Well, i could help you with that. But you would need to give a linux test installation a try, but i am sure you have one harddisk lying arround.
in linux you start and stop services with init scripts, wich is /etc/init.d/boinc in that case. to start, you will have to run as root "/etc/init.d/boinc start", to stop its "/etc/init.d/boinc stop".
now linux has somthing called cron, to quote wikipedia: "cron is a time-based scheduling service in Unix-like computer operating systems."
so you just add the following lines to the /etc/crontab file:
Code:
0 * * * * /etc/init.d/boinc start
30 * * * * /etc/init.d/boinc stop
Which results in boinc getting started every 0th Minute, and stopped every 30th minute, which should be enough time to cool down and heat up.
If you want to try this and need help, feel free to ask

(ps: maybe there is the possibility to write such a script which remote controls other clients, and thus only needs to run in a virtual machine, i could try out that tomorrow

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