ACEDB data release for C. elegans

Richard Durbin rd at mrc-lmb.cam.ac.uk
Mon Sep 12 23:59:54 EST 1994



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ACEDB data updates 2-11, 2-12, 2-13, 2-14 for C. elegans
========================================================

A set of four new data update files are available for the C. elegans
database.  I apologise for the long delay.  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).

There are 4 update files because there is a large amount of new data,
in particular sequence data, and we have also rearranged some of the
information.  The total database size is now approximately 90Mbytes.

The main items in this data release are:
       77 new cosmids from the genomic sequencing project, making
	over 6Mb of completed sequence (211 separate entries), plus 
	corrections and updates to old sequences.
       Over 5000 new cDNA EST sequences from Yuji Kohara.  These are
	now clustered by Yuji into groups for mapping, based on
	identity of sequence (usually identity of 3' end sequence).
	There are 1508 groups, named YK1 to YK1508, almost all of
	which have been placed on the physical map.  Thank you Yuji.
       The text of the gazette articles for issues 12.2 to 13.2, 
	obtained with the help of the WCS project and Leon Avery
	(thanks to both).  In release 2-10 gazette issue 13.2 was
	systematically named 13.1 by mistake.  This has been corrected.
       Ronald Pasterk's group are now maintaining sequence data around
	Tc1 insertion points for inclusion in ACEDB as the
	corresponding genomic sequence is finished.  If you have data 
	to contribute please contact Ronald at rplas at ron.nki.nl.
       Plus other regular updates to the map data, bibliography, 
	EMBL sequences etc.  Because Mary O'Callaghan left in June 
	(see below), changes sent to cgc at mrc-lmb.cam.ac.uk since then 
	are not reflected in this release.  They have not been lost 
	and will be incorporated in future releases.

New curator needed
==================

Mary O'Callaghan, who managed most of the genetic and bibliographic
information in ACEDB, left the project in June.  I'd like to thank
Mary for everything she has done over the last couple of years.  We
are in the process of looking for a replacement; we would like
somebody with a biology background who likes working with computers.
For further information contact me at the email address given below.

Code
====

There is no new code release.  You should use your existing version of
the binary (2_0).  We hope to release a significantly new version of
the ACEDB code, version 4.0, this fall.  If you use the Macintosh
version and are not already on the macace mailing list, please contact
Frank Eeckman (eeckman at genome.lbl.gov) to be placed on his list, which
will announce macace code and binary compressed databases.

		******	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.

		**************************

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/ace2
  cele.mrc-lmb.cam.ac.uk (131.11.84.1) in England, in pub/acedb/ace2
  lirmm.lirmm.fr (193.49.104.10) 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.

Example:

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

quit

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

If updating an existing system
------------------------------
Just get the last update.tar.Z file, 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". 

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 (program or data), to

Richard Durbin (rd at mrc-lmb.cam.ac.uk)

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