Where can I set the timeout of a web application?

I've got an iterative-intensive app (Monte Carlo simulation for risk 
management of construction company) with upwards from 50000 iterations per 
node (can be hundresds of nodes).
The db query is simple, then the heavy work follows in a class. 
Often I get the message "Server Application Unavailable" on my web, after 
about 3 minutes.
I've set the timout on both the webserver (VBScript timeout) and the SQL 
server at 14400.
I also reset the applicationTimeout in the machine.config file.
It seems the client request times out.
dirk