ACEDB 4-8 update for C. elegans

Richard Durbin rd at mrc-lmb.cam.ac.uk
Wed Aug 30 12:22:56 EST 1995

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ACEDB data update 4-8 for C. elegans

As promised, we are now making more frequent releases.  The principle
is to make data available more quickly, and fix errors as they are
found.  Please let us know if you find errors -- they will be fixed in
a subsequent release.  You can add several update files at once if you
want to get them less often, or if you fall behind.  Because they are
more frequent, updates will now be smaller, and so faster to transfer
and load into acedb.

Update 4-8 should be used in conjunction with version 4_1 of the ACEDB
program.  You can add it as an update to a 4-7 database using "Add
update".  The total database size is now approximately 190 Mbytes.

The additions since 4-7 are:
  - more genomic sequence data (there are now 595 cosmids totalling
18,334,987 bases).
  - a physical map update (last one was April 1995).
  - some genetic map updates.
  - some more expression data, including some pictures for the first
      time in the worm database (see below).
  - a new type of map display (X-Sequence etc.), showing the status of
      cosmids being sequenced.  Colour codes are: 
	DARKRED(BROWN)  = submitted, sequence in ACEDB,
	RED             = finished, sequence in ACEDB,
	LIGHTRED        = finished, sequence on ftp server, 
	BLUE            = shotgun, sequence may be on ftp server.
    You can get a key to this information by clicking on the green bar
      at the bottom of the map display, under the coloured cosmid region.
    The endpoints of cosmids in this map are derived from the physical
      map, and are not accurate in detail (in particular duplicate 
      regions are not being sequenced, as suggested by this map!).
  - a number of errors and problems have been fixed.


This update includes some pictures, which will be stored as JPEG files
in the subdirectory pictures/.  In order to see these from acedb, you
must have another program able to view JPEG files.  We recommend xv,
which can be obtained for private use from many anonymous ftp sites
(e.g. wuarchive.wustl.edu).  This must be installed on your computer,
and in your executable path.  You may have it already.  To check if it
is there and working, go to your acedb home directory after installing
update 4-8, and type:
	xv pictures/b0523_5_vul.jpeg

To access pictures from inside acedb, display an Expr_pattern object
(e.g. Expr35), click on one of the Picture titles in bold lettering
next to the tag word Picture (e.g. b0523_5_vul.jpeg).  This brings up
another textual record, corresponding to the Picture object.  Click on
the words Pick_me_to_call and WAIT.  A khaki worm picture with dark
blue staining (lacZ) should appear in an xview window.  To remove the
image, click with left mouse anywhere on the picture. this brings up
the xview menu window. Click on quit.

<< Technical note: If you have another program than xv, or want to
store the files differently, you will need to edit the file

We would like to thank Ian Hope and Andy Lynch of Leeds University for
starting the "ball rolling" and giving us their worm pictures.  We
hope that lots more folk will follow suit especially people working on
cDNA expression patterns.

Good viewing,  Sylvia Martinelli and Eric Sonnhammer.

Macintosh version

A set of Macintosh self-extracting archive files for 4-8 is available
in the macace/ subdirectory of the standard ftp sites.  Follow the
instructions in the README file there.  Pictures are not yet available
in the Macintosh version - if you follow the instructions above I am
told you crash.  We hope they will be working in the next release.

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 ( in the USA, in repository/acedb
  ftp.sanger.ac.uk in England, in pub/acedb
  lirmm.lirmm.fr ( 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.


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
cd ace4				# change to ace4 directory
get bin.sunos.4_1.tar.Z		# get program
cd ../celegans			# change to worm data directory
mget update*			# get all update files


Get any update.4-n.tar.Z 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 at sanger.ac.uk).

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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