Forums

Hello Mike,

You are right I suggest an even less constraint alternative, which would
allow the the result of kinetic laws, i.e., particle fluxes to be used
in assignment rules and the result of an assignment rules to be used as
an input in the kinetic law. It seems to me not only by the choices that
both are desirable features. To allow for both we need to implement an
ordering scheme across reactions and assignment rules. If this choice
would be given, it would definitely get my vote. I recognize that it
becomes more complicated to detect loops however the freedom to
express models is greatly increased.

Thanks,
Stefan



On Sun, 08 Jan 2006 22:03:47 -0800
Michael Hucka <mhucka@caltech.edu> wrote:

> Hi Stefan,
>
> I'm not sure I am following what you're saying below -- do
> you mean that in addition to the 4 alternatives already
> presented, you wanted to see a 5th consisting of the 3
> parts you have listed there?
>
> MH
>
> >>>>> On 19 Dec 2005, Stefan Hoops <shoops@vbi.vt.edu> wrote:
> shoops> It seems to me that the set of options I have to choose from
> is shoops> not complete I would like the following:
> shoops>
> shoops> (I) Remove the ordering constraints on assignment rules.
> shoops> (II) Introduce a similar ordering constraint on reactions
> and shoops> AssignmentRules combined.
> shoops> (III) Allow assignment rules to be functions of reaction
> fluxes AND vice shoops> versa.


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu