From owner-celegans@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.celegans Subject: acedb release 4_5 Date: 3 Sep 1997 19:29:00 +0100 Lines: 158 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5uka9c$93r@mserv1.dl.ac.uk> Original-To: celegans@dl.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 mieg@kaa.crbm.cnrs-mop.fr, rd@sanger.ac.uk. ACEDB code release 4_5 ====================== A new version of acedb is available at ncbi and the usual mirror sites Ace 4_5 is fully compatible with ace.4_3, if you download this code, you do not need to reconstruct your database. New features ============ The overall quality of the code has been improved, the system is faster and uses much less memory when exporting large relational tables. The non graphic code has been extensivelly checked and should be very reliable. A number of graphics have changed, in particular the help system, which now uses an http browser and the key-set display, which now offers many submenus. There is a new Forest display, available from the more-info button of the keyset window, which offers a custom view of sets of objects, and a new Peptide display for proteins. Jo Dicks' comparative map displays have been added. Most other displays have been fixed and/or improved. The sequence display now offers asynchronous access to blast, biomotif and oligo-search, via external calls using scripts in wscripts. The genefinder options now have controllable parameters. The blixem display has many additions. The map display has several new columns. The printer and file chooser are more flexible and easier to control. And so on. Data curators should note the new file wspec/layout.wrm which now controls wysiwyg the class layout of the main window. Unix Binaries ============= The distributed code has a subrelease letter, presently 4_5d/e, which may continue to change a little while we build for more platforms, but is irrelevant otherwise. The code itself is now fixed. Binaries are available for SUN, SOLARIS, Silicon, DEC, Linux; more binaries will appear soon for IBM and HP, and since the source code is available, you may also recompile for your platform if it is not on this list. Windows version =============== For the fist time, we include a binary for windows-95 and windows-NT intel machines. This code was prepared by Richard M. Bruskiewich, from Vancouver from the same souce code. Please let us know of any problems and also if you are happy with it. It seemed to be very fast on pentium-200 machines. To install winace, read the document WinAce.*.txt Mac version =========== Unfortunately, we are not able to port ace.4_5 for the mac. So the last Mac version remains ace.4_1. We hope that Cyrus Hammon, who built the current macace release will be able to recompile 4_5 for the mac, or give us his latest source code, but there is no guarantee. If you are a mac programmer and would like to help, please let us know. Server/Client ============= Ace.4_5 server client capability have been substentially improved. To gain space, and since any person installing a server is most probably able to recompile, the servercode is not part of the binaries but must be recompiled with the command: make aceserver gifaceserver other However, we do distribute the SOLARIS server, because the make command on solaris produces an aceserver which does not work in daemon mode. (help welcome if you are a solaris/rpc expert) There is now a graphic client, xaceclient, with a start-up script called xcl which will act exactly like xace, but getting its data transparently form a remote server. The gifaceserver can export postscript or gif files equivalent to the standard graphic xace. It will be used by the forthcoming revised webace release. The jade program can export the data to the Web using the recent java language. 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 (130.14.25.1) in the USA, in repository/acedb ftp.sanger.ac.uk 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.xxx.4_5d.tar.Z # get correct precompiled code get source.4_5d.tar.Z # and/or get the source code quit -------------------------------- If you want the C.elegans data, get any update.4-n.tar.Z that you do not have already from the directory ../celegans. 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 "chmod 755 INSTALL ; INSTALL". Start acedb (normally by typing "acedb"), click "Yes" to accept initialising the database if starting from scratch. If you imported the update files, 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 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 -------------------- .