ACEDB release 2-10: C. elegans data

Richard Durbin rd at mrc-lmb.cam.ac.uk
Thu Apr 14 07:57:38 EST 1994


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**** For Sun Sparc users, note the *IMPORTANT* message below. ****

ACEDB data update 2-10
======================

There is available a new data update for the C. elegans database.
This does not affect version 3 of ACEDB, which is designed for human
and other organism data.

This is an incremental update, with new data but no change to the
program.  The next release will be a major release, including a new
version of the program.  Because this release is late it does in fact
include the updated version of the genetic map (thank you Jonathan).
However the external database of protein matches (proteins.???.tar.Z)
has not been updated; it will be in the quarterly update.

The main items in this data release are:
       Genetic map 3/94
       Physical map 12/4/94	
       C. elegans DNA sequences in EMBL release 37
       Mapping data sent to cgc at mrc-lmb.cam.ac.uk
       A major update of genes and rearrangements mentioned in papers
	listed in the CGC bibliography (thanks Theresa Stiernagle,
	Mark Edgeley and Larissa)
       New sequences from the genomic sequencing project, and changes
	to old ones.  There are now 137 cosmids finished (about 4Mb).
       General edits and fixes (e.g. EMBL references brought up to date,
	and some sequences)

New tutorial/manual
===================

Bruno Gaeta and others at the Australian National Genome Information
Service (ANGIS) wrote a very nice macintosh tutorial for ACEDB, full of
screen images.  They have kindly made this available for us to
redistribute, and it is available in both postscript and compressed
macintosh forms (angistute.*.*).

Code
====

There is no new code release.  You should use your existing version of
the binary (2_0).

		******	IMPORTANT  ******

There is a bug in version 2_0 of the code that causes the program to
crash ("bus error" or "segmentation violation") in some versions of
the binary (particularly sparc) at the very end of reading the
updates.  This does not lose any data.  It does remove the
precalculation of the genetic and physical maps, which should speed up
their display.  You can do this precalculation by hand as follows:

After adding the update, as the administrator (the person who
installed ACEDB)
	Select "Write Access" from the main menu
	Select "Align Maps" from the main menu
	Press the "Make pMaps" button to make the physical maps
	Press the "Make gMaps" button to make the genetic maps
	Select "Save" from the main menu.

		**************************

Solaris versions
================

There are two Solaris versions, one for people with more recent
Solaris releases that contain the X11R5 libraries
(bin.solaris.2_0.tar.Z) and one for older releases with the X11R4
libraries (bin.solaris.2_0A.tar.Z).  Some people have had continuing
problems with Solaris libraries.  If neither of these versions work, a
more drastic solution is to establish symbolic links from /usr/lib to
/usr/openwin/lib/libXaw.5*.

Macintosh version
=================

I understand the Macintosh version is now working in a number of labs.
Again, the archive anonymous ftp site is genome.lbl.gov, folder
pub/macace, and detailed enquiries should go to Frank Eeckman
(eeckman at llnl.gov).  Thank you again, Frank.

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/ace2
  cele.mrc-lmb.cam.ac.uk (131.11.84.1) in England, in pub/acedb/ace2
  lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb/ace2

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 email address'
cd repository/acedb/ace2
binary
mget *
get README  y/n   answer yes   etc
..
..

quit

If installing for the first time
--------------------------------
Get all the update tar.Z and read the files README and NOTES before
proceeding further.

If updating an existing system
------------------------------
Just get the last update.tar.Z file, plus INSTALL.

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". 

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.

******************************************************************

Please send any comments, especially about anything you think is
wrong (program or data), to

Richard Durbin (rd at mrc-lmb.cam.ac.uk)		program
Mary O'Callaghan (moc at mrc-lmb.cam.ac.uk)	data

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