[Richard Finney]

Don't forget: monitor, keyboard, mouse.

Verify: CPU works with MB. Memory is compatible with MB (check MB manufacturers list of supported chips). Power supply is sufficient. Network IF will work with your network.
Check out driver support for your graphics card (may not be that important).

What is your data back up plan?

[atcghelix]

Thanks for the price breakdown and advice, Wallysb01. I'd definitely prefer to offload stuff to an external builder if the markup is < $1,000 and comes with better warranty coverage and easier support. We're at UCLA--I'll check about vender lists. That markup might be putting us into the E5-2630 v2 territory in terms of what we can afford, but maybe still worth it? Or maybe we should wait a few weeks for the E5-2630 v3? Lots to think about...

We currently back up our raw data to a Synology 1812+ in RAID 6 (still on campus, but in a different building), and will be archiving in Amazon Glacier.

[Wallysb01]

Thanks for the price breakdown and advice, Wallysb01. I'd definitely prefer to offload stuff to an external builder if the markup is < $1,000 and comes with better warranty coverage and easier support. We're at UCLA--I'll check about vender lists. That markup might be putting us into the E5-2630 v2 territory in terms of what we can afford, but maybe still worth it? Or maybe we should wait a few weeks for the E5-2630 v3? Lots to think about...

Brain's comments above about core count vs clock speed in bioinformatics should help you guage how worth it each CPU upgrade might be. If you're doing a lot of aligning, maximizing core count * GHz in your bugdet is what you should shoot for.

Personally, I don't think waiting for v3 is that big of deal. For the 2630, you'll pick up 2 more cores (8 total), but lose 200 GHz, plus the maybe 5% clock-for-clock performance increase (2.6 * 6 = 15.6 GHz vs. 2.4 * 8 * 1.05 = 20.16 v2 equivalent GHz). So its a nice bump (~33% faster if you can use all cores), however, those v3 systems will be a bit more expnsive since you have to use DDR4, which is about $100 more than DDR3 per 16GB stick right now.

[jpummil]

Vendor recommendations allowed?

http://www.advancedclustering.com/products/horizon-workstations.html

I've known these guys a long time and are pretty impressed with their stuff as well as their support and service.