ACEDB update 2-9 data for C. elegans

Richard Durbin rd at mrc-lmb.cam.ac.uk
Wed Feb 9 13:51:56 EST 1994


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ACEDB data update 2.9
=====================

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.

We plan to have an incremental data update every month, with code
updates every three months.  The quarterly updates may also contain
more complete data, e.g. the genetic map locations have not been
updated in this version, although there is more mapping data.  We
tentatively plan a map revision for the March release.  We also have
not updated the file of matching proteins (proteins.2-8.tar.Z).

********************************************************************
IMPORTANT: you must get a new copy of INSTALL as well as the update.
********************************************************************

The main items in this data release are:
       Physical map 18/1/94	
       C. elegans DNA sequences in EMBL release 36
       Mapping data sent to cgc at mrc-lmb.cam.ac.uk
       Latest CGC strain and subscriber listings and bibliography
       Abstracts and keywords for many papers
       27 cosmid sequences from the genomic sequencing project
       General edits and fixes (e.g. yk* clones are now on the pmap)
       Cell lineage and fates
       Neural wiring data

The last two items are entirely new.  The cell lineage data is
currently preliminary.  What we have comes from combining files from
Barney Hilken and Thomas Burglin (thank you Thomas).  Currently we
have division times for embryonic divisions, but not postembryonic
ones.  Does anybody have these?  There is no tool to draw the lineage,
but we are thinking about it.

The neural wiring data come from two ring reconstructions (the JSH and
N2U series of White, Southgate, Thomson and Brenner, 1986).  For each
cell, there is a list the number of synapses of each type to each
target in each reconstruction.  Types Send, Send_joint, Receive,
Receive_joint refer to chemical synapses; the "_joint" variants
indicate that more than one potential post-synaptic partner was
present at the synapse (see White et al. for further explanation).
The other type, "Gap_junction" refers to a potential direct electrical
junction.  I have a memory that the Send and Receive numbers don't
exactly crosscheck - I haven't checked recently.

Remember that you can search all the abstracts (CGC, Worm Meeting and
now for many papers) using the "Long Search" button.

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).

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

There is now a tested Macintosh version.  You need a Macintosh with
16Mb of memory and a decent monitor.  You also need some way of
obtaining the files from an ftp site (e.g. NCSA telnet, Versaterm
Pro...) and Stuffit Deluxe, which I am told costs $65 in the USA, and
is useful anyway for compressing/decompressing files.  It turns out
that Stuffit Deluxe can decompress Unix .tar.Z archive files.  Frank
Eeckman has now made available a .tar.Z archive of a complete C.
elegans ACEDB database, with updates already read in.  Ftp to 
genome.lbl.gov, folder pub/macace, and follow the instructions in
README.  Thank you 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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