Hi folks,
It's me again -- I wrote a few months ago about collecting data for a
review on metabolic simulation (the "Metabolic Simulation and
Informatics" thread). I got a lot of very useful responses and I am
very grateful for the time people have taken to give me their
viewpoints.
I am currently worked on the section about rate-equation based kinetic
simulations, in particular those that game out of the Garfinkel lab in
the early 80s by people like Michael Kohn and Murray Achs. These seam
to be the only pathway-level models I have come across at the level of
resolution of kinetic simulation. I have a few questions that I'd like
to post to group:
1. I am curious to read what people think of as the legacy of this
work. How did it influence your work and what do you see as its most
significant contributions, biologically or computationally?
2. The eighties and early nineties saw a proliferation of software
packages for metabolic simulation, yet these seam to nearly outnumber
the number of models actually constructed at the pathway level. Why is
this? Who are the primary users of, for instance, SCAMP, Gepasi,
Kinsim, DBsolve, SCoP, etc.
3. Between a 1985 simulation of Purine Metabolism by Franco and Canela
and a 1995 update of the same model by Curto et al, it seams as if the
field of (pathway-level) kinetic simulation disappeared. Why the gap?
Or am I missing something? (also if anyone wants to comment on the
purine work, feel free...)
Thanks again for all your help. I am trying as best as I can to present
the work of this community to the bioinformatics world in this review,
so if anyone wants a particular piece of information to get reported,
feel free to drop me a line.
-mike
