500.11820/1b2fc55b-d3b0-4e6b-8b60-6614254b020a
156:The SED-ML format is built of five major blocks:
17:Simulation Experiment Description Markup Language
427:
8:
16:
434:
420:
412:
347:"Computational Systems Neurobiology Group"
22:
366:
364:
330:
320:
529:Science and technology in Cambridgeshire
253:
251:
247:
15:
179:Kinetic Simulation Algorithm Ontology
137:is a representation format, based on
7:
14:
204:European Bioinformatics Institute
1:
534:South Cambridgeshire District
67:Level 1 Version 2, Release 1
560:
372:"SED-ML-discuss Info Page"
349:. EMBL-EBI. 1 October 2012
21:
394:"Current SED-ML Editors"
290:10.1038/npre.2011.5846.1
322:10.1186/1752-0509-5-198
234:SED-ML is part of the
71:; 10 years ago
48:; 13 years ago
544:XML markup languages
210:accordance with the
143:computational models
69:2 December 2013
309:BMC Systems Biology
18:
95:Extended from
46:25 March 2011
32:Filename extension
516:
515:
282:Nature Precedings
131:
130:
551:
436:
429:
422:
413:
406:
405:
403:
401:
390:
384:
383:
381:
379:
368:
359:
358:
356:
354:
343:
337:
336:
334:
324:
300:
294:
293:
277:
271:
270:
268:
266:
255:
230:SED-ML Community
127:
124:
110:
79:
77:
72:
56:
54:
49:
26:
19:
559:
558:
554:
553:
552:
550:
549:
548:
539:Systems biology
519:
518:
517:
512:
481:
445:
440:
410:
409:
399:
397:
392:
391:
387:
377:
375:
370:
369:
362:
352:
350:
345:
344:
340:
302:
301:
297:
279:
278:
274:
264:
262:
257:
256:
249:
244:
232:
200:
154:
121:
105:
89:Markup language
80:
75:
73:
70:
68:
52:
50:
47:
43:Initial release
38:
12:
11:
5:
557:
555:
547:
546:
541:
536:
531:
521:
520:
514:
513:
511:
510:
505:
500:
495:
489:
487:
483:
482:
480:
479:
474:
469:
464:
459:
453:
451:
447:
446:
441:
439:
438:
431:
424:
416:
408:
407:
385:
360:
338:
295:
272:
246:
245:
243:
240:
231:
228:
199:
196:
192:
191:
188:
185:
182:
174:
153:
150:
129:
128:
119:
115:
114:
111:
102:
101:
96:
92:
91:
86:
85:Type of format
82:
81:
66:
64:
62:Latest release
58:
57:
44:
40:
39:
36:
34:
28:
27:
13:
10:
9:
6:
4:
3:
2:
556:
545:
542:
540:
537:
535:
532:
530:
527:
526:
524:
509:
508:BioModels.net
506:
504:
501:
499:
496:
494:
491:
490:
488:
484:
478:
475:
473:
470:
468:
465:
463:
460:
458:
455:
454:
452:
448:
444:
437:
432:
430:
425:
423:
418:
417:
414:
395:
389:
386:
373:
367:
365:
361:
348:
342:
339:
333:
328:
323:
318:
314:
310:
306:
299:
296:
291:
287:
283:
276:
273:
260:
254:
252:
248:
241:
239:
237:
229:
227:
225:
220:
216:
213:
207:
205:
197:
195:
189:
186:
183:
180:
175:
172:
168:
164:
159:
158:
157:
151:
149:
146:
144:
140:
136:
126:
120:
116:
112:
108:
103:
100:
97:
93:
90:
87:
83:
65:
63:
59:
45:
41:
35:
33:
29:
25:
20:
471:
398:. Retrieved
388:
376:. Retrieved
351:. Retrieved
341:
312:
308:
298:
281:
275:
263:. Retrieved
233:
221:
217:
208:
201:
193:
155:
147:
134:
132:
107:Open format
523:Categories
242:References
76:2013-12-02
53:2011-03-25
486:Standards
152:Structure
396:. SED-ML
374:. SED-ML
353:24 April
261:. SED-ML
450:Formats
443:COMBINE
315:: 198.
224:COMBINE
198:History
171:NeuroML
118:Website
74: (
51: (
493:MIRIAM
477:CellML
472:SED-ML
457:BioPAX
400:6 July
378:6 July
265:6 July
167:CellML
123:sed-ml
503:KiSAO
212:MIASE
181:term.
467:SBML
462:SBGN
402:2017
380:2017
355:2014
267:2017
163:SBML
133:The
125:.org
37:.xml
498:SBO
327:hdl
317:doi
286:doi
139:XML
113:Yes
99:XML
525::
363:^
325:.
311:.
307:.
284:.
250:^
169:,
165:,
435:e
428:t
421:v
404:.
382:.
357:.
335:.
329::
319::
313:5
292:.
288::
269:.
109:?
78:)
55:)
Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
