EMBL CD-ROM - some answers
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:
>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
>1) price compared to tape?
Academic (EMBL/EC nation) DM 150
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.
EMBL Data Library
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