Re: [SOSlib-discuss] sink reactions

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

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outdated.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.