Re: [SOSlib-discuss] sink reactions

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

On Fri, May 30, 2008 at 9:25 AM, Michael Lawrence <mfl...@fh...>
wrote:

>
>
> 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...
>

Also, my results seem similar to what is happening here:

http://www.biouml.org/_biomodels/relativeErrors/BIOMD0000000015.xml.html



>
> And sorry for presuming there was a bug in the reaction handling.
>
> Michael
>
>
>> Thanks,
>> Rainer
>>
>>
>>> Thanks,
>>> Michael
>>>
>>>
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>>
>>
>