Acedb data updates 4-9, 4-10, 4-11 for C.elegans

Richard Durbin rd at mrc-lmb.cam.ac.uk
Sun Oct 29 14:00:47 EST 1995

This is a broadcast message to the ACEDB mailing list and related
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to be, please send email to rd at sanger.ac.uk.

ACEDB data updates 4-9, 4-10 and 4-11 for C. elegans

It is nearly two months since update 4-8.  We are making three new
updates available at once to keep them a reasonable size.  These
should be used in conjunction with version 4_1 of the ACEDB program.
The total database size after adding updates 4-1 to 4-11 is
approximately 240 Mbytes.

The additions since 4-8 are:
  - more genomic sequence data (there are now 707 cosmids totalling
      21,762,318 bases).
  - over 12000 more cDNA EST sequences from Yuji Kohara, more than
      doubling the number available.  Thank you Yuji and colleagues.
  - Worm Breeders Gazette issue 14.1, plus some old missing abstracts
  - coordinate data for an embryonic lineage from Harald Hutter (most 
      cells up to 270mins, some up to 430 mins).  We plan to link 
      images to this data directly in a future version of acedb.  In the 
      mean time, we propose making TIFF images available packed up
      into timepoint-based ftp archives (700 images at 28 timepoints; 
      more details in a future email).
  - the new CGC subscribers list
  - various other new data, including more genetic and expression data.
  - a physical map update (October 13).
  - a number of errors and problems have been fixed -- in particular 
      a whole set of Df/Dup data were behaving incorrectly.

Macintosh version

There will be a macace.4-11 shortly.  There will be a further broadcast
email message announcing this.

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_1.tar.Z		# get program
cd ../celegans			# change to worm data directory
mget update*			# get all update files


Get any update.4-n.tar.Z 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"), 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)

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