EMBL CD-ROM - some answers

Peter Stoehr Peter.Stoehr%EMBL at PUCC.PRINCETON.EDU
Fri Aug 10 08:17:00 EST 1990


Rob Harper has asked me the following about EMBL CD-ROMs:

>Hei Peter,
>
>I have just taken over the task of handling the tapes from EMBL
>I do not know if CD-ROM would be a more elegant solution, but fill
>me in on the advantages.
>If you want to answer these questions in a public forum then
>please do.
>
>RGDS Rob.
>
>1) price compared to tape?

   Academic (EMBL/EC nation)   DM 150
   Academic                       300
   Commercial                     600
   This includes both EMBL Nucleotide and SWISS-PROT sequence databases,
   also retrieval s/w for MS-DOS. Tapes cost half these prices, but only
   include single databases (and no s/w).

>2) CD drive price

   The following are ball-park figures, obviously variable:-
   MS-DOS : DM 1500-1900   (Hitachi or Philips).
   MAC    : DM 2000
   VAX    : DM 4000 (SCSI, eg for vaxstation 3100)
            DM 7000 (Q-Bus)
   SUN    : DM 2000 (Sun SPARCstation 1, 4/60)

>3) Software for getting database from CD drive to VAX.

   A sore point !. Currently there is no CD-ROM driver s/w that allows
   VMS to read ISO-formatted (or High Sierra) CD-ROM's. sigh..
   A standalone program, CD_ACCESS, has been made available which allows
   'dir', 'type' and 'copy' operations on ISO CD-ROM's. Thanks to Peter
   Stockwell, Otago, New Zealand, for this contribution. It is available
   from the EMBL File Server.

>4) Speed of CD drive compared to Hard disk assuming I want to
>   look at data on a PC.

   CD-ROM is slower of course, but its high capacity gives scope
   for extensive indexing which can often overcome the slow access. We are
   very satisfied with the performance of the query/retrieval s/w (for MS-DOS)
   on our CD, for instance.
    As a further clue to whether the CD-ROM can be used a working medium, I
   include some rough figures from some FASTA homology searches. Database
   files used were located on the CD, and were in NBRF-format. The latest
   versions of FASTA for the MAC and MSDOS from Bill Pearson can read these.

   MAC IIcx, 220aa test sequence vs SWISSPROT 13          5 mins cpu
   IBM PC-AT ('real')                                    10 mins cpu

   MAC II cx, 907 bp test vs EMBL 21, Mammal div.         3 mins cpu
                                 EMBL 21, Complete       45 mins cpu

   Of course, there is always the option of copying files from CD-ROM
   to floppy/hard disk if you have space and need to work faster.


Peter Stoehr
EMBL Data Library



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