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Mike Hucka


Posts: 961
Registered:
October 2003
Re: SBML L2v2 specification vote #4: References to controlled vocabularies 02 Jan '06 20:20 Go to previous messageGo to previous message

[Getting back to this after the holidays.]

bshapiro> Here's my point: reactions may include more than
bshapiro> one parameter, and we need to identify which
bshapiro> parameter is which. For example, suppose we know
bshapiro> that a reaction is Michaelis-Menten-Henri, and
bshapiro> we know the k1 and the kD. We can not specify
bshapiro> this information without giving the entire math
bshapiro> field, because even though the kineticlaw is
bshapiro> optional, if the kineticLaw is present the math
bshapiro> is required, and the parameters are inside of
bshapiro> the kinetic law.

Bruce, I understand your point now, and you are right; if
there are local parameters in an SBML kinetic law, then
sboTerms attached to those local parameters will not be
optional separately from the math.

This applies only to local parameters, not global
parameters.

But, it's an issue to take into consideration.

MH

      

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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