Problem in Adding events

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Parvathy Sarma

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Sep 11, 2022, 12:09:16 PM9/11/22
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Hi,

As a beginner in COPASI tool, I am finding difficulty in adding an event to a reaction set. For example, consider a reaction where 

C <- A -> B,  Here A can yield two products based on some conditions. I would like to add a condition, when damage 9global quantity) is greater than 50% A favours the reaction towards C and not B. But when it is less it favours the reaction B and not C.

I tried adding this in event section but my time course simulation dosent show any change in results. the plots are indifferent both in the precense or absence of events. Can you help me how to rectify this.

Thanks in advance

Hoops, Stefan (sh9cq)

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Sep 11, 2022, 1:03:57 PM9/11/22
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Hello Parvathy,

Without seeing your model I have only a couple of comments:

What is the target or what are the targets of your events? Please note
that events only get triggered when the trigger condition changes from
false to true.

Thanks,
Stefan
--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911

Phone: +1 540 570 1301
Email: sho...@virginia.edu

Matthias König

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Sep 12, 2022, 4:33:48 AM9/12/22
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Hello Parvathy,

I would probably model this as two reactions:
v1: A -> B
v2: A -> C
where you make the rates v1 and v2 dependent on some condition. I.e. this could just be a function f(p1, p2, p3, ..) which you add as a factor to the kinetic law or you could also use some event to change v1 and v2.

As an alternative: If you have a reaction A -> s1 * A + s2 * B, with s1 and s2 being the stoichiometric coefficients you could also make the coefficients non-constant, i.e. depening on a condition. This would shift your reaction either to A or B. As far as I know COPASI does not support variable stoichiometric coefficients (as do many other SBML tools). So I would probably go with the first suggestion here.

Hope this helps.
Best Matthias
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