ACEDB 4 C.elegans data release

Richard Durbin rdurbin at WATSON.WUSTL.EDU
Sat May 27 17:54:42 EST 1995



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

ACEDB data updates 4-1 to 4-6 for C. elegans
============================================

There is a new version of the C. elegans ACEDB database.  This uses   
version 4_0 of the ACEDB code (subversion beta4).  There will be a 
separate email message about the code for those using ACEDB for other 
organisms. To build the C. elegans database you will need to get all 
six update files update.4-1.tar.Z to update.4-6.tar.Z.

The total database size is now approximately 160Mbytes.  As well as a 
large amount of new sequence data, this contains all the genetic mapping
data submitted to the CGC in Cambridge up to April 1995, together with
a draft new map, and the abtracts for the 1995 Worm Meeting with links
to Gene, Rearrangement and Sequence objects.  

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.

Macintosh version
=================

There will be a new macace self-extracting archive containing this
data.  It can be obtained by anonymous ftp from genome.lbl.gov/pub/macace. 

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 (130.14.20.1) in the USA, in repository/acedb/celegans
and in a few days from
  sanger.ac.uk in England, in pub/acedb/celegans
  lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb/celegans

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.

Example:

ftp ncbi.nlm.nih.gov
login: anonymous
password 'your email address'
cd repository/acedb/ace4
binary
mget *
get README  y/n   answer yes   etc
..
..

quit

--------------------------------

Get all the update.4-n.tar.Z and read the files README and 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") 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 Celegans mailing list