From owner-celegans@net.bio.net Thu May 15 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.celegans Subject: ACEDB worm data release WS2.4-20 and WG2.4-4 Date: 16 May 1997 08:16:31 +0100 Lines: 106 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5lh1kf$a9n@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk 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@sanger.ac.uk. ACEDB data updates WG2.4-3 to 4-4 and WS2.4-17 to 4-20 for C. elegans ===================================================================== You should be using these in conjunction with release 4_3 of the acedb software. **** WARNING **** Unfortunately, these update files increase the WS2 database size on disk to around 700Mb. We have been trying to find a way to reduce this, which has led to the delay in this release. We plan to make another release before the Madison Worm Meeting (May 28 - June 1), and hope that will use less disk space. ***************** Reminder: there are now two versions of the C.elegans database. The WS2 update series contains everything, whereas WG2 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. The additions since WG2.4-2 and WS2.4-16 are: for both types of update - a fix to the map displays which were behaving oddly - the expression pictures with the display script from wscripts/ that was missing in the initial WS/G2 release. (the next update will have bibliography, genetics, embl etc (as usual) and for just the complete database including sequences (WS2.4-17 plus) Data fom St Louis and Sanger Sequence databases taken in mid-Apr: - There are now 2177 ( 2020 before) cosmids totalling 65222006 (60615799 before) bases. - Peptides have been updated only to include new ones. The total database sizes after adding these updates are around 700Mb for the WS2 database and around 65Mb for the WG2 database. It will take time to read in the WS2 updates, perhaps 2-3 hours. 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@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- .