[Biodevelopers] Re: Biodevelopers digest, Vol 1 #95 - 5 msgs

[Allen Henry]

To all new in this field, please get some advise from
a friend who's been in IT or engineering for many
years and keeps up with price/performance ratios of
the various vendors.

A little known fact is that the SDSC is running on
Linux clusters for performance reasons, this is much
faster/cheaper than any windows solution since Linux
is FREE!

I, personally, am technology agnostic and do not
participate in any religous wars over such matters,
since I have to deliver products 'on-time and under
budget', and do not have the luxury of working in
'research' or 'academic' environments where this does
not seem to be a concern.

A new report (Dr. Dobbs ?), concludes that the total
cost of ownership (over time), for Linux is
substantially higher than the windows solution. Why?
Because of the maintenance costs. Linux revs every
month, there are different flavors of Linux, etc...

The code that I've seen out of research and academia
are autrocious, thus, any personnel turn-over is also
extremely costly. Please remember to comment all code,
initailize all variables, identify all variables in
comments, and comment any 'tricky' code, and this will
reduce your maintenance costs substantially. Following
good programming practices will save you up to 25% of
the total cost of ownership. 

The other major factor in this price/performance ratio
is how long this code/hardware be around. These are
typical engineering questions that I would hate to see
any bio person make in the dark.

So in summary, get a software friend who can give you
advise on the applications. R my ass, statistical
packages have been around for decades and cost a
fraction of writing/maintaining your own. 

Find another friend who understands the differences in
the chips (int vs float math, and performance ratios),
since these differ by manufacturer/ chip/ and changes
every 18-24 months.

Then get the software and the chip friends together
and communicate. This seems to be more of an
engineering question than a bio one, so maybe your
friends should answer it, and you just go along... :-)

Hope this helps


--- biodevelopers-request at bioinformatics.org wrote:
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> When replying, please edit your Subject line so it
> is more specific
> than "Re: Contents of Biodevelopers digest..."
> 
> 
> Today's Topics:
> 
>    1. Workstation Selection for Bioinformatics
> Research (Chip Coward)
>    2. Re: Workstation Selection for Bioinformatics
> Research (Malay Kumar Basu)
>    3. Re: [Bioclusters] Workstation Selection for
> Bioinformatics Research (Chris Dagdigian)
>    4. Re: [Bioclusters] Workstation Selection for
> Bioinformatics Research (Joe Landman)
>    5. Re: [Bioclusters] Workstation Selection for
> Bioinformatics Research (Joseph Landman)
> 
> --__--__--
> 
> Message: 1
> From: "Chip Coward" <ccoward at jersey.net>
> To: <bioclusters at bioinformatics.org>,
> 	<biodevelopers at bioinformatics.org>
> Date: Thu, 10 Apr 2003 12:39:34 -0400
> Subject: [Biodevelopers] Workstation Selection for
> Bioinformatics Research
> Reply-To: biodevelopers at bioinformatics.org
> 
> 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.
> 
>          Chip Coward
> 
> 
> 
> 
> 
> 
> --__--__--
> 
> Message: 2
> Date: Thu, 10 Apr 2003 22:54:23 +0630
> From: Malay Kumar Basu <curiouser at ccmb.res.in>
> To: biodevelopers at bioinformatics.org
> Cc: bioclusters at bioinformatics.org
> Subject: Re: [Biodevelopers] Workstation Selection
> for Bioinformatics Research
> Reply-To: biodevelopers at bioinformatics.org
> 
> On Thu, 10 Apr 2003, 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.
> > 
>  
> Good choice. Almost all bioinformatics software
> nowadays have Linux
> support. And noone can beat GNU/Linux when it comes
> to software
> development. And Linux really scale very well to
> move to cluster
> computing. It is so easy, one of our Indian
> distribution actually modified
> RedHat 8 to give cluster installtion as standard
> installation option.
> Except for some legacy proprietary software you can
> virtually manage to do
> all your bioinformatics on Linux.
> 
> Cheers,
> 
> Malay
> 
> 
> 
> 
> --__--__--
> 
> Message: 3
> Date: Thu, 10 Apr 2003 13:23:44 -0400
> From: Chris Dagdigian <dag at sonsorol.org>
> To: bioclusters at bioinformatics.org,
> biodevelopers at bioinformatics.org,
> 	ccoward at jersey.net
> Subject: [Biodevelopers] Re: [Bioclusters]
> Workstation Selection for Bioinformatics Research
> Reply-To: biodevelopers at bioinformatics.org
> 
> 
> 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 
=== message truncated ===


=====

=================================================================

An ounce of prevention is worth a pound of cure

 

Allen Henry
408 799-9404 
10am - 10pm PST


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