[Bioclusters] Journalist request: linux cluster user feedback

bioclusters@bioinformatics.org bioclusters@bioinformatics.org
Fri, 10 Jan 2003 10:03:36 +1100

Hello again Bernadette, Happy New Year.

Quick question for you. In your survey you asked if anyone was using
specific implementations of blast on their clusters, such as beoblast. I am
interested to know how many were as we are thinking to implement it, but I'd
like to find out if many people use it.



Gavin Kennedy
Software Engineer - Bioinformatics
CSIRO Mathematical and Information Sciences
ph: 612-6246-4929

-----Original Message-----
From: Bernadette Toner [mailto:btoner@genomeweb.com]
Sent: Friday, 20 September 2002 2:44 AM
To: bioclusters@bioinformatics.org
Subject: [Bioclusters] Journalist request: linux cluster user feedback

Hi everybody -

I'm conducting an informal survey on user trends for bioinformatics Linux
clusters for BioInform newsletter and I'm looking for as much input as

The set of questions below has already been sent out to around 40 people who
use Linux clusters for bioinformatics. If anyone on this list has a few
minutes to add their two cents, that would be really helpful. Feel free to
forward this e-mail to anyone else you know of who may be interested in

I'll post the results to this list once the article comes out - probably in
about two weeks.

Here's the questions (please respond directly to btoner@genomeweb.com):

- How long have you had your Linux cluster running?

- How many nodes was your cluster originally? How many nodes is it now? Do
you have plans to add more in the future?

- Did you build your cluster yourself or use an independent consultant or
hardware vendor (If so, please specify who)?

- What type of processors make up your cluster?

- What type of distributed resource management software (ie, LSF, PBS, Sun
Grid Engine) do you use?

- What bioinformatics/life science applications do you run on the cluster?
Has this changed at all in the time you've had it running?

- Do you use a parallel Blast application? If so, which one (ie, BeoBlast,
NBlast, Blackstone PowerBlast, TurboBlast, Paracel Blast)?

- Is the price/performance of your Linux cluster better or worse than you
expected it to be? Please elaborate, if possible.

- Is the total cost of ownership of your Linux cluster (including air
conditioning/cooling, sys-admin costs, downtime, footprint, etc.) better or
worse than you expected it to be? Please elaborate, if possible.

- Overall, what are the biggest advantages to using a Linux cluster in
bioinformatics? What are the biggest drawbacks?

- What future improvements would be on your wish list for Linux cluster
technology for bioinformatics applications?

All responses will be treated as confidential. If you're willing and have
the time to discuss any of these questions further, please let me know what
day and time would be most convenient for a follow-up discussion.

Thanks in advance to all -

Bernadette Toner

Bernadette Toner
Editor, BioInform
GenomeWeb LLC

Bioclusters maillist  -  Bioclusters@bioinformatics.org