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ACEDB data release for C.elegans WS4.4-26 and WG4.4-4

Richard Durbin rd at sanger.ac.uk
Mon Feb 16 12:51:31 EST 1998

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New ACEDB data release WG4 and WS4 for C. elegans 
*** A Macace version is available for WG4 (without sequences only just now) ***

With this release we are again starting a new series of database
updates from scratch, rather than adding on to WS3.  The new series is
called WS4 (and correspondingly WG4 for the version without

Because both series are new, you must get all the updates from the
series you want (WS4 or WG4), and rebuild a new database using them.

If you have a working acedb version built with the WS3 or a previous
series, you must remove your current database/ directory (ideally
after backing it up in case of difficulties).  As well as removing the
database directory, you can also remove any update.WS3...tar.Z or
rawdata/update.WS3... files.

If you do not remove the contents of the database directory, when
you start up acedb it will still say "WS3" in the title bar, and will
not be able to load the WS4 updates.  When you have emptied it
properly, it will ask if you want to reinitialise, and put WS4 in
title bar.

You should be using these updates in conjunction with release 4_5 of
the acedb software (released in August 1997).

Reminder: there are now two versions of the C.elegans database.  The
WS4 update series contains everything, whereas the WG4 update series
contains all data except sequences and directly related material
(proteins, motifs etc.), for those with limited resources.

(N.B. at the end of this file is a list of the contents of each
update file).

The additions since the last release are :

for both types of update				

  - a physical map update with a lot of  changes (mid Jan)
    all but one chromosome is now a single contig
  - accumulated genetic data corrections, inclusion of phenotypes
    from C. elegans II
  - from  CGC : bibliography, wbg subscribers and strains
  - from Leon Avery : wbg15.1 contents and abstracts
  - Expression patterns from Julie Ahringer and Ian Hope, 
	many more pictures form Ian Hope

and for just the complete database including sequences (WS4)

  Data fom St Louis and Sanger Sequence databases taken in mid-December:	
  - there are now 2520 (2237 before) cosmids totalling 75458714 (66969575
        before) bases.
  - there are also many new ESTs from Yuji Kohara.
The total database directory sizes after adding these updates are
around 870MB for the WS4 database and around 75MB for the WG4.


We have made a macace version of WG4, the database without sequence
data.  This can be obtained as a self-extracting archive from
subdirectory macace on the ftp site, file name macace.WG4.sea.bin.  We
will try to build a macace.WS4, but this will need to be distributed
in multiple self-extracting archive files, with instructions on how to
put the resulting files back together.  This will be the subject of a
future message.

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.*		# get all WS1 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"), 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 installation procedure, should be sent to Richard
Durbin (rd at sanger.ac.uk)




20045766 Feb  3 16:31 dna.1.ace			update.WS4.4-1
20002743 Feb  3 16:32 dna.2.ace                 update.WS4.4-2
20041832 Feb  3 16:32 dna.3.ace                 update.WS4.4-3
20020535 Feb  3 16:33 dna.4.ace                 update.WS4.4-4
20000377 Feb  3 16:33 dna.5.ace                 update.WS4.4-5
20009870 Feb  3 16:34 dna.6.ace                 update.WS4.4-6
 5039173 Feb  3 16:34 dna.7.ace                 update.WS4.4-7

 2196036 Jan 29 12:17 LongText.9801.ace		update.WS4.4-8
 2046998 Jan 29 12:22 Motif.9801.ace		update.WS4.4-8

20000250 Feb  3 17:18 prot.1.ace                update.WS4.4-9
20001473 Feb  3 17:18 prot.2.ace                update.WS4.4-10
20024947 Feb  3 17:19 prot.3.ace                update.WS4.4-11
 7927522 Feb  3 17:19 prot.4.ace                update.WS4.4-12

20000092 Feb  3 17:02 pep.1.ace                 update.WS4.4-13
 4625232 Feb  3 17:03 pep.2.ace                 update.WS4.4-14

20051234 Feb  3 17:26 seq.1.ace                 update.WS4.4-15
20029307 Feb  3 17:27 seq.2.ace                 update.WS4.4-16
20000589 Feb  3 17:28 seq.3.ace			update.WS4.4-17
20007206 Feb  3 17:28 seq.4.ace			update.WS4.4-18
20005199 Feb  3 17:29 seq.5.ace			update.WS4.4-19	
20000782 Feb  3 17:29 seq.6.ace			update.WS4.4-20
16893242 Feb  3 17:30 seq.7.ace			update.WS4.4-21

		      gene.1.ace		update.WS4.4-22 update.WG4.4-1
		      gene.2.ace                update.WS4.4-23 update.WG4.4-2
		      gene.3.ace                update.WS4.4-24 update.WG4.4-3

 1564442 Feb  2 16:52 seq_AC_numbers.ace	update.WS4.4-25
    1374 Feb  3 13:40 stl.seq.nospp.ace		update.WS4.4-25
    1274 Feb  4 12:03 xmap.fix.ace		update.WS4.4-25 update.WG4.4-3
     264 Feb  4 12:03 yseqmap.delete.ace	update.WS4.4-25 update.WG4.4-3
	              link.fix.ace              update.WS4.4-25
                      Clonegrid.ace		update.WS4.4-25 update.WG4.4-3
                      Picture.fix.ace		update.WS4.4-25 update.WG4.4-3

		      methods.ace + pictures	update.WS4.4-26 update.WG4.4-4

gene.1.ace, gene.2.ace, gene.3.ace contain the bulk of acedb classes
and form the basis of WG4 database. They deliberately exclude
proteins, motifs, dna, and the bulk of sequence annotations.

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