[Oscill8-devel] .net simdriver

[Emery C. <ec...@vt...>]

Frank,

I notice that SimDriver plots and labels data according to the order in 
which it found the species IN THE SBML file, not in the order that the 
Simulator says they are in... that's not GOOD! A simulator may, for 
reasons of speed or whatever, decide to order things it's own way. In 
the case of Oscill8, the XPPTranslator outputs things in a different 
order than that found in the SBML file AND THIS IS NECESSARY for speed, 
since floating species and dependent species are handled as two 
separate, CONTIGUOUS blocks of memory, and therefore increases speed 
when copying data etc.

Can this be fixed?

Also, you mentioned that the Oscill8 simulator sometimes returns more 
data than was requested... 1001 instead of 1000. This is correct, and is 
especially necessary when we model with events. The simulator needs the 
flexibility to return more data to reflect the shape of the graph (at 
discrete events there is usually a huge jump, and it's very helpful to 
have extra data points to do this). The other alternative is to bail out 
when you've got enough points, BUT THAT is much worse from a user 
standpoint, since that would stop the simulation BEFORE reaching the end 
time.

One last question:

What methods must I implement to have the continuous timecourse in the 
SimDriver work?

BTW, just about done with testing new Oscill8; I'll upload it shortly.

Emery