[SciPy-user] integrate.odeint problem

Peter Cimermančič peter.cimermancic@gmail....
Thu Feb 19 03:25:38 CST 2009


Thank you, Johann. Now it works. However, results, compared to those gotten
from Jarnac, are quite different (initial slope or steady state value differ
two times). Do you know, is this "normal" (since I used modified Jarnac
script directly I can exclude transcriptional mistakes)? I will try with
PySCes, as well.
Regards,

Peter

2009/2/16 Johann Rohwer <jr@sun.ac.za>

> Hi Peter
>
> Try increasing the parameter mxstep (default is 500) in the odeint
> function call to a higher value (such as 1000 or 3000). We are using
> SciPy's odeint in our Python based systems biology simulation
> software PySCeS (http://pysces.sf.net) and have found quite regularly
> for biological models that an mxstep value of 500 is insufficient.
> Incidentally, when PySCeS encounters this situation, it automatically
> increments the mxstep value and re-simulates....
>
> In general, we have been able to get good agreement with PySCeS and
> Jarnac simulating the same model, so I'd be surprised if this does
> not fix it.
>
> Regards
> Johann
>
> On Monday, 16 February 2009, Peter Cimermančič wrote:
> > Hi!
> >
> > Using 60 differential equations, I am trying to simulate some
> > biological process. After running the script, I've got next
> > message:
> >
> > lsoda-- at current t (=r1), mxstep (=i1) steps
> >        taken on this call before reaching tout
> >        In above message, I1 =                  500
> >        In above message, R1 = 0.857...E+01
> > Excess work done on this call (Perhaps wrong Dfun type).
> > Run with full_output = 1 to get quantitative information.
> >
> > After running with full_output = 1, additional information was:
> > KeyError: 0.
> >
> > The same equations and parameters were run in Jarnac (simulation
> > software) and I've got correct results, assuming equations and
> > parameters are right. What else could go wrong to produce above
> > error message?
> >
> > Thank you in advance,
> >
> > Peter
>
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