From owner-celegans@net.bio.net Mon Jul 15 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.celegans Subject: ACEDB data release for C.elegans Date: 16 Jul 1996 04:03:14 +0100 Lines: 134 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4sf0pi$2tn@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 WG1.4-4 and WS1.4-9 to 4-12 for C. elegans ============================================================= You should be using these in conjunction with release 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 WG1.4-3 and WS1.4-8 are: for both types of update - a physical map update with many changes (June 24th) - some cgc references have been added (April 11th) also a new set of connections between references and Loci - cgc strains update (May) - wbg subscribers update (May) - wbg14.3 citations and abstracts - genetic data left over from submissions for the new Worm map last year (although a few outstanding points need clearing up next time) - a set of transgenic strains from David Baillie has been added - more expression data from Ian Hope and Donna Albertson and more pictures and for just the complete database including sequences WS1.4-9 Data fom St Louis and Sanger Sequence databases taken in mid-June: - There are now 1464 cosmids totalling 44,150,616 bases. We are nearly half way! - We are switching from using the PIR protein database for homology searches to the TREMBL database, hence many PIR homologies are being deleted and TR ones added. The total database sizes after adding these updates are 370Mb 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 4-12. All four updates took us several hours. APOLOGIES ========= For some reason, some of the Sequence-* map displays, which show the status of the cosmids being sequenced, are not automatically updated properly. If no coloured boxes are displayed when you show a Sequence map, then please select "Recalculate" from the main menu. To avoid you from having to do this every time, you should get write access first, then save after recalculating. Sorry, we inadvertently left out Restriction enzymes last time when we were re-building the whole database. This meant that enzyme sites could not be specified by name when using the DNA analysis tool. Poetic justice caught up with Sylvia when teaching ACeDB to a class. They have been added in this release. We failed in the initial WG1 and WS1 releases to include the wscripts directory containing the display_script for viewing the expression pictures. They are included this time. The DNA became inaccessible in the Macintosh version of WS1. We are trying to resolve this problem before the next mac release. The abstracts for the regional worm meetings 1996 did not make this release, but will be in the next one. Plus further transposon mapping data. 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 -------------------- .