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Thread Subject:
Negative feedback loop in SimBiology

Subject: Negative feedback loop in SimBiology

From: Jerry

Date: 11 Apr, 2013 13:43:05

Message: 1 of 4

Hello,

How could I connect two species using a negative feedback loop within SimBiology?

Thanks,
Jerry

Subject: Negative feedback loop in SimBiology

From: Arthur Goldsipe

Date: 11 Apr, 2013 22:39:08

Message: 2 of 4

Hi Jerry,

SimBiology includes an example model of an mitotic oscillator that includes negative feedback.

You can see the example here:
http://www.mathworks.com/help/simbio/ug/minimal-cascade-model-for-a-mitotic-oscillator.html

You can also load this model directly in the desktop. The project is located under your MATLAB folder in toolbox\simbio\simbiodemos, and the filename is Goldbeter_Mitotic_Oscillator_with_reactions.sbproj

You can see the negative feedback in the way that more cyclin (species C) leads to more cyclin protease (species M), but more cyclin protease leads to less cyclin.

-Arthur

"Jerry " <jerrycholo@gmail.com> wrote in message <kk6el9$2o3$1@newscl01ah.mathworks.com>...
> Hello,
>
> How could I connect two species using a negative feedback loop within SimBiology?
>
> Thanks,
> Jerry

Subject: Negative feedback loop in SimBiology

From: Jerry

Date: 15 Apr, 2013 17:31:08

Message: 3 of 4

There are seven reactions in this model (Goldbeter_Mitotic_Oscillator_with_reactions.sbproj). I am wondering if which one includes the negative feedback loop and how we could define this loop in a SimBiology diagram.

Thanks,
Jerry

Subject: Negative feedback loop in SimBiology

From: Arthur Goldsipe

Date: 16 Apr, 2013 22:06:08

Message: 4 of 4

Hi Jerry,

It's hard to give you a good answer, because there is no single way to implement negative feedback. I tried to provide you with a biologically meaningful example. All of the reactions in that model are required to get the expected system dynamics. However, I guess I would say that the negative feedback between X and C is primarily introduced in reaction r3 (C -> null), with the fact that the rate is proportional to species X.

To distill this down even more, let me show a smaller example. Let's say you want to create a negative feedback loop between species X and Y. Specifically, you want increasing X to increase the production rate of Y, and increasing Y to decrease the production rate of X. You could do this by creating the following 2 reactions:

X -> X + Y, with reaction rate = k1*X
X + Y -> Y, with reaction rate = k2*Y

Note that if you simulate this system with non-zero X and Y, you quickly product Y and deplete all the X. In a more realistic model, you would probably have additional reactions that are producing and consuming X and Y.

"Jerry " <jerrycholo@gmail.com> wrote in message <kkhdgs$1gi$1@newscl01ah.mathworks.com>...
> There are seven reactions in this model (Goldbeter_Mitotic_Oscillator_with_reactions.sbproj). I am wondering if which one includes the negative feedback loop and how we could define this loop in a SimBiology diagram.
>
> Thanks,
> Jerry

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