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Howard,

I admit that I've not explored new architectures, but under old
architectures compilers and assemblers had the ability to produce memory
maps which had the positions of variables in the binaries produced. Thus
you could compile your model ONCE and produce a binary image of your
program, which could be modified (in C or similar by changing only the
relevant individual bytes) before being run. This does not depend on
object-orientation or interpretation (beyond some operating system
commands which are so basic that they are practically inescapable).

This is less expensive than re-evaluating the sboTerm many
thousands of times and does not prevent you using your special libraries
for optimisation. The time to evaluate the algebraic expression once is
truly negligible.
The time to read in a binary image is going to be less than to
read an SBML file.
The time to alter and write a new version of the binary image is
going to be less than to parse an SBML file.

Maybe the new architectures preclude this, but it would appear to
the uninitiated to be a retrograde step.



Hugh Spence
GSK Scientific Computing and Mathematical Modelling
Medicines Research Centre
Gunnels Wood Road
Stevenage
UK
SG1 2NY