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September 2003
 RE: Multiple kineticLaw Sections Per Reaction 10 Mar '06 18:01 I also think there is a real problem, how would one know that a given rate law in an SBML model is valid for a stochastic model? As far as I know, and I please correct me if I am wrong, there are only a very small number of rate laws that have been shown to be usable for stochastic simulations. I can't blindly read a SBML file, Level 1 or 2 (and we use level 2), and just plug all the equations into a, say, Gillespie simulator. I think this is what the SBO idea will solve? Herbert -----Original Message----- From: Stefan Hoops [mailto:shoops@vbi.vt.edu] Sent: Friday, March 10, 2006 3:05 PM To: sbml-discuss@caltech.edu Subject: Re: [sbml-discuss] Multiple kineticLaw Sections Per Reaction Hello Darren, On Fri, 10 Mar 2006 21:51:42 +0000 (GMT) Darren Wilkinson wrote: > --- Herbert Sauro wrote: > > Seems to make sense to me. I would agree that there is a real > > problem with representing stoachstic models in the current SBML, we > > are confronted with this problem almost every week. > > Actually, there is no problem representing stochastic models in SBML > Level 2. I am not sure about that. Actually I think it is impossible if we interpret what is said in the kinetic law section strictly :( The kinetic law section states in paragraph 3: The expression in math may refer to species identifiers; in that case, as discussed in Section 3.6.3, the units of each species reference are those of concentration. However section 3.6.3 somewhat contradicts that and says that it may also be substance units depending on the species definition. The minimum we need to do is to correct the paragraph 3 in 4.9.7 and add this to the errata. Thanks, Stefan -- Stefan Hoops, Ph.D. Senior Project Associate Virginia Bioinformatics Institute - 0477 Virginia Tech Bioinformatics Facility I Blacksburg, Va 24061, USA Phone: (540) 231-1799 Fax: (540) 231-2606 Email: shoops@vbi.vt.edu

SubjectPosterDate
Multiple kineticLaw Sections Per Reaction Bill Denney09 Mar '06 10:14
Re: Multiple kineticLaw Sections Per Reaction Hiroyuki Kuwahara09 Mar '06 16:18
RE: Multiple kineticLaw Sections Per Reaction Herbert Sauro09 Mar '06 17:09
RE: Multiple kineticLaw Sections Per Reaction Bill Denney09 Mar '06 18:30
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 01:01
RE: Multiple kineticLaw Sections Per Reaction Bill Denney10 Mar '06 04:15
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 09:54
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 10:16
Re: Multiple kineticLaw Sections Per Reaction Stefan Hoops10 Mar '06 10:28
Re: Multiple kineticLaw Sections Per Reaction Mike Hucka10 Mar '06 11:24
Re: Multiple kineticLaw Sections Per Reaction Tomas Radivoyevitch10 Mar '06 05:32
Re: Multiple kineticLaw Sections Per Reaction Bill Denney10 Mar '06 10:32
RE: Multiple kineticLaw Sections Per Reaction Mike Hucka10 Mar '06 11:02
RE: Multiple kineticLaw Sections Per Reaction Herbert Sauro10 Mar '06 09:39
RE: Multiple kineticLaw Sections Per Reaction Bill Denney10 Mar '06 10:36
RE: Multiple kineticLaw Sections Per Reaction Mike Hucka10 Mar '06 11:10
Re: Multiple kineticLaw Sections Per Reaction Mike Hucka10 Mar '06 11:07
RE: Multiple kineticLaw Sections Per Reaction Herbert Sauro10 Mar '06 13:00
RE: Multiple kineticLaw Sections Per Reaction Herbert Sauro10 Mar '06 13:03
RE: Multiple kineticLaw Sections Per Reaction Darren J Wilkinson10 Mar '06 13:51
Re: Multiple kineticLaw Sections Per Reaction Stefan Hoops10 Mar '06 15:04
Re: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 16:21
Re: Multiple kineticLaw Sections Per Reaction Stefan Hoops13 Mar '06 05:55
Re: Multiple kineticLaw Sections Per Reaction Darren J Wilkinson13 Mar '06 12:09
Re: Multiple kineticLaw Sections Per Reaction Stefan Hoops14 Mar '06 05:08
Re: Multiple kineticLaw Sections Per Reaction Darren J Wilkinson14 Mar '06 11:21
response to "fast" attribute action item... Schaff29 Mar '06 08:22
response to "fast" attribute action item Schaff29 Mar '06 11:58
RE: Multiple kineticLaw Sections Per Reaction Bill Denney10 Mar '06 14:28
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 15:10
stochastic/ODE models Eric Mjolsness10 Mar '06 14:44
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 14:55
RE: Multiple kineticLaw Sections Per Reaction  Herbert Sauro10 Mar '06 18:01
RE: Multiple kineticLaw Sections Per Reaction Mike Hucka11 Mar '06 00:41
RE: Multiple kineticLaw Sections Per Reaction Darren J Wilkinson11 Mar '06 05:29
RE: Multiple kineticLaw Sections Per Reaction Bill Denney11 Mar '06 05:37
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere11 Mar '06 15:23
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