[Bioclusters] Journalist request: linux cluster user feedback

[bioclusters@bioinformatics.org]

Hi there!

I would like to find out the advantages of using Linux clusters as opposed to 
Grid computing and/or Supercomputers for genomic research or any research for 
that matter in the biotech industry.

Thank you,
Ravi Subramanian

> 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.
> 
> Regards,
> 
> Gavin
> 
> Gavin Kennedy
> Software Engineer - Bioinformatics
> CSIRO Mathematical and Information Sciences
> Gavin.Kennedy@CSIRO.AU
> 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
> possible.
> 
> 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
> participating.
> 
> 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
> 212-651-5636
> btoner@genomeweb.com
> www.bioinform.com
> 
> 
> 
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