[Biodevelopers] Standalone WWW Blast server

Joseph Landman landman at scalableinformatics.com
Wed Oct 30 21:53:36 EST 2002

Hi Jacquelyn:

  You should be able to use a Linux machine to do this quite cost

  The configuration of the machine depends strongly upon which databases
you will be using, what type of searches you will be performing, and how
many query sequences you have.

  Some simple rules of thumb:

1) Memory is cheap, and BLAST loves memory.  Without knowing details, I
cannot really guess where you need to be, but I tend to try to configure
a minimum of 1 GB RAM.  "Excess" RAM is used as a disk cache, which
speeds up the calculation.  I have used a machine for searches where 4GB
was insufficient for all the indices of all the databases.  This is
problem dependent.  Don't work with anything less than 512 MB.

2) Disk IO speed is cheap (using IDE RAID0), and databases can be
indexed/manipulated faster on a better file system.

3) Network speed is important, hopefully you have a GigE connection for
pulling down big databases, if not, a nice Intel EtherExpress Pro 100
Network card is a good choice.

4) CPU choice can incite "religious" wars, much like editor choice,
etc.  I use AMD Athlon XP's in my desktop boxes, Athlon MP's in my
servers.  You can use Pentium 4 with equal success.  Just remember that
CPU MHz does not correlate well with performance on all codes.  Lower
MHz does not mean slower, and higher MHz does not mean higher.


On Wed, 2002-10-30 at 16:12, Nguyen, Jacquelyn wrote:
> Here is the email message that I sent to NCBI:
> At this time the Standalone WWW Blast server is only available on UNIX web servers.  We don't have a UNIX server in-house and would like to buy one to use for the Standalone WWW Blast server.  What is the minimum requirements (memories, hardware, software) to deploy the software? What kind of UNIX machine (HP or Sun) do I need?  What kind of web server (weblogic or websphere)?  
> I haven't received a response from them yet and I need the answer soon.  So does anyone know the answer?  Did anyone try to put the software on a LINUX server?  If so, were there any difficulties versus on a Sun Unix server?
> Thanks
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Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman at scalableinformatics.com
  web: http://scalableinformatics.com
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