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

Genome Database acedb at gps.leeds.ac.uk
Thu Apr 9 08:15:29 EST 1998


> From rd at sanger.ac.uk Mon Feb 16 17:50 GMT 1998
> From: Richard Durbin <rd at sanger.ac.uk>
> Date: Mon, 16 Feb 1998 17:28:15 GMT
> To: acedb_distrib at sanger.ac.uk
> Subject: ACEDB data release for C.elegans WS4.4-26 and WG4.4-4
>
>
> 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.
>
> 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
> sequences).
>
> 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.
> database.
>
> Macace
> ======
>
> 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 (130.14.20.1) in the USA, in repository/acedb
>   ftp.sanger.ac.uk (193.60.84.11) in England, in pub/acedb
>   lirmm.lirmm.fr (193.49.104.10) 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.
>
> Example:
>
> 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
> get README
> get NOTES
> get INSTALL
> 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
> quit
>
> --------------------------------
>
> 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)
>
> ********************************************************************
>
> FILE DIVISIONS FOR UPDATE WS4 FEB 98
> ====================================
>
> UPDATE.WS4.4-1.TAR.Z AND UPDATE.WG4.4-1.TAR.Z BOTH
> CONTAIN THE WSPEC/, WSCRIPTS, PICTURES, WGF/ AND WHELP/
> DIRECTORIES.
>
>
> 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.
>
> -------------------- end of message --------------------
>





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