Re: [SOSlib-discuss] sink reactions

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

Rainer Machne wrote:
> 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.

I just realized that the figure caption states that this change was 
introduced at t=10. However, I think this is a typo, as I get exactly 
the published results for this change at t=0, also for values between 
t=0 and t=10. I am just writing a comment to biomodels about this.

r


> 
> 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
>>
>>
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