IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

ACEDB data update for worm - data only

Richard Durbin rd at mrc-lmb.cam.ac.uk
Mon Apr 10 16:22:10 EST 1995

This is a broadcast message to the ACEDB mailing list and related
newsgroups.  If you are on the mailing list and do not want to be,
please send email to rd at sanger.ac.uk.

ACEDB data updates 2-15, 2-16, 2-17, 2-18 for C. elegans

A set of four new data update files are available for the C. elegans
database.  Once again they are incremental updates, with new data but
no change to the program.  This means Sparc users will again have to
build the maps by hand after adding the updates (see below).

As with the previous release, there are 4 update files because there
is a large amount of new data.  The total database size is now
approximately 140Mbytes.

This release is fully up to date with respect to the physical map, the
CGC information, and gene/genetic map information prior to that
resulting from the recent call for data (which we are working on now).
We have also added over 200 Medline references and a significant
number of missing Gazette pages.  There is also a lot of new genomic
sequence information.

There will be a further release with at least the worm meeting
abstracts and further sequence data three weeks before the worm


There is no new code version.  You should continue to use your
existing version of the binary (2_0).  We are close to a version 4
code release (most of the kernel bugs have been fixed), but did not
want to wait even longer to make this data available.  That has not
turned out to be a good strategy!

		******	IMPORTANT  ******

There is a bug in version 2_0 of the code that causes the program to
crash ("bus error" or "segmentation violation") in some versions of
the binary (particularly sparc) at the very end of reading the
updates.  This does not lose any data.  It does remove the
precalculation of the genetic and physical maps, which should speed up
their display.  You can do this precalculation by hand as follows:

After adding the update, as the administrator (the person who
installed ACEDB)
	Select "Write Access" from the main menu
	Select "Align Maps" from the main menu
	Press the "Make pMaps" button to make the physical maps
	Press the "Make gMaps" button to make the genetic maps
	Select "Save" from the main menu.


Macintosh version

There will be a new macace self-extracting archive containing this
data, ready in approximately a week from now (Frank is away just now).
It will be announced separately on the celegans and acedb newsgroups,
and to the macace mailing list (contact Frank Eeckman if you wish to
be added to this: eeckman at genome.lbl.gov).

Instructions for obtaining updates/the whole thing

All the files are available in the following public access accounts
(anonymous ftp sites) accessible over internet:

  ncbi.nlm.nih.gov ( in the USA, in repository/acedb/ace2
  cele.mrc-lmb.cam.ac.uk ( in England, in pub/acedb/ace2
  lirmm.lirmm.fr ( in France, in directory genome/acedb/ace2

In each case, log in as user "anonymous" and give a user identifier
as password.  Remember to transfer the files in BINARY mode by
typing the word "binary" at the start of your ftp session.  Many
thanks to NCBI for letting us share in their excellent resource.


ftp ncbi.nlm.nih.gov
login: anonymous
password 'your email address'
cd repository/acedb/ace2
mget *
get README  y/n   answer yes   etc


If installing for the first time
Get all the update.2-n.tar.Z and read the files README and NOTES before
proceeding further.

If updating an existing system
Just get the update.2-n.tar.Z files that you are missing, plus INSTALL.

Always get a copy of the INSTALL script.  Move it and the .tar.Z files
into the home directory in which you are installing ACEDB.  Type
"source INSTALL".  Start acedb (normally by typing "acedb") and choose
"Add Update File" from the menu (right button), and press "All
updates" with the left mouse button.

If you have a problem making the program work, look at the section
on problems in NOTES, and if that fails to help, let us know.


Please send any comments, especially about anything you think is
wrong to one of us:

Richard Durbin (rd at sanger.ac.uk)
Sylvia Martinelli (sylvia at sanger.ac.uk)

-------------------- end of message --------------------

More information about the Acedb mailing list

Send comments to us at biosci-help [At] net.bio.net