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SBML Discussions » sbml-discuss » SBML L2v2 specification vote #4: References to controlled vocabularies
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Nicolas Le Novere


Posts: 469
Registered:
October 2003
Re: SBML L2v2 specification vote #4: References to controlled vocabularies 16 Dec '05 10:11 Go to previous messageGo to previous message


> I
> could imagine that there are some programs out there that will just read
> the sboTerm because this is simpler
> So programs would have to evaluate both the formula and the sboTerm.

But in most of the case, that will hardly be sufficient to run the
simulation. sboTerm are not meant to replace kineticLaw. In the case of a
wrong sboTerm, it is likely that there will be inconsistencies between
sboTerms of parameters, speciesReferences and kineticLaws. Therefore, the
simulator clever enough to reconstruct kineticLaws based on sboTerms won't
be able to. In the event where sboTerms are consistent, there are great
chances that the mistake is actually in the kineticLaw!



--
Nicolas LE NOVÈRE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov


      

SubjectPosterDate
Read Message   SBML L2v2 specification vote #4: References to con... Mike Hucka13 Dec '05 14:21
Read Message   Re: SBML L2v2 specification vote #4: References t... Ralph.Gauges15 Dec '05 06:57
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence15 Dec '05 10:02
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges16 Dec '05 00:27
Read Message   Re: SBML L2v2 specification vote #4: References to...  Nicolas Le Novere16 Dec '05 10:11
Read Message   Re: SBML L2v2 specification vote #4: References to... Sven Sahle19 Dec '05 04:53
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence16 Dec '05 10:56
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard16 Dec '05 11:43
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence19 Dec '05 04:00
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard19 Dec '05 09:19
Read Message   Re: SBML L2v2 specification vote #4: References to... Martin Ginkel21 Dec '05 12:26
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard21 Dec '05 15:30
Read Message   Re: SBML L2v2 specification vote #4: References t... Nicolas Le Novere16 Dec '05 01:27
Read Message   Re: SBML L2v2 specification vote #4: References t... Mike Hucka20 Dec '05 11:31
Read Message   Re: SBML L2v2 specification vote #4: References t... Nicolas Le Novere20 Dec '05 16:05
Read Message   Re: SBML L2v2 specification vote #4: References t... Mike Hucka20 Dec '05 19:42
Read Message   Re: SBML L2v2 specification vote #4: References t... bshapiro15 Dec '05 12:15
Read Message   Re: SBML L2v2 specification vote #4: References t... Mike Hucka20 Dec '05 19:50
Read Message   Re: SBML L2v2 specification vote #4: References t... Ben Bornstein21 Dec '05 09:25
Read Message   RE: SBML L2v2 specification vote #4: References to... Ralph.Gauges17 Dec '05 09:11
Read Message   RE: SBML L2v2 specification vote #4: References to... Nicolas Le Novere19 Dec '05 08:52
Read Message   RE: SBML L2v2 specification vote #4: References to... Mike Hucka20 Dec '05 15:11
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges21 Dec '05 02:04
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka02 Jan '06 23:33
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere03 Jan '06 00:21
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 15:30
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere04 Jan '06 03:08
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere06 Jan '06 10:37
Read Message   Re: SBML L2v2 specification vote #4: References to... Martin Ginkel05 Jan '06 01:44
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere03 Jan '06 00:50
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence05 Jan '06 05:29
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere05 Jan '06 11:01
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence06 Jan '06 02:48
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere06 Jan '06 10:32
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence03 Jan '06 04:30
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 20:55
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro03 Jan '06 12:52
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops03 Jan '06 14:16
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 15:39
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere04 Jan '06 03:02
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops04 Jan '06 09:46
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 14:24
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere04 Jan '06 02:55
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard19 Dec '05 09:22
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges20 Dec '05 01:48
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard20 Dec '05 11:13
Read Message   RE: SBML L2v2 specification vote #4: References to... Mike Hucka20 Dec '05 19:56
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro20 Dec '05 20:18
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka20 Dec '05 23:55
Read Message   Re: SBML L2v2 specification vote #4: References to... hugh.d.spence21 Dec '05 02:18
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka21 Dec '05 05:48
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro21 Dec '05 11:35
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard21 Dec '05 15:44
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 07:30
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard22 Dec '05 09:22
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 10:12
Read Message   Re: SBML L2v2 specification vote #4: References to... Pedro Mendes22 Dec '05 10:23
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard22 Dec '05 11:18
Read Message   Re: SBML L2v2 specification vote #4: References to... zucker22 Dec '05 11:54
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard22 Dec '05 12:13
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges23 Dec '05 01:02
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka02 Jan '06 20:49
Read Message   Partial compliance [was] SBML L2v2 specification ... Nicolas Le Novere03 Jan '06 00:08
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro22 Dec '05 12:05
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard22 Dec '05 12:21
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka23 Dec '05 09:07
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard23 Dec '05 10:07
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere22 Dec '05 05:23
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 08:25
Read Message   Re: SBML L2v2 specification vote #4: References to... Nicolas Le Novere22 Dec '05 10:19
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 10:31
Read Message   Re: SBML L2v2 specification vote #4: References to... bshapiro22 Dec '05 10:58
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka22 Dec '05 12:29
Read Message   Re: SBML L2v2 specification vote #4: References to... Darren J Wilkinson23 Dec '05 12:12
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka23 Dec '05 15:46
Read Message   Re: SBML L2v2 specification vote #4: References to... Hiroyuki Kuwahara24 Dec '05 22:01
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka03 Jan '06 00:33
Read Message   Re: SBML L2v2 specification vote #4: References to... Hiroyuki Kuwahara04 Jan '06 10:27
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka04 Jan '06 11:49
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka02 Jan '06 22:23
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka02 Jan '06 20:20
Read Message   Re: SBML L2v2 specification vote #4: References to... Howard21 Dec '05 10:29
Read Message   Re: SBML L2v2 specification vote #4: References to... Sven Sahle22 Dec '05 01:56
Read Message   RE: SBML L2v2 specification vote #4: References to... Nicolas Le Novere21 Dec '05 10:08
Read Message   RE: SBML L2v2 specification vote #4: References to... zucker21 Dec '05 11:02
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges22 Dec '05 02:53
Read Message   Re: SBML L2v2 specification vote #4: References to... Ralph.Gauges22 Dec '05 02:57
Read Message   Re: SBML L2v2 specification vote #4: References to... Stefan Hoops22 Dec '05 08:10
Read Message   RE: SBML L2v2 specification vote #4: References to... Herbert Sauro22 Dec '05 13:08
Read Message   Re: SBML L2v2 specification vote #4: References to... zucker23 Dec '05 22:28
Read Message   Re: SBML L2v2 specification vote #4: References to... Mike Hucka26 Dec '05 09:11
Read Message   Results of SBML L2v2 specification survey vote #4 Mike Hucka04 Jan '06 23:37
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