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Mike Hucka


Posts: 961
Registered:
October 2003
Change to conversion factors in L3 Core 24 Jul '09 10:58 Go to previous message

While writing the SBML Level 3 Core specification, we
realized that the conversion factor attribute probably
should be placed on the species, rather than species
references in reactions. The reason is that, with all
kinetic laws in a model having the same units (by design),
it does not appear that there's any way for a given species
to ever need anything except one conversion factor.

The changes affect several pages in the descriptions of
Level 3 Core changes:

http://sbml.org/Community/Wiki/SBML_Level_3_Core/Species_changes
http://sbml.org/Community/Wiki/SBML_Level_3_Core/Reaction_changes/Changes_to_stoichiometry
http://sbml.org/Community/Wiki/SBML_Level_3_Core/Improvements_to_the_interpretation_of_reactions

(Note: make sure to refresh your browser window in case the
pages have been cached from the last time you visited them
-- this particularly affects the UML diagrams.)

An additional related change is the introduction of an
optional global conversion factor on <model>. This is
explained here:

http://sbml.org/Community/Wiki/SBML_Level_3_Core/Model_changes

We very much welcome people's comments about these proposed
changes.

Best regards,
MH
(on behalf of everyone)


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SubjectPosterDate
Read Message   Change to conversion factors in L3 Core  Mike Hucka24 Jul '09 10:58
Read Message   Re: Change to conversion factors in L3 Core Schaff26 Jul '09 15:31
Read Message   Re: Change to conversion factors in L3 Core Sven Sahle27 Jul '09 01:06
Read Message   Re: Change to conversion factors in L3 Core Stefan.Hoops27 Jul '09 06:25
Read Message   Re: Change to conversion factors in L3 Core Sven Sahle27 Jul '09 08:38
Read Message   Re: Change to conversion factors in L3 Core Schaff30 Jul '09 12:35
Read Message   Re: Change to conversion factors in L3 Core Mike Hucka31 Jul '09 18:57
Read Message   Re: Change to conversion factors in L3 Core Sven Sahle01 Aug '09 02:34
Read Message   Re: Change to conversion factors in L3 Core Schaff01 Aug '09 12:16
Read Message   Re: Change to conversion factors in L3 Core Sven Sahle02 Aug '09 03:50
Read Message   Re: Change to conversion factors in L3 Core Nicolas Le Novere03 Aug '09 16:41
Read Message   Re: Change to conversion factors in L3 Core Sven Sahle04 Aug '09 01:17
Read Message   Re: Change to conversion factors in L3 Core Nicolas Le Novere31 Jul '09 16:26
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