From owner-acedb@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!hgmp.mrc.ac.uk!mbishop From: mbishop@hgmp.mrc.ac.uk (Martin Bishop) Newsgroups: bionet.software.acedb Subject: Re: Workshop and Class Date: 2 May 1996 08:37:28 GMT Organization: UK HGMP Resource Centre Lines: 83 Distribution: world Message-ID: <4m9s88$3ad@mercury.hgmp.mrc.ac.uk> References: <199605011534.LAA11795@ussun4e> NNTP-Posting-Host: hydrogen.hgmp.mrc.ac.uk Please see http://www.hgmp.mrc.ac.uk/ ACEDB Workshop Course duration : 3 days Course outline : Advanced use of acedb. For those wanting to use acedb to manage their experimental data. Organiser Richard Durbin. ACeDB is a software tool to manage and provide easy access to large collections of genomic data. It is available from the HGMP Resource Centre computers, where it provides a read only front end to C. elegans, human and arabidopsis genomic data. ACeDB, with many of the sets of genomic data it is used to present, is available over anonymous ftp. Users acquiring their own copies of the program can use it to manage their own collections of genomic data. The objectives of the workshop are: - to provide a comprehensive introduction to the use of ACeDB as a tool for researchers requiring easy access to C.elegans genomic data. - to show how ACeDB has been used to provide a front end to other collections of a genomic data. - to provide an introduction to the use of ACeDB as a tool to manage genomic data Day 3) Provisional Topic: IGD: The Integrated Genomic Database (IGD) is an international project to develop an information management system for human genome researchers which interconnects existing molecular biology databases and analysis tools. It is a joint project between DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). As a database, IGD integrates and references genome-related data from public sources, including GDB, OMIM, EMBL, SWISS-PROT, RLDB, DNA Probe Bank, and several other databases, including in the future mouse and farm animals. These databases are very heterogeneous in terms of the way in which the data is organised and managed. They are also completely autonomous, so that no collaboration is required from any of these database to become integrated into IGD. Provisional Timetable: 9:30-10.15 Introduction into IGD 10.15-11.15 Navigating through the system: text and graphics display 11.15-13.00 Querying the system Query by example Query builder 13.00-14.00 Lunch 14:00-15:00 Data Structure Query Language Defining Tables 15:00-17:30 Reading in Update Files Modifying Data Installation of your own system Questions 19-21 June 96 (Cambridge) ---------------------------------------------------------------------------- From owner-acedb@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!USSUN4E.GLAXO.COM!ehl21107 From: ehl21107@USSUN4E.GLAXO.COM (Eric Lai) Newsgroups: bionet.software.acedb Subject: Re: xcontigview (!) Date: 2 May 1996 07:41:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605021433.KAA12715@ussun4e> NNTP-Posting-Host: net.bio.net Hi Newsgroup, Where can I download Xcontigview? Thanks. Eric Lai From owner-acedb@net.bio.net Mon May 13 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB release: 4_3 code plus data Date: 14 May 1996 21:33:17 +0100 Lines: 116 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4naqmd$n5p@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. New ACEDB software and data =========================== Acedb version 4_3 is now available in both binary and source form from our standard ftp distribution sites (see end of this messsage). It replaces version 4_1 as the current official acedb release. The new version contains a large number of efficiency and consistency improvements and some interface changes, e.g. a much improved bibliography display tool. There are also some critical bug fixes. In particular, it fixes the bug that prevented the most recent C.elegans data updates being loaded on Solaris machines. Version 4_3 is compatible with databases produced by 4_1. It also supports named databases with their own named series of update files (see below for C.elegans usage of this). New C.elegans data releases WS1-8 and WG1-3 =========================================== The last series of updates (4-1 to 4-14) became extremely cumbersome to load in, and we decided to start again from scratch. We also realise that the database is becoming too large for some users with limited disk space or memory. There are therefore now two alternative database versions: WS1: updates WS1.4-1 to WS-8. This contains all information, as up until now. The current genomic sequence total in WS-8 is 35,483,730 bases. The current size of this database is 220 Mb. It will continue to grow, probably over 500 Mb. WG1: update WG1.4-1 to WG1.4-3. This does not contain the genomic sequence and material directly related to that. It will however allow people with limited resources to access genetic and physical maps and the CGC data, and gives a version of the physical map showing the state of the sequencing, and EMBL/Genbank accession numbers for sequenced clones and a map. The size of this database is 46 Mb, and it should stay around 50 Mb in the future. You should make a decision which version you want, and get update files only for that version. If you choose to get WG-1, then in place of getting update files you can get a preloaded database, currently in the file database.WG1.4-3.tar.Z. ***************************** IMPORTANT ****************************** To correctly install and load the new updates, either WS1 or WG1, you need to get acedb 4_3, and an up to date copy of the INSTALL script. ********************************************************************** 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 ftp.sanger.ac.uk in England, in pub/acedb lirmm.lirmm.fr (193.49.104.10) 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. Example: 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 get README get NOTES get INSTALL cd ace4 # change to ace4 directory get bin.sunos.4_3.tar.Z # get program cd ../celegans # change to worm data directory mget update.WS1.4-*.tar.Z # get all update files quit -------------------------------- Get any update files 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"). If you have installed database.WG1.4-3 then you should be fine now. If starting from scratch with update files, when you first start up you are asked to confirm initialising the database; click "Yes". Then to load the updates into the database 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@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- From owner-acedb@net.bio.net Mon May 13 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!news.sprintlink.net!newsfeed.internetmci.com!in2.uu.net!newsflash.concordia.ca!canopus.cc.umanitoba.ca!news.magic.mb.ca!news2.insinc.net!pegasus.odyssee.net!pool30_12.odyssee.net!user From: pinotte@odyssee.net (Christiane Beaulieu) Newsgroups: bionet.software.acedb Subject: where can I find the speech manager Date: 11 May 1996 21:09:45 GMT Organization: Odyssee Internet Lines: 4 Message-ID: NNTP-Posting-Host: pool30_12.odyssee.net where can I find the speech manager,If you know that ...please send me a E-mail -- Philippe Roy From owner-acedb@net.bio.net Mon May 20 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: embl entry Date: 21 May 1996 13:56:31 +0100 Lines: 3 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4nsehv$nhj@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk please, who has a good embl to ace script ? merci From owner-acedb@net.bio.net Tue May 21 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.kth.se!sibirien.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: embl entry Date: 22 May 1996 08:30:55 +0200 Organization: Biochemistry, KTH, Stockholm Lines: 30 Distribution: bionet Message-ID: <4nucav$9al@sibirien.physchem.kth.se> References: <4nsehv$nhj@mserv1.dl.ac.uk> NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article <4nsehv$nhj@mserv1.dl.ac.uk> mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) writes: > >please, who has a good embl to ace script ? >merci Jean (and anyone else that wants :-) Check out ftp://ftp.biochem.kth.se/pub/acetools/embl2ace.pl.gz This is a perl script I use for automatically pulling in EMBL records from our xndt feed into MycDB. It is currently in a state of flux (the 'published version' is 2.1, but I'm currently reworking it completely, to a more 'object'-oriented version, or I guess HASH-oriented is a better word... Unfortunately I haven't got this in a working state yet.) embl2ace.pl will take one or more records and perform all the conversion into Sequence, Paper and DNA ace objects; it splits out CDS's and other subsequences. Any questions and suggestions to Staffan Bergh Biochemistry, KTH, S-100 44 Stockholm, Sweden email: staffan@biochem.kth.se + Don't let that horse eat that violin phone: int+46 8 790 9230 + cried Chagall's mother fax: int+46 8 24 54 52 + but he kept right on painting + -- Lawrence Ferlinghetti Webmaster and MycDB maintainer From owner-acedb@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: printing Date: 31 May 1996 17:12:42 +0100 Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4on5pq$bqf@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk I had a question about printing from the xace program. When I print via the 'print screen' command my postscript handling package 'transcript' dumps the print job because of a non-conforming "trailer"... or missing "trailer" in PS file. If I dump the image to a postscript file, then try and print the same problem. After examining the %%Trailer tag on the end of the file, it is written as "%%trailer". If I change this to "%%Trailer" it will then print, but I get two copies of each print job. I examined the source code file "graphps.c" and it outputs a '%%trailer" tag. Is there a problem with my particular postscript handling package 'Transcript', or is this a bug for some systems, since all postscript handling packages would probably not have a problem with "%%Trailer" rather than "%%trailer" Thanks Stephen Hauskins UCSC Biology From owner-acedb@net.bio.net Fri May 31 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 1 Jun 1996 02:01:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199606010900.CAA12249@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ----------------------------------------------------------------------