From owner-celegans@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!mrc-lmb.cam.ac.uk!rd From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.celegans Subject: ACEDB data release for C. elegans Date: 12 Sep 1994 21:59:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 134 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409130447.AA13202@cele.mrc-lmb.cam.ac.uk> NNTP-Posting-Host: net.bio.net This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the mailing list and do not want to be, please send email to rd@mrc-lmb.cam.ac.uk. ACEDB data updates 2-11, 2-12, 2-13, 2-14 for C. elegans ======================================================== A set of four new data update files are available for the C. elegans database. I apologise for the long delay. Once again they are incremental updates, with new data but no change to the program. This means Sparc users will again have to build the maps by hand after adding the updates (see below). There are 4 update files because there is a large amount of new data, in particular sequence data, and we have also rearranged some of the information. The total database size is now approximately 90Mbytes. The main items in this data release are: 77 new cosmids from the genomic sequencing project, making over 6Mb of completed sequence (211 separate entries), plus corrections and updates to old sequences. Over 5000 new cDNA EST sequences from Yuji Kohara. These are now clustered by Yuji into groups for mapping, based on identity of sequence (usually identity of 3' end sequence). There are 1508 groups, named YK1 to YK1508, almost all of which have been placed on the physical map. Thank you Yuji. The text of the gazette articles for issues 12.2 to 13.2, obtained with the help of the WCS project and Leon Avery (thanks to both). In release 2-10 gazette issue 13.2 was systematically named 13.1 by mistake. This has been corrected. Ronald Pasterk's group are now maintaining sequence data around Tc1 insertion points for inclusion in ACEDB as the corresponding genomic sequence is finished. If you have data to contribute please contact Ronald at rplas@ron.nki.nl. Plus other regular updates to the map data, bibliography, EMBL sequences etc. Because Mary O'Callaghan left in June (see below), changes sent to cgc@mrc-lmb.cam.ac.uk since then are not reflected in this release. They have not been lost and will be incorporated in future releases. New curator needed ================== Mary O'Callaghan, who managed most of the genetic and bibliographic information in ACEDB, left the project in June. I'd like to thank Mary for everything she has done over the last couple of years. We are in the process of looking for a replacement; we would like somebody with a biology background who likes working with computers. For further information contact me at the email address given below. Code ==== There is no new code release. You should use your existing version of the binary (2_0). We hope to release a significantly new version of the ACEDB code, version 4.0, this fall. If you use the Macintosh version and are not already on the macace mailing list, please contact Frank Eeckman (eeckman@genome.lbl.gov) to be placed on his list, which will announce macace code and binary compressed databases. ****** 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. ************************** 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@mrc-lmb.cam.ac.uk) -------------------- end of message -------------------- .