[Bioclusters] Workstation Selection for Bioinformatics Research

Elia Stupka bioclusters@bioinformatics.org
Tue, 15 Apr 2003 16:53:05 +0800


> They're grossly annoying because there are still things they either 
> can't do or seem to not want you to do.

I sit back quietly on the list but once in a while I need to voice 
out.... we are running a large Xserve bioinformatics cluster for all 
sorts of applications, from back-end to front-end, from research to 
services, from genome annotation pipelines (read repeatmasking, 
blasting, genewising, hmmering,etc.etc.) to promoter characterisation, 
and...

...yes we did have some pains, yes we did have to recompile here and 
there and yes, my sysadmin is adored and admired by all of us, but none 
of the issues we had were unsurmountable, and so far we have not had a 
showstopper.

So I would be very interested to know more about what they "can't do 
and don't want you to do" (except, of course, commercial packages where 
the vendor has not provided a binary for OS X, in which case I'd be 
happy to challenge whether their product can be emulated with open 
source software and a bit of good old programming glue)

Now interestingly I notice the discussion was not even about server 
machines in the farm but about desktops. While there might be some 
reasons not to use Xserves for a large farm (though we do it 
successfully) there is definitely no reason I see to get a dual boot in 
one machine -> OS X rather than nightly patches, VMWare,etc. It is not 
just about getting a dual boot in one system, it is also about getting 
people that like user-friendly OSs to use tools usually available only 
in UNIX (and its reliability).

> That probably answered no ones question and will just get the 
> workstation/apple/stinkpad people mad at me. Oh well.

;) Not mad, just interested. Mind you, before OS X came out I'd have 
used a Mac only as a heavy paper-holder and an iMac as a football... :)

Elia

---
Bioinformatics Program Manager
Temasek Life Sciences Laboratory
1, Research Link
Singapore 117604
Tel. +65 6874 4945
Fax. +65 6872 7007