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ACEDB data update 4-7 for C. elegans
This update should be used in conjunction with updates 4-1 to 4-6, and
version 4_1 of ACEDB, which is being made available at the same time
(see other email). You should rebuild the database when you get
code version 4_1.
The total database size is now approximately 190Mbytes.
The major additions since 4-6 are:
- a lot more genomic sequence data (there are now 581 cosmids
totalling 17,910,882 bases).
- the 1995 worm meeting entries have been renamed according to page
numbers, and 3 missing abstracts have been read in.
- the CGC bibliography has been updated, with 106 new entries.
- Tc1 insertion data from Ronald Pasterk's group has been put back;
it was missing in the first version 4 release (sorry Ronald, et al.).
Mapped Tc1 insertion sites are now visible on the sequence and
- a new Expr_pattern class has been created to show expression data,
and some has been added. Please see wbg13.5p89, and send
comments/data to sylvia at sanger.ac.uk.
- a number of errors and problems have been fixed.
We are planning much more frequent releases in the future.
The macintosh update is not yet available, but should be released
shortly. We plan to have multiple self-extracting archive files, to
avoid the problem of transferring one very large file.
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 (220.127.116.11) in the USA, in repository/acedb
ftp.sanger.ac.uk in England, in pub/acedb
lirmm.lirmm.fr (18.104.22.168) 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.
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 all the update.4-n.tar.Z and read the file NOTES before proceeding
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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