Re: [SOSlib-discuss] sink reactions

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

Michael Lawrence wrote:
> 
> 
> On Fri, May 30, 2008 at 10:00 AM, Rainer Machne <ra...@tb... 
> <mailto:ra...@tb...>> wrote:
> 
>     Michael Lawrence wrote:
> 
>            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
> 
>     ...
> 
> 
>         Also, my results seem similar to what is happening here:
> 
>         http://www.biouml.org/_biomodels/relativeErrors/BIOMD0000000015.xml.html
> 
> 
>     Strange!
> 
>     Which version of the odeSolver are you using?
> 
> 
> 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.
>  
> 
> 
>     Are you using other options additionally to --time 70
> 
> 
> Nope, just --time and the filename.
> 
> 
>     I have just freshly recompiled 1.6.0 and don't get these results.
> 
> 
> I haven't tried 1.6.0, yet. Perhaps I should though.

Which version are you using? I don't have the old libSBML versions, and 
currently sbml.org is down, so i can't test 1.5.0pre, but it is easily 
possible that this bug existed back then, or even still in 1.6.0pre.

Please check the correct libSBML and SUNDIALS (not Scott Cohen's CVODE 
anymore) libraries for 1.6.0 at
http://www.tbi.univie.ac.at/~raim/odeSolver/doc/

If you want to go for the CVS version use the latest versions of both 
libSBML and SUNDIALS (CVS has several bugs fixed, and is much faster, 
with a on-line compiler which should already work, but needs to be 
activated by commenting in some line).

Rainer


>  
> 
> 
>     Rainer
> 
>