Summary: Easier data installation?

Mike Cherry cherry at genome.Stanford.EDU
Sat Jun 26 10:58:29 EST 1993

In article <C94q1A.A2A at usenet.ucs.indiana.edu> gilbertd at bio.indiana.edu (Don Gilbert) writes:
>The general answer here is that updating acedb data sets & software
>is not hard nor time consuming.   I more or less knew that, but haven't
>updated local ace data yet because as I said I haven't enough time
>to do everything that people want me to.

Its really very easy. Since you say you haven't tried it I can assure
you that there is nothing technical about the updates that ACEDB uses.
1) ftp the update file. 2) run a canned csh script to extract the
files 3) start the database and choose the Add Update option.

>Let me expand my belly-ache about time spent maintaining/updating
>biology data (ace & non-ace) at local biocomputing centers & by
>biologists without much computer expertise.  Would it be feasible for
>acedb software to incorportate a homeserver-localserver-client scheme of
>automatic network data retreival?   This is something perhaps like
>Worm Community System envisioned (aside: I haven't seen any updates
>in WCS for > a year -- am I looking in wrong place? place being

WCS used rdist to update their files, and I believe WCS hasn't had an
update since Feb 1992. Which does mean the local WCS admin doesn't do
anything except initially setup the software and leave access to your
machine open to the database administrators.  Thats fine if all the
local copies of your database are on the network and available. We'll
still need to use other methods of updating.  The update procedure
used by ACEDB databases (note the correct spelling is all caps) allows
local users to add there own private data into the database. If no
local data is being added then other methods would be possible. For
example we could create a compressed tar file of changed files,
including the blocks.wrm the binary database file which for AAtDB is
around 50MB, for many other ACEDB based database its much larger. This
would remove step 3 from the list above and require more temporary
free space during an update.

>It would make the life of overworked sys admins and undertrained biologists
>simpler if acedb software could incorportate network links to
>a home server which would update local data automatically, more or less.
>I'd hope to see this scheme considered for many biology databases, esp.
>if they include tailored software like acedb does.

We, the AAtDB Project, haven't heard many (if any) complains about the
update process. We have biologists without any experience with
computers doing the AAtDB updates around the world. Do others have
suggestions for making the process easier than it already is? Is this
a problem that others are concerned about?

I should also note that work is underway for a network client/server
version of ACEDB. We'll all know more after the ACEDB workshop next
month in Boston.

J. Michael Cherry                       Project Manager, Yeast Genome Database
Stanford Genome Sequencing Center,      Department of Genetics
Stanford University School of Medicine, Stanford, CA 94305-5120
Voice: 415-723-7541  FAX: 415-723-7016  Internet: cherry at genome.stanford.edu

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