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New ACEDB data release WG3.4-3 and WS3.4-18 and 19 for C. elegans
THE NEW DATA RELEASE CAN ONLY BE INSTALLED WITH NEW CODE VERSION 4_5,
WHICH HAS JUST BEEN RELEASED.
With this release we are still using the series of updates called
WS3 (and correspondingly WG3 for the version without sequences). If
you have not changed from WS2 to WS3, please get and read the
instructions in letter.may97 from the ftp directories.
The software has changed. You should be using these updates in
conjunction with release 4_5 of the acedb software. Instructions for
obtaining this are given below. You will see changes in the main
window (classes displayed) and quite radical changes in the Keyset
window. Several other display windows have a new look, for example DNA
analysis and bibliography. The new layout on the main window will not
be fully realised until you have updated, saved, exited and re-opened
Reminder: there are now two versions of the C.elegans database. The
WS3 update series contains everything, whereas the WG3 update series
contains all data except sequences and directly related material
(proteins, motifs etc.), for those with limited resources.
The additions since the last release are:
for both types of update
- a physical map update (mid July)
- accumulated genetic data corrections
- a re-build of the genetic maps after adding new map-data
(submitted by end of april.)
- from CGC : bibliography, wbg subscribers and strains (July)
- from Ian Hope's lab.: more expression patterns and many more images
and for just the complete database including sequences (WS3.4-18 to 19)
Data fom St Louis and Sanger Sequence databases taken in mid-July:
- There are now 2303 (2237 before) cosmids totalling 68938124
(66969575 before) bases.
The total database sizes after adding these updates are around 560MB
for the WS3 database and around 60MB for the WG3 database.
We apologise for the delay between finalising the data and
distribution for these updates, caused by delays in releasing the new
THE CELEGANS DIRECTORY
This contains 3 additional directories in response to a request from
worm users: wscripts/, wspec.WS3.4-19/ and pictures/ . The wscripts
directory has the executable script for viewing the expression images
and the pictures directory contains ALL images submitted to date. The
wspec.WS3.4-19/ directory has many changes which can only be used with
version 4-5 code.
All three have been bundled into the current update files and will
come automatically therefore to people who have taken copies of
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 (126.96.36.199) in the USA, in repository/acedb
ftp.sanger.ac.uk (188.8.131.52) in England, in pub/acedb
lirmm.lirmm.fr (184.108.40.206) 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.
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.solaris.4_5e.tar.Z # get program (use relevant operating system)
cd ../celegans # change to worm data directory
get update.WS3.4-18.tar.Z # get relevant updates
get update.WS3.4-19.tar.Z # or "mget update.WS3.*" to get all updates
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" (or if you are working with the bash shell in Linux,
type "csh INSTALL"). Start acedb (normally by typing "acedb"), click
"Yes" to accept initialising the database if starting from scratch,
then 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.
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)
UPDATE FILE CONTENTS (BRIEFLY)
ws3.4-1 = geneace 1st half (i.e. non sequence material)
ws3.4-2 = geneace 2nd half (i.e. non sequence material)
ws3.4-3 = file1 (sequence_ace bits & pieces)
ws3.4-4 = peptide file
ws3.4-5 = dna1
ws3.4-6 = dna2
ws3.4-7 = dna3
ws3.4-8 = dna4
ws3.4-9 = dna5
ws3.4-10 = protein1
ws3.4-11 = protein2
ws3.4-12 = protein3
ws3.4-13 = sequence1
ws3.4-14 = sequence2
ws3.4-15 = sequence3
ws3.4-16 = sequence4
ws3.4-17 = sequence5 & motif & general fixes
ws3.4-18 = non-sequence material
ws3.4-19 = corrections to sequence material.