From owner-celegans@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.celegans Subject: ACEDB data updates for C.elegans Date: 3 Dec 1996 19:44:46 -0000 Lines: 105 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <581vve$p5l@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 WG1.4-7 and WS1.4-21 to 4-26 for C. elegans ============================================================== ****** IMPORTANT NOTICE: you must get a new copy of INSTALL ******** Versions of the INSTALL script from before December 1996 will not unpackage these update files correctly. ******************************************************************** You should be using these updates in conjunction with previous WS1 and WG1 releases, and version 4_3 of the acedb software. Reminder: there are now two versions of the C.elegans database. The WS1 update series contains everything, whereas WG1 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. The additions since WG1.4-6 and WS1.4-20 are: for both types of update - a physical map update with a few changes (mid Nov) - accumulated genetic data including a substantial number of new gene_classes and loci, also some mapping data - from CGC: bibliography, strains and subscribers (late Oct) - from Leon Avery: wbg14.4 with connections to genes etc. and for the first time connections to Cells and Cell_groups (any comments ??) and for just the complete database including sequences (WS1.4-16) Data fom St Louis and Sanger Sequence databases taken in mid-Nov: - There are now 1777 (1714 before) cosmids totalling 53695369 (51655842 before) bases. The total database sizes after adding these updates are around 480Mb for the WS1 database (we said it would grow!) and around 65Mb for the WG1 database. It will take a long time to read in the WS1 updates, particularly WS1.4-22 to 4-24. All six updates took us several 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 -------------------- .