ACEDB release: 4_3 code plus data

Richard Durbin rd at mrc-lmb.cam.ac.uk
Tue May 14 15:33:17 EST 1996

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New ACEDB software and data

Acedb version 4_3 is now available in both binary and source form from
our standard ftp distribution sites (see end of this messsage).  It
replaces version 4_1 as the current official acedb release.

The new version contains a large number of efficiency and consistency
improvements and some interface changes, e.g. a much improved
bibliography display tool.  There are also some critical bug fixes.
In particular, it fixes the bug that prevented the most recent
C.elegans data updates being loaded on Solaris machines.

Version 4_3 is compatible with databases produced by 4_1.  It also
supports named databases with their own named series of update files
(see below for C.elegans usage of this).

New C.elegans data releases WS1-8 and WG1-3

The last series of updates (4-1 to 4-14) became extremely cumbersome
to load in, and we decided to start again from scratch.  We also
realise that the database is becoming too large for some users with
limited disk space or memory.  There are therefore now two alternative
database versions:

WS1: updates WS1.4-1 to WS-8.  This contains all information, as up
until now. The current genomic sequence total in WS-8 is 35,483,730
bases.  The current size of this database is 220 Mb.  It will continue
to grow, probably over 500 Mb.

WG1: update WG1.4-1 to WG1.4-3.  This does not contain the genomic
sequence and material directly related to that.  It will however allow
people with limited resources to access genetic and physical maps and
the CGC data, and gives a version of the physical map showing the
state of the sequencing, and EMBL/Genbank accession numbers for
sequenced clones and a map.  The size of this database is 46 Mb, and
it should stay around 50 Mb in the future.

You should make a decision which version you want, and get update
files only for that version.  If you choose to get WG-1, then in place
of getting update files you can get a preloaded database, currently
in the file database.WG1.4-3.tar.Z.

***************************** IMPORTANT ******************************
To correctly install and load the new updates, either WS1 or WG1, you
need to get acedb 4_3, and an up to date copy of the INSTALL script.

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
  ftp.sanger.ac.uk in England, in pub/acedb
  lirmm.lirmm.fr ( in France, in directory genome/acedb

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 user id or email address
cd repository/acedb             # change to relevant directoy
binary				# IMPORTANT
dir				# display files in this directory
cd ace4				# change to ace4 directory
get bin.sunos.4_3.tar.Z		# get program
cd ../celegans			# change to worm data directory
mget update.WS1.4-*.tar.Z	# get all update files


Get any update files that you do not have already and read the file
NOTES before proceeding further.

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").  If you
have installed database.WG1.4-3 then you should be fine now.  If
starting from scratch with update files, when you first start up you
are asked to confirm initialising the database; click "Yes".  Then to
load the updates into the database choose "Add Update File" from the
menu (right button), and press "All updates" with the left mouse

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.


Comments about the data should be sent to the data curator, Sylvia
Martinelli (sylvia at sanger.ac.uk).

Comments about the program, or the installation procedure, should be
sent to one of us:

Richard Durbin (rd at sanger.ac.uk)
Jean Thierry-Mieg (mieg at kaa.cnrs-mop.fr)

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