Non-physical behavior near zero copy number for SSA

[0u812]

The Gillespie simulator allows the copy numbers of molecules to go negative, which should not happen.

[luciansmith]

There's no reason to require species to not go negative in the simulator,
since some models are modelling things that can actually go negative like
charge or debt. A warning is probably appropriate, though.
On Oct 11, 2015 9:36 AM, "Kyle Medley" notifications@github.com wrote:

The Gillespie simulator allows the copy numbers of molecules to go
negative, which should not happen.

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#215.

[0u812]

True, but some models like the Mycoplasma whole-cell model apparently rely on the simulation algorithm stopping reactions before the copy number can go negative, so I'll put it behind a config flag.

[hsauro]

In that case its a bad model. The biophysics should be correct so that
concentration will naturally not go negative. It means the model is not a
good physical representation.

H

On Sun, Oct 11, 2015 at 9:48 AM, Kyle Medley notifications@github.com
wrote:

True, but some models like the Mycoplasma whole-cell model apparently rely
on the simulation algorithm stopping reactions before the copy number can
go negative, so I'll put it behind a config flag.

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#215 (comment).

[0u812]

Fixed. Python syntax is:

r.setIntegrator('gillespie')
r.getIntegrator().setValue('nonnegative', True)

[luciansmith]

I have to agree that that is a crappy model, and not an issue with the
simulator. And in fact, I'm not convinced that adding a special option
that makes the simulator behave incorrectly in response is a good solution,
as the model will continue to be unexchangeable, and exchangeability is
kind of the whole point of SBML, etc.

However, I could see a translator from that crappy model to a slightly
better (but still unrealistic) model that converted reaction rates from:

f(x,y)

to:

piecewise(0, S1<=0, f(x,y))

-Lucian

On Sun, Oct 11, 2015 at 10:26 AM, Kyle Medley notifications@github.com
wrote:

Closed #215 #215 via 8a50677
8a50677
.

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#215 (comment).