Re: [SOSlib-discuss] sink reactions

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

On Fri, May 30, 2008 at 11:14 AM, Rainer Machne <ra...@tb...>
wrote:

> Michael Lawrence wrote:
>
>  I stated above:
>>
>> I am using the CVS as of about a week ago. Don't think it's changed since
>> then. And I believe those BioUML test results (for what they call
>> SBWODESolver) are from the CVS back in December.
>>
>>
> Oh I am sorry! I have overread that!
>
> In that case, the only thing i can think of is that the model is outdated.
> Could that be? I have tried before to get the model they used at BioUML, but
> it is not online anymore. Also they don't have a model version history at
> biomodels, or at least i couldn't find any.
> Could you send me your version, or try to get the current from Biomodels?
>
> I have just removed all changes I had towards the CVS and I don't get this
> behaviour but the apparently correct results, see values below.
>
> It would be strange if it was somehow platform-dependent. What are you
> using?
>
> Also, while we did commit changes during the last week, I can't imagine
> that they should have this effect. But to make sure, could you update the
> CVS, please?
>
> (also, while you are on it and if you are using SOSlib for long and heavy
> runs, you might be interested in testing the new compiler ;) just comment in
> #define ARITHMETIC_TEST in src/sbmlsolver/arithmeticCompiler.h which gives
> can give you a 3-4x speedup ;) )
>
> Rainer
>
>
> odeSolver --time 70 BIOMD0000000015.xml
>
> #t      HX
> ##CONCENTRATIONS
> 0       9.51785
> 1.4     9.51785
> 2.8     9.51786
> 4.2     9.51786
> 5.6     9.51786
> 7       9.51786
> 8.4     9.51786
> 9.8     9.51786
> 11.2    9.51786
> 12.6    9.51786
> 14      9.51786
> 15.4    9.51786
> 16.8    9.51786
> 18.2    9.51786
> 19.6    9.51786
> 21      9.51786
> 22.4    9.51786
> 23.8    9.51786
> 25.2    9.51786
> 26.6    9.51786
> 28      9.51786
> 29.4    9.51786
> 30.8    9.51786
> 32.2    9.51786
> 33.6    9.51786
> 35      9.51786
> 36.4    9.51786
> 37.8    9.51786
> 39.2    9.51786
> 40.6    9.51786
> 42      9.51786
> 43.4    9.51786
> 44.8    9.51786
> 46.2    9.51786
> 47.6    9.51786
> 49      9.51786
> 50.4    9.51786
> 51.8    9.51786
> 53.2    9.51786
> 54.6    9.51786
> 56      9.51786
> 57.4    9.51786
> 58.8    9.51786
> 60.2    9.51786
> 61.6    9.51786
> 63      9.51786
> 64.4    9.51786
> 65.8    9.51786
> 67.2    9.51786
> 68.6    9.51787
> 70      9.51787
> ##CONCENTRATIONS
> #t      HX
>
> ... and the same with the corrected initialAmount:
>
> odeSolver --time 70 BIOMD0000000015.xml.corrected.xml
>
> #t      HX
> ##CONCENTRATIONS
> 0       9.51785
> 1.4     7.29934
> 2.8     8.75094
> 4.2     9.76402
> 5.6     10.4581
> 7       10.9211
> 8.4     11.2168
> 9.8     11.3914
> 11.2    11.4791
> 12.6    11.505
> 14      11.4878
> 15.4    11.4411
> 16.8    11.3749
> 18.2    11.2966
> 19.6    11.2116
> 21      11.123
> 22.4    11.0339
> 23.8    10.9458
> 25.2    10.8604
> 26.6    10.7786
> 28      10.7008
> 29.4    10.6274
> 30.8    10.5582
> 32.2    10.4931
> 33.6    10.4319
> 35      10.3744
> 36.4    10.3207
> 37.8    10.2706
> 39.2    10.2242
> 40.6    10.1811
> 42      10.1408
> 43.4    10.103
> 44.8    10.0674
> 46.2    10.0343
> 47.6    10.0038
> 49      9.97568
> 50.4    9.94967
> 51.8    9.92517
> 53.2    9.90191
> 54.6    9.87989
> 56      9.85958
> 57.4    9.84113
> 58.8    9.82448
> 60.2    9.80886
> 61.6    9.79395
> 63      9.77958
> 64.4    9.76607
> 65.8    9.75357
> 67.2    9.74221
> 68.6    9.73176
> 70      9.72204
> ##CONCENTRATIONS
> #t      HX
>
> ... which corresponds to the published figure 2.
>


Looks like I've figured this one out. I had passed the XML through libsbml
and its MathML to formula routines. Apparently, it got confused between the
constant pi and the symbol for inorganic phosphate Pi. That's kind of funny.


Sorry for taking up so much of your time.

Michael