Re: [SOSlib-discuss] sink reactions

[Rainer M. <ra...@tb...>]

Michael Lawrence wrote:
> I just posted a bug to the tracker about apparent lack of support for 
> sink reactions (those with only reactants). See e.g. the behavior of HG 
> in BIOMD0000000015. Does not match up with the expected.

Hi Michael,

SOSlib should actually handle sink (and creation) reactions correctly.

Do you mean HX? I can't find HG in the model.

You are right, that the default version of BioModels #15 simulated in 
SOSlib (both version 1.6.0 and current CVS) does not reproduce e.g. 
figure 2 in the publication or the online simulation results at 
biomodels database showing species HX.

However, for figure 2 the initial concentration of PRPP has been 
increased from 5 to 50 uM.

If I increase PRPP accordingly in the SBML from 5.01742 to 50.1742, I 
can reproduce the published results (dashed line for GMA version), both 
with SOSlib v1.6.0 and current CVS.

Can you confirm this or did you mean another error?

Thanks,
Rainer

> 
> Thanks,
> Michael
> 
> 
> ------------------------------------------------------------------------
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> sbmlsolver-discuss mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss