Re: [SOSlib-discuss] sink reactions

[Michael L. <mfl...@fh...>]

On Fri, May 30, 2008 at 8:11 AM, Rainer Machne <ra...@tb...>
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.
>

Yes sorry HX.


>
> 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?
>

When I run odeSolver --time 70 on the model, I get the following results for
HX:

 9.51785  37.57650  57.50690  71.10390  80.45370  87.07900  92.03690
 96.01670  99.44160 102.55900 105.51100 108.37200 111.18700 113.97600
116.75000 119.51500 122.27100 125.01900 127.75700 130.48400 133.19800
135.89700 138.57900 141.24200 143.88600 146.50800 149.10600 151.68100
154.22900 156.75100 159.24500 161.71000 164.14600 166.55000 168.92400
171.26500 173.57500 175.85000 178.09300 180.30100 182.47500 184.61400
186.71800 188.78700 190.82000 192.81800 194.78000 196.70600 198.59500
200.44900 202.26700

As you can see just by eye, those numbers are monotonically increasing.
So what is going on here? I must not know what I am doing...

And sorry for presuming there was a bug in the reaction handling.

Michael


> Thanks,
> Rainer
>
>
>> Thanks,
>> Michael
>>
>>
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