[Biodevelopers] Re: [Bioclusters] Workstation Selection for Bioinformatics Research

Chris Dagdigian dag at sonsorol.org
Thu Apr 10 13:23:44 EDT 2003

Hi Chip,

My $.02 of course...

I lean in favor of the dual-booting Intel workstations. The scientific 
software developers and bioinformatics researchers will like Linux 
because of the development environment and wide variety of algorithims 
and tool suites. The researchers interested in visualization and data 
mining will also like Linux but they can benefit from Windows as well 
when/if they want to run apps like Spotfire which are Windows-only.

You need to be careful with your hardware selection if you expect to do 
serious visualization work on your workstations. Make sure that whatever 
graphics card / monitor combination you get is _well_ supported by the 
X11/Linux distro you plan to use. It may be worth aquiring a test 
machine before you actually commit dollars to a bigger purchase. It is 
probably also worthwhile to try to find people who are currently using 
any workstation combo you plan to aquire to see what real users think.

Dell tends to be not that great with Linux at the presales / tech 
support level (sometimes I get lucky) but their Linux guru's hang out on 
the dell-poweredge mailing list and have been amazingly helpful with 
supporting Linux across the entire Dell server line. As an example, 
check out Matt Domsch's website at http://www.domsch.com/linux/ -- that 
site is the first place I check when I'm cluster building with Dell 
PowerEdge boxes.

Not sure if that expertise is also offered for the workstation line though.

Someone else mentioned building your own -- that may be fine for cluster 
nodes but it may not be worth the effort just for workstation machines. 
Especially in an academic lab where there may not be a huge amount of 
steady IT support to run/fix the machines.  People may be suprised at 
the price Dell quotes for workstations. Last time I checked into a 
'build it myself' vs 'buy from Dell' for a personal machine it turned 
out that the Dell box was about the same price as what it would have 
cost me to purchase componants on my own. When you add in the fact that 
Dell will come onsite and fix your box for three years running then that 
seriouly tilts the purchase decision for business/academic users.


Chip Coward wrote:
> Greetings,
>     I am a researcher in bioinformatics at Drexel University and we are
> setting up a computational lab for research and teaching in Computational
> Systems Biology/Bioinformatics. We are looking for workstations for our lab
> using existing software tools or developing new tools to perform molecular
> modeling/visualization (e.g. RasMol/Protein Explorer), searching the genome,
> stochastic modelling/cellular automata, ect. We are considering both SUN
> workstations and Dell workstations (Precision 450/Precision 650) although we
> would be open to consider other platforms if there are compelling reasons. I
> am writing to get input/information that will help us make a decision on
> platform selection. I am leaning toward selecting the Dell Workstation due
> to the theme that prevades these email lists about use of Linux which seems
> to be the way the bioinformatics community is heading. If we purchased the
> Dell system I would configure it to support both Windows and Linux under the
> assumption that by supporting both operating systems, we would have more
> options/flexibility for tool selection.
>    I would appreciate any thoughts or opinions that would help in our
> platform selection.
>    Thanks.

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