acedb release 4_5

Danielle et jean Thierry-Mieg mieg at kaa.crbm.cnrs-mop.fr
Wed Sep 3 13:28:16 EST 1997


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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 at sanger.ac.uk)
Jean Thierry-Mieg (mieg at kaa.cnrs-mop.fr)

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