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Mike Hucka


Posts: 961
Registered:
October 2003
RE: Multiple kineticLaw Sections Per Reaction 10 Mar '06 11:02 Go to previous messageGo to previous message

denney> This is what I've been doing, but it doesn't
denney> really seem like the best solution, and I was
denney> thinking this would be a place where the standard
denney> could use some improvement. I didn't know why the
denney> flag was there-- it seems a bit specific (and it
denney> could be detected other ways).

Well, the specification does try to make clear why the flag
is there: e.g., in section 4.9.3 in L2v2, it explains that
the reversibility of a reaction may be evident from the rate
expression, but that the flag has to be there because the
rate expression is *optional*. (If a reaction does not have
a rate expression, then obviously it wouldn't be possible to
use it to infer reversibility :).)

In more qualitative models lacking rate expressions, the
information about reversibility might be available even when
a rate expression is absent, so (we think) the flag has
utility despite that there is some duplication of
information. Some analysis tools may also be able to do
useful work on a model but not be designed to parse rate
expressions.

The spec uses elementary mode analysis as an example, but
presumably there are other applications.

It is critical that the software tool writing out a model
take care to make the 'reversible' flag consistent with the
reaction. This is just a necessary requirement, but
hopefully not an unusual one. There are other places where
bits of a model have to be consistent with each other.

MH

      

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