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You nailed a fear I have with specialised hardware, but I think for the most part the hardware would be transparent to the astro data acquisition apps like focusmax, pinpoint, maximdl, blah blah. If it wasn't transparent, then the OS isn't doing its job IMO. The problem I have is the current system is a tower case. The CPU fan gets choked up with considerable dust. Over time it falls down onto the PCI wireless adapter causing me grief shorting things out. There's always a cheap or expensive way of solving this. The PC in the Obs is never turned off unless there's a power failure as its also used to log weather station information from the Davis Vantage Pro and Weather Envoy data logger.
Looking at some of great suggestions here has given further insight. I think I'm better off with a system that it's external case/enclosure is one giant heat sink instead of a fan operated unit. Some operate on 48VDC would may also lend itself well with future solar power plans, but I'm not pushing for a "green" observatory as yet.
I should note that I don't use this system for processing. Solely data acquisition.
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