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Posts: 170
Registered:
December 2006
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Re: assignments
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14 May '10 09:48
 
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On Fri, 14 May 2010 08:34:21 -0700
Frank Bergmann <fbergman@u.washington.edu> wrote:
> Hello Stefan,
>
> sorry for confusing you ... all I wanted to ensure, is that use cases
> that we have now where one would like to iterate through all rules of
> the model would still work as before.
>
> In the scheme lucian and you suggest, asking for all rules would also
> give me initial assignments and event assignments, and would thus
> change my expectation. An initial assignment simply is no rule!
This is about semantics and the use case you mention relates only to the
Semantics Test Suite. To distinguish between the abstract classes and
the semantics we should not use the names Rule and Assignment instead
these constructs could be named RuleBase and AssignmentBase which would
be similar to SBase indicating that only derived classes may be
instantiated.
>
> Anyway ... i guess the next thing to work out would be the
> unification of specifying the target attribute, which right now is:
>
> Initial Assignment: symbol
> Assignment Rule / Rate Rule / Event Assignment: variable
>
> if all of them are supposed to be 'assignments' then this might have
> to change.
I agree, it should be called the same in all cases. Since variable is
already used in 3 cases I suggest to adopt it for the initial
assignment to. For conversion from L2 to L3 the attribute is simply
renamed. libsbml may choose to allow access to both attribute names to
ease conversion.
Thanks,
Stefan
--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility II
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu
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