IUBio

PC/Mainframe - data vs. storage

goldman at mbcl.rutgers.edu goldman at mbcl.rutgers.edu
Tue Jun 23 14:21:11 EST 1992


In article <1992Jun22.162120.1 at hmivax.humgen.upenn.edu>, bailey at hmivax.humgen.upenn.edu (Charles Bailey) writes:
> In article <1992Jun19.122907.12041 at athena.cs.uga.edu>, russell at dogwood.botany.uga.edu writes:
>> 1.  The amount of data in GenBank, EMBL etc. must be going up rapidly,
>>     and someone must be projecting this into the future.
> 
> Last I heard, GenBank was increasing at ~25% of total size per quarterly
> release.  The specific figure for the current release of EMBL (31) is 14%.
. stuff deleted to conserve bandwidth..

> 
> 
>> These two trends could resolve in several ways -
>> 
>>     There might be so much sequence information that local computers
>>     would not be able to handle the storage, and we would all have
>>     to rely on the big facilities for searching, homologies, etc.
>> 
>>     The improvement in data storage and its lowered price might
>>     reach the point where PCs and Macs could reasonably handle
>>     all the required tasks, including storage of all sequence data.
>> 
>> Has anyone projected these kind of thoughts for 5 years from now, as
>> opposed to what is the optimum system for the size of GenBank right
>> now.
> 
> Actually, I think that the limiting factor in most cases will be cycles, not
> storage space.  This is especially true as smallish minis and largeish micros
> use more and more of the same mass storage technology (e.g. a SCSI chain filled
> with 1-2 Gbyte disks will be adequate for a while :-)).  As the data expands,
> however, and as techniques for analysis become more sophisticated,  micros like
> the Mac and IBM PC will suffer more severely from CPU performance limitations. 
> I expect that for the near future they will perform well for tasks like
> restriction mapping, contig assambly, and perhaps simple pattern searches or
> alignments, and may in fact have an advantage in these areas since most of the
> packages I've seen have nicer interfaces than the mini/mainframe sw.  The
> faster processors in the minis, however, will substantially outperform micros
> in tasks like database searching, multiple alignments, etc.  (For the *real*
> processing nuts, there's always parallel machines, but I don't expect to see
> them in general-use analysis facilities for a while.)  Particularly as the
> prices for small minis and workstations drop, I'd recommend that any site which
> plans to do significant database searching or complex alignment locally but as
> much CPU as they can reasonably afford.
> 
I basically concur, except that I don't really think the bottleneck on PCs
and MACs is the CPU.  High-end machines PCs and MACS have fairly respectable
compute power.  What they don't have is I/O bandwidth.  So they can't
really drive their disks that fast, and they certainly can't drive (for
instance) a stripe set at its rated speed.  So that's why I think minis
will outperform micros in data-intensive searches.

               Adrian

-- 
Adrian Goldman                         |  Internet:  Goldman at MBCL.Rutgers.Edu
Molecular Biology Computing Laboratory |  Bitnet:    Goldman at BioVAX
Waksman Insitute,                      |  Phone:     (908) 932-4864
Rutgers University,                    |  Fax:       (908) 932-5735
Piscataway, NJ 08855 USA               |




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