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SBML Discussions » sbml-discuss » SBML L2v2 specification vote #6: Reaction Ids and Assignment Rules
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Mike Hucka


Posts: 961
Registered:
October 2003
Results of SBML L2v2 specification survey vote #6 10 Jan '06 21:50 Go to previous message

The topic of this vote was:
REACTION IDENTIFIERS AND ASSIGNMENT RULES

Thank you all for your participation in the SBML electronic
vote on this issue. The voting on this topic is closed.
For reference, the call for votes can be found at this URL:
http://www.sbml.org/forums/index.php?t=msg&th=731&start=0&rid=2

The total number of votes cast was 20; all votes were
unique. The results are the following (where the
descriptions of options a-d are excerpted below, for
convenience):

# of votes for option (a) -- no reaction id's in math: 2
# of votes for option (b, see below): 5
# of votes for option (c, see below): 4
# of votes for option (d) -- remove ordering constraints: 9

The results show that a majority of voters prefer option
(d), keeping the ability to use reaction identifiers and
removing the ordering constraints on assignment rules.

Here are the excerpts of the description of the options:

> Alternative 1: Back out this part of the SBML L2V2
> proposed specification, that is, do *not* introduce the
> ability to use reaction flux identifiers, and leave the
> ordering constraints on AssignmentRules structures as they
> are specified in SBML Level 2 Version 1. (This would
> leave the burden of sorting the rules only on the SBML
> generator, as it is now.)
>
> Alternative 2: (i) Retain the specific constraints on
> ordering of AssignmentRules in L2V2 as they are in L2V1;
> (ii) introduce a separate, similar ordering on reactions;
> and (iii) allow reaction fluxes to be functions of
> variables assigned values by AssignmentRules, but not vice
> versa. One implication of this is that fluxes could not
> be used in the calculations made by assignment rules. (As
> in the alternative above, this would also leave the burden
> of sorting the rules only on the SBML generator, as it is
> now.)
>
> Alternative 3: (i) Retain the specific constraints on
> ordering of AssignmentRules in L2V2 as it is in L2V1; (ii)
> introduce a separate, similar ordering on reactions; and
> (iii) allow assignment rules to be functions of reaction
> fluxes but not vice versa. (Again, this would leave the
> burden of sorting the rules on the SBML generator, as it
> is now.)
>
> Alternative 4: Remove the ordering constraints on
> assignment rules. This would mean that numerical
> applications will in general need to perform a topological
> sort upon reading an SBML model, on the combined set of
> kinetic laws and assignment rules. This will shift the
> burden onto the SBML reader rather than the writer. (But,
> it is worth noting that the sort would only have to be
> performed *once* per model.)

MH

      

SubjectPosterDate
Read Message   SBML L2v2 specification vote #6: Reaction Ids and ... Mike Hucka18 Dec '05 19:35
Read Message   Re: [sbml-discuss] SBML L2v2 specification vote #6... Stefan Hoops19 Dec '05 12:47
Read Message   Re: [sbml-discuss] SBML L2v2 specification vote #6... Mike Hucka08 Jan '06 22:03
Read Message   Re: [sbml-discuss] SBML L2v2 specification vote #6... Stefan Hoops09 Jan '06 05:05
Read Message   Re: SBML L2v2 specification vote #6: Reaction Ids ... Sarah Keating20 Dec '05 02:11
Read Message   Results of SBML L2v2 specification survey vote #6  Mike Hucka10 Jan '06 21:50
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