From owner-acedb@net.bio.net Sun Feb 01 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!206.117.63.12!diablo.interworld.net!news.claremont.edu!nntp-server.caltech.edu!xux From: xux@cco.caltech.edu (Xuequn Xu) Newsgroups: bionet.software.acedb Subject: Re: despair with webace2? Date: 2 Feb 1998 23:09:17 GMT Organization: California Institute of Technology, Pasadena Lines: 27 Distribution: world Message-ID: <6b5jmt$i9@gap.cco.caltech.edu> References: <9801211718.AA28290@greengenes.cit.cornell.edu> NNTP-Posting-Host: accord.cco.caltech.edu X-Newsreader: TIN [version 1.2 PL2] I have successfully implemented webace on Solaris 2 and Linux (PC) platforms. There were some pitfalls in compiling perl with aceclient extension and in the configuration of those perl CGI scripts, but finally it worked for me. I used acedb version 4.3. My site is at http://www.tree.caltech.edu (follow the link "Web-BAC-Ace"). Xuequn Xu (Robert) Dave Matthews (matthews@GREENGENES.CIT.CORNELL.EDU) wrote: : Last I heard, about a month ago, webace2 was robustly nonfunctional and the : debugging was being performed by Sean Walsh, sean@nasc.nott.ac.uk. Is : this still the status Sean? : - Dave : > From: Nicolas Pollet : > Subject: despair with webace2 : > Date: Wed, 21 Jan 1998 16:00:45 +0100 : > : > We installed the Aceclient extension to perl5.x from webace2. : > I made a test using the simple perl aceclient pacecl.pl and I got: : > pollet@wuhan:/opt/www/axeldb/ace/wrpc <0>pacecl.pl wuhan 56789 : > ld.so.1: /usr/local/bin/perl: fatal: relocation error: symbol not found: : > openServer: referenced in : > /usr/local/lib/perl5/site_perl/sun4-solaris/auto/Aceclient/Aceclient.so : > Killed From owner-acedb@net.bio.net Thu Feb 05 22:00:00 1998 Path: biosci!bsu.bashedu.ru!Veselov From: Veselov@bsu.bashedu.ru (Stanislav Y. Veselov) Newsgroups: bionet.software.acedb Subject: Hantavirus Date: 6 Feb 1998 04:30:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <19980206133313.AAB13793@default> NNTP-Posting-Host: net.bio.net Hantavirus in BASHKIARIA From owner-acedb@net.bio.net Thu Feb 05 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!131.103.1.116!news2.chicago.iagnet.net!qual.net!iagnet.net!128.255.56.80!news.uiowa.edu!news.physics.uiowa.edu!newsrelay.iastate.edu!news.iastate.edu!macgrant.agron.iastate.edu!user From: dgrant@iastate.edu (David Grant) Newsgroups: bionet.software.acedb Subject: ACE98 Date: Fri, 06 Feb 1998 10:12:12 -0600 Organization: USDA-ARS and Iowa State University Lines: 7 Message-ID: NNTP-Posting-Host: macgrant.agron.iastate.edu X-Newsreader: MT-NewsWatcher 2.3.1 I've heard some rumors about ACE98 but nothing definite. Does anyone have any details? Thanks, David Grant dgrant@iastate.edu USDA-ARS and Iowa State University From owner-acedb@net.bio.net Sat Feb 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!europa.clark.net!128.230.129.106!news.maxwell.syr.edu!streamer1.cleveland.iagnet.net!qual.net!iagnet.net!198.6.0.87!uunet!in1.uu.net!ozemail!news.mel.aone.net.au!newsfeed-in.aone.net.au!news.mel.connect.com.au!not-for-mail From: "jonathan" Newsgroups: bionet.software.acedb Subject: quark Date: 8 Feb 1998 05:47:10 GMT Organization: Customer of Connect.com.au P/L, Melbourne, Australia Lines: 1 Message-ID: <01bd3455$51b19920$6a0108d2@j-and-a> NNTP-Posting-Host: acc4-ppp42.mel.enternet.com.au X-Newsreader: Microsoft Internet News 4.70.1155 anyone know where to get Quark? From owner-acedb@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!194.72.7.126!btnet-peer!btnet!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: Matt Couchman Newsgroups: bionet.jobs,bionet.software.acedb,bionet.plants,uk.jobs.offered Subject: Bioinformaticist Co-ordinator Date: Tue, 10 Feb 1998 10:16:41 +0000 Organization: The John Innes Centre Lines: 31 Message-ID: <34E02909.167E@bbsrc.ac.uk> NNTP-Posting-Host: jiio5.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.04Gold (X11; I; OSF1 V3.2 alpha) To: grains@greengenes.cit.cornell.edu, cje2@york.ac.uk, Andy.Brass@man.ac.uk Xref: biosci bionet.software.acedb:1604 bionet.plants:17818 JOHN INNES CENTRE Bioinformaticist Co-ordinator Bioinformatics Co-ordinator (ref. no. MDG/315) to work jointly on two EU Biotechnology projects on comparative mapping of monocot and dicot plant genomes: EGRAM (European Graminieae Mapping Project) and EuDicot Map (European Dicotyledonous Mapping Project). The post will involve ensuring that the work of all groups fro 9 European countries is databased from the outset in ways compatible with and linked to the international plant genome and DNA databases. The postholder will also provide means of information flow between groups including the organisation of meetings as required. The post is funded by AMICA (Advanced Molecular Initiative in Community Agriculture) and will be based at the John Innes Centre at Norwich in the UK where the postholder will interact closely witl the several bioinformaticists at JIC already working on comparative, brassica and cereals bioinformatics. The successful candidate will have experience in plant genome research or bioinformatics and will have the opportunity to travel abroad in this capacity. The post will be appointed between $15,800 to £19,000 depending on qualifications and experience. For an application form and further particulars contact Pauline Stephenson, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK or email: Pauline.Stephenson@bbsrc.ac.uk quoting the appropriate reference number. The closing date for application forms will be 2nd March 1998. The John Innes Centre is a registered charity (no. 511709) grant-aided by the Biotechnology and Biological Research Council and is an Equal Opportunities Employer. From owner-acedb@net.bio.net Wed Feb 11 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!newsfeed.eerie.fr!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!pollet From: Nicolas Pollet Newsgroups: bionet.software.acedb Subject: webace Date: Thu, 12 Feb 1998 13:15:04 +0100 Organization: "GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France" Lines: 34 Message-ID: NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, As you may have observed during the last months, some recurrent questions about webace2 and webace appeared in the newsgroup. Being one of those which asked questions, I felt it would be of interest to have more tips and hints from those which are succesfully running a web interface to their database. For example,it would be of interest to know which platform/aceversion are actually running succesfully. Of interest, for example, is if somebody has a 4_5 acedb running succesfully with webace. Another point which will help all those willing to make a web interface to their favourite database, is to know what kind of problems have been encountered, for example during the compilation of perl with aceclient extension and the configuration of the perl CGI script (see Robert mail). I thought that since the web is certainly the way by which most of acedb database will be queried, it would be nice that the establishment of a web interface is as easy as the making of acedb, and that the pitfalls are clearly marked. I will likely make a compilation of all answers, but the responses posted to the newsgroup will certainly profit to more people. I hope not to be the only one to learn a lot in this, Best wishes to all Nicolas Dr Nicolas Pollet e-mail: n.pollet@dkfz-heidelberg.de Division of Molecular Embryology DKFZ Tel: (+49)-6221-42-4694 INF 280 Fax: (+49)-6221-42-4692 D-69120 Heidelberg http://www.dkfz-heidelberg.de/abt0135/hpeng.htm From owner-acedb@net.bio.net Wed Feb 11 22:00:00 1998 Path: biosci!presence4u.com!associat From: associat@presence4u.com (Alan Alvarez) Newsgroups: bionet.software.acedb Subject: ADV: International Equipment Financing Date: 12 Feb 1998 15:24:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802121407.JAA00217@morrison.mlmail.com> Reply-To: associat@presence4u.com NNTP-Posting-Host: net.bio.net ////////////////////////////////////////////////////////// You have been carefully selected to receive this Message. If you wish to be "Removed" from any future mailings, please reply with the subject "Remove" and this software will automatically block you from our future mailings. \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ International Financing Boosts Up Foreign Sales! Let us help you increase your foreign sales. Attention: Exporters & Importers We have streamed lined the approval process for foreign companies to obtain term financing for US manufactured products and services. The rates & terms we offer are very attractive. The minimum transaction size is $150,000. We also offer rates in the 10% range for domestic transactions over $100,000. This offer is also for importers of US manufactured products or services who would like financing without having to guaranty the loan with a LC or other collateral. Our finance programs are based on the credit worthiness of the borrower. Please contact me for all details. We have an info package we can fax or email you at your request. Contact: Alan Alvarez. Email: associat@presence4u.com Tel: 305-632-7332 Fax: 305-870-9610 Thank You For Your Time Alan Alvarez --------------- To never receive commercial emails or offerings from any vendor at this site again, please go to: http://www.aoci.com/removal for instructions and free software. From owner-acedb@net.bio.net Wed Feb 11 22:00:00 1998 Path: biosci!sanger.ac.uk!rd From: rd@sanger.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: webace, perl module Date: 12 Feb 1998 05:29:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802121328.NAA21252@mull.sanger.ac.uk> NNTP-Posting-Host: net.bio.net There have been several messages on the newsgroup recently about the problems of making the perl component of webace, and making webace itself run. We have recently managed to produce a makefile that will compile a stand alone perl module that can be dynamically linked into your existing perl, without requiring recompilation of perl itself as with the previous NAL version. This follows the approved way now to create such extensions. We intend to make this available on the acedb ftp sites in the near future (the next few days) and mail the newsgroup when we do so. Tim Hubbard here has also been working extensively on extending and developing webace, using the latest acedb code. Various experimental services on the Sanger Web site are using this. I expect that in a few weeks we will have a version that can be stabilised and made available to others. This uses gifaceserver to make .gif files, and is complementary to the Java approaches of Jean and Licoln Stein. Richard From owner-acedb@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!ETMP.COM!etmp From: etmp@ETMP.COM Newsgroups: bionet.software.acedb Subject: Eventemp Stock(ETMP) Heating Up - Huge Orders Coming In!! Date: 13 Feb 1998 13:05:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802132059.PAA12730@apollo.redcomet.net> NNTP-Posting-Host: net.bio.net You have been carefully selected to receive the following as a person obviously interested in this subject based upon your previous internet postings, or visits to one of our affiliate web sites. If you have received this message in error, please accept our apology as a responsible e-mailer, and reply with the word REMOVE in the subject line. You will be automatically excluded from future e-mailings. Thank you for your consideration and help in making the Internet spam-free. ***** *** News Flash *** 01/30/98 - Eventemp receives 27 million dollar contract - Company expects net profit of 5 to 6 million dollars. Other large contracts pending. Huge profit potential. Analyst say look for Eventemp (Symbol OTC BB: ETMP) to go as high as $10.00 by March 1. Analysts predict that stock could shoot to $6.00 in the next few days. Stock rose over 41% on 01/30/98 - Get in while there is still time. For complete info, visit http://www.etmp.com Now you can call your car from any available telephone and start the air conditioner or heater and have it pre-cooled or pre-heated for your comfort when you arrive....WITH THE VEHICLE'S ENGINE STILL OFF! THE TECHNOLOGY EXISTS! THE SYSTEM WORKS! THE COMPANY IS EVENTEMP! THE STOCK (OTC BB: ETMP) currently trades at about $4.25 and could possibly reach $10.00 by March 1, 1998! EVENTEMP owns the exclusive patent rights to this revolutionary system which will be available as an option on luxury cars this year. Deals are in the works to make this available on all new cars by the year 2000! Look for some exciting news to be released soon! Visit EVENTEMP'S web site at http://www.etmp.com for more information! The temperature in your car may be cool, but this stock is going to be one of the HOTTEST of 1998! From owner-acedb@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Pascal Hingamp x4533 Newsgroups: bionet.software.acedb Subject: Automated updating of acedb mirrors Date: Fri, 13 Feb 1998 14:13:52 +0000 Organization: UK MRC Human Genome Mapping Project Resource Centre Lines: 18 Message-ID: <34E45520.9575D7F9@hgmp.mrc.ac.uk> NNTP-Posting-Host: copper.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; SunOS 5.6 sun4m) Dear Ace managers, If you're maintaining at least one acedb mirror at your site (we currently hold 16 public mirrors at the HGMP-RC!), then please feel free to help yourself to UPace. This is a fully automated acedb updating Perl script for UNIX suitable for peace of mind cron jobs... The three upace.* files are available from: ftp://ftp.hgmp.mrc.ac.uk/pub/phingamp/ Enjoy! Pascal -- Dr. Pascal Hingamp mailto:phingamp@hgmp.mrc.ac.uk UK MRC Human Genome Mapping Project Resource Centre Bioinformatics Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SB Tel:(+44) 01223 494533 Fax: ~4512 http://www.hgmp.mrc.ac.uk From owner-acedb@net.bio.net Sun Feb 15 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Richard Durbin Newsgroups: bionet.software.acedb Subject: ACEDB data release for C.elegans WS4.4-26 and WG4.4-4 Date: 16 Feb 1998 17:51:31 -0000 Lines: 186 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6c9ub3$da3@mserv1.dl.ac.uk> Original-To: acedb_distrib@sanger.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 data release WG4 and WS4 for C. elegans ================================================= *** A Macace version is available for WG4 (without sequences only just now) *** With this release we are again starting a new series of database updates from scratch, rather than adding on to WS3. The new series is called WS4 (and correspondingly WG4 for the version without sequences). Because both series are new, you must get all the updates from the series you want (WS4 or WG4), and rebuild a new database using them. If you have a working acedb version built with the WS3 or a previous series, you must remove your current database/ directory (ideally after backing it up in case of difficulties). As well as removing the database directory, you can also remove any update.WS3...tar.Z or rawdata/update.WS3... files. If you do not remove the contents of the database directory, when you start up acedb it will still say "WS3" in the title bar, and will not be able to load the WS4 updates. When you have emptied it properly, it will ask if you want to reinitialise, and put WS4 in title bar. You should be using these updates in conjunction with release 4_5 of the acedb software (released in August 1997). Reminder: there are now two versions of the C.elegans database. The WS4 update series contains everything, whereas the WG4 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. (N.B. at the end of this file is a list of the contents of each update file). The additions since the last release are : for both types of update - a physical map update with a lot of changes (mid Jan) all but one chromosome is now a single contig - accumulated genetic data corrections, inclusion of phenotypes from C. elegans II - from CGC : bibliography, wbg subscribers and strains - from Leon Avery : wbg15.1 contents and abstracts - Expression patterns from Julie Ahringer and Ian Hope, many more pictures form Ian Hope and for just the complete database including sequences (WS4) Data fom St Louis and Sanger Sequence databases taken in mid-December: - there are now 2520 (2237 before) cosmids totalling 75458714 (66969575 before) bases. - there are also many new ESTs from Yuji Kohara. The total database directory sizes after adding these updates are around 870MB for the WS4 database and around 75MB for the WG4. database. Macace ====== We have made a macace version of WG4, the database without sequence data. This can be obtained as a self-extracting archive from subdirectory macace on the ftp site, file name macace.WG4.sea.bin. We will try to build a macace.WS4, but this will need to be distributed in multiple self-extracting archive files, with instructions on how to put the resulting files back together. This will be the subject of a future message. 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 (193.60.84.11) 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.* # get all WS1 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"), 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@sanger.ac.uk). Comments about the installation procedure, should be sent to Richard Durbin (rd@sanger.ac.uk) ******************************************************************** FILE DIVISIONS FOR UPDATE WS4 FEB 98 ==================================== UPDATE.WS4.4-1.TAR.Z AND UPDATE.WG4.4-1.TAR.Z BOTH CONTAIN THE WSPEC/, WSCRIPTS, PICTURES, WGF/ AND WHELP/ DIRECTORIES. 20045766 Feb 3 16:31 dna.1.ace update.WS4.4-1 20002743 Feb 3 16:32 dna.2.ace update.WS4.4-2 20041832 Feb 3 16:32 dna.3.ace update.WS4.4-3 20020535 Feb 3 16:33 dna.4.ace update.WS4.4-4 20000377 Feb 3 16:33 dna.5.ace update.WS4.4-5 20009870 Feb 3 16:34 dna.6.ace update.WS4.4-6 5039173 Feb 3 16:34 dna.7.ace update.WS4.4-7 2196036 Jan 29 12:17 LongText.9801.ace update.WS4.4-8 2046998 Jan 29 12:22 Motif.9801.ace update.WS4.4-8 20000250 Feb 3 17:18 prot.1.ace update.WS4.4-9 20001473 Feb 3 17:18 prot.2.ace update.WS4.4-10 20024947 Feb 3 17:19 prot.3.ace update.WS4.4-11 7927522 Feb 3 17:19 prot.4.ace update.WS4.4-12 20000092 Feb 3 17:02 pep.1.ace update.WS4.4-13 4625232 Feb 3 17:03 pep.2.ace update.WS4.4-14 20051234 Feb 3 17:26 seq.1.ace update.WS4.4-15 20029307 Feb 3 17:27 seq.2.ace update.WS4.4-16 20000589 Feb 3 17:28 seq.3.ace update.WS4.4-17 20007206 Feb 3 17:28 seq.4.ace update.WS4.4-18 20005199 Feb 3 17:29 seq.5.ace update.WS4.4-19 20000782 Feb 3 17:29 seq.6.ace update.WS4.4-20 16893242 Feb 3 17:30 seq.7.ace update.WS4.4-21 gene.1.ace update.WS4.4-22 update.WG4.4-1 gene.2.ace update.WS4.4-23 update.WG4.4-2 gene.3.ace update.WS4.4-24 update.WG4.4-3 1564442 Feb 2 16:52 seq_AC_numbers.ace update.WS4.4-25 1374 Feb 3 13:40 stl.seq.nospp.ace update.WS4.4-25 1274 Feb 4 12:03 xmap.fix.ace update.WS4.4-25 update.WG4.4-3 264 Feb 4 12:03 yseqmap.delete.ace update.WS4.4-25 update.WG4.4-3 link.fix.ace update.WS4.4-25 Clonegrid.ace update.WS4.4-25 update.WG4.4-3 Picture.fix.ace update.WS4.4-25 update.WG4.4-3 methods.ace + pictures update.WS4.4-26 update.WG4.4-4 gene.1.ace, gene.2.ace, gene.3.ace contain the bulk of acedb classes and form the basis of WG4 database. They deliberately exclude proteins, motifs, dna, and the bulk of sequence annotations. -------------------- end of message -------------------- From owner-acedb@net.bio.net Sun Feb 15 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!newsxfer3.itd.umich.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!news.clara.net!nnrp1.clara.net!not-for-mail From: "A Tan" Newsgroups: alt.binaries.w-software,alt.geo-software,at.tuwien.software,att.gis.software,att.gis.software.leadership,att.gis.software.leadership.group,att.software-dev,att.software-dev.metatool,bionet.software,bionet.software.acedb,bionet.software.gcg,bion Subject: Help ! Real Time Compression Recording ! Date: 16 Feb 1998 04:00:47 GMT Lines: 8 Message-ID: <01bd3a8f$c382b760$825008c3@default> NNTP-Posting-Host: 195.8.80.130 X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.software:20505 bionet.software.acedb:1614 bionet.software.gcg:2990 Hi Does anyone know are there any Real Time Compression Recording, like Effect Phase's PC Deck ? Thanks A Tan From owner-acedb@net.bio.net Mon Feb 16 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Pascal Hingamp x4533 Newsgroups: bionet.software.acedb Subject: UPace 1.02 (Automated acedb mirror updating) Date: Tue, 17 Feb 1998 14:34:22 +0000 Organization: UK MRC Human Genome Mapping Project Resource Centre Lines: 8 Message-ID: <34E99FEE.15840C0A@hgmp.mrc.ac.uk> NNTP-Posting-Host: copper.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; SunOS 5.6 sun4m) For those interested in automated acedb mirror updating: I've fixed a couple of bugs in UPace as well as added a new update method ("new-worm") to deal with c. elegans style "right from scratch" updating. UPace 1.02 is available from ftp://ftp.hgmp.mrc.ac.uk/pub/phingamp/ Pascal From owner-acedb@net.bio.net Mon Feb 16 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Richard Durbin Newsgroups: bionet.software.acedb Subject: fix for ACEDB INSTALL problem with WS4.4-24 Date: 17 Feb 1998 09:45:35 -0000 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6cbm7v$8vp@mserv1.dl.ac.uk> Original-To: celegans@dl.ac.uk, acedb@dl.ac.uk Lines: 18 This message is relevant to people who obtained the latest ACEDB updates and INSTALL script from NCBI yesterday (Monday Feb 16). The update file update.WS4.4-24.tar.Z which is part of the data release announced yesterday did not install properly with the INSTALL script obtained from NCBI. Unfortunately the script there was out of sync with that in England. I have now fixed this at NCBI, so anyone who obtained the updates yesterday and was unable to install update 24 should get a new copy of INSTALL from the NCBI ftp site and proceed as usual. If you have already loaded updates 1 to 23, that is fine - you can add in 24 to 26 on top of that. If you have not yet obtained the updates and tried to load them, then you can proceed as usual, but make sure to get a copy of the new INSTALL script to replace any that you currently have. Richard Durbin From owner-acedb@net.bio.net Tue Feb 17 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Martin Fleischmann Newsgroups: bionet.software.acedb Subject: update Date: 18 Feb 1998 12:32:28 -0000 Lines: 24 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6cekcs$abc@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Hello I tried to install the new data release of acedb on our sparcstation (older releases were running well). I did a ftp session to get all the updates, I did uncompress and tar of these updates. When I tried to update the database (all updates), the programm (4_5) was looking for update.4-1 instead of looking for update.WS4.4-1 which is present in the rawdata directory. Can anybody tell me what went wrong? Shall I rename the rawdata files? Martin ___________________________________ Martin Fleischmann Institut de Zoologie Universite de Fribourg Perolles 1700 Fribourg Switzerland Tel *41 26 300 88 63 Fax *41 26 300 97 41 e-mail Martin.Fleischmann@unifr.ch http://zoops1.unifr.ch From owner-acedb@net.bio.net Wed Feb 18 22:00:00 1998 From: "Lars Fritsch" Newsgroups: bionet.software.acedb Subject: WinOnCD 3.5 Date: Tue, 17 Feb 1998 21:47:19 +0100 Organization: BergNet GmbH Lines: 9 Message-ID: <6ccsub$hvu$1@toe.berg.net> NNTP-Posting-Host: ws-039.berg.net X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Path: biosci!news.ic.sunysb.edu!news-pen-15.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!209.6.107.173!tuco.xcom.net!cam-news-hub1.bbnplanet.com!atl-news-feed1.bbnplanet.com!news.bbnplanet.com!news.planetc.com!news.berg.net!not-for-mail I need the serial nr. for WinOnCD 3.5 Kann mir einer weiter helfen???? Ich bräuchte dringend die Serien Nummer von WinOnCD 3.5!!! eMail: fritsch@berg.net From owner-acedb@net.bio.net Thu Feb 19 22:00:00 1998 Path: biosci!agate!howland.erols.net!Cabal.CESspool!bofh.vszbr.cz!serra.unipi.it!bigarea.area.ba.cnr.it!massimo@area.ba.cnr.it From: valenzi@iigbna.iigb.na.cnr.it (Marco Valenzi) Newsgroups: bionet.software.acedb Subject: FATAL ERROR :System error 5 . WHY? Date: 20 Feb 1998 10:37:52 GMT Organization: CNR - Area di Ricerca - Bari,Italy Lines: 12 Sender: -Not-Authenticated-[6946] Message-ID: <6cjme0$lc2@bigarea.area.ba.cnr.it> NNTP-Posting-Host: valenzi.iigb.na.cnr.it X-Posted-From: InterNews 1.1@valenzi.iigb.na.cnr.it Xdisclaimer: No attempt was made to authenticate the sender's name. hello acedb-exspert, We have Enterprise 3000 with Solaris system 2.5. when we install the new update WS4 in acedb all go well as far as update.WS4.4-10 but running update.WS4.4-11 at line 69276 (17%) we see litle window with message FATAL ERROR :System error 5 I/O error diskblock.write cannot actually write the disk ,n=-1 What means ? have you any suggestions ? thanks Marco Valenzi From owner-acedb@net.bio.net Thu Feb 19 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!portc04.blue.aol.com!audrey02.news.aol.com!not-for-mail From: comic62@aol.com (Comic62) Newsgroups: bionet.software.acedb Subject: FREE SOSTWARE Date: 20 Feb 1998 10:33:04 GMT Lines: 1 Message-ID: <19980220103300.FAA09552@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com http://members.spree.com/placez/ From owner-acedb@net.bio.net Fri Feb 20 22:00:00 1998 Path: biosci!agate!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Curator) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 21 Feb 1998 19:42:50 GMT Organization: Dept. Plant Breeding, Cornell University Lines: 1323 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <6cnanq$kc0@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w021.psw.fs.fed.us Summary: Frequently Asked Questions about finding and getting started with the URL: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html Archive-name: acedb-faq Last-modified: 19 Feb 98 Version: 1.41 _________________________________________________________________ ACEDB FAQ _________________________________________________________________ Curated by: Dave Matthews _________________________________________________________________ Frequently Asked Questions about ACEDB Q0 : What is ACEDB? Q1 : ! What is the current version of ACEDB? Q2 : Where can I get ACEDB? Q3 : What hardware/software do I need to run ACEDB? Q4 : Can ACEDB be networked? Q5 : What documentation exists for ACEDB? Q6 : What newsgroups and mailing lists are available for ACEDB? Q7 : ! Is there a repository of software tools for ACEDB curators? Q8 : When and where is the next ACEDB Workshop? Q9 : How does ACEDB compare to commercial relational DBMS's? Q10 : How should ACEDB be cited? Q11 : What ACEDB databases exist? Q12 : Who prepared this document & where is the current version? Questions marked with '+' are new, those with '!' have substantially changed answers. _________________________________________________________________ Q0: What is ACEDB? A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning in 1989. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions _________________________________________________________________ Q1: What is the current version of the ACEDB software? A1: The current Unix version is ace.4_5d/e, released 28 August 1997. Enhancements added during the ACE97 Workshop will be incorporated in the next release. The very latest development version is always available at ftp://ftp.sanger.ac.uk/pub/acedb_src/. This is unsupported and not to be redistributed. New! The current Windows 95/NT version 4.5.3d, 15 January 1998, corresponds to Unix test.ace.4_5c. For the latest documentation see the WinAce Web page at http://mendel.medgen.ubc.ca/rbrusk/winace.html. A Macintosh version is available as version 4.1b1, August 1995. Return to List of Questions _________________________________________________________________ Q2: Where can I get ACEDB? A2: Source code and Unix binaries are available in the following anonymous ftp sites: * ncbi.nlm.nih.gov in repository/acedb * ftp.sanger.ac.uk in pub/acedb * lirmm.lirmm.fr in pub/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb Linux binaries in ELF and a.out format, from Jeff Bryer: * ncbi.nlm.nih.gov in repository/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb Windows 95/NT, from Richard Bruskiewich: * ftp.sanger.ac.uk in pub/acedb/winace * bioinformatics.weizmann.ac.il in pub/databases/acedb * Documentation: http://mendel.medgen.ubc.ca/rbrusk/winace.html MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin: (Note: The authors are not currently able to support MacAce. Latest version was 4.1b1.) * genome.lbl.gov in pub/macace * ncbi.nlm.nih.gov in repository/acedb/macace * bioinformatics.weizmann.ac.il in pub/databases/acedb NEC EWS4800 binaries: * http://www.labs.nec.co.jp/freesoft/freesofte.html Return to List of Questions _________________________________________________________________ Q3: What hardware/software do I need to run ACEDB? A3: The software is available in binary (pre-compiled) format for a variety of machines. * Unix: + Sun/SunOS 4.x + Sun/Solaris + DEC DECstation3100, 5100 etc. + DEC Alpha/OSF-1 + Silicon Graphics Iris series 4, 5, 6 + IBM RS-6000 + PC 386/486/Pentium with Linux + NEC EWS4800 + NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu + There exist, or have existed, ports onto Alliant, Hewlett- Packard, Convex. You may have to contact the developer responsible for the port to make these real. * Windows 95/NT * Macintosh (not currently supported) The software is also available as source code, so you may be able to get it working on any machine. Memory requirements (from Richard Durbin, aug 97) The amount of memory you require for ACEDB depends very much on how big the database is (i.e. the disk space used by the database/ subdirectory). Our rule of thumb is that one typically uses 5-10Mb plus up to 10% of the disk space size of the database. So with a 200Mb database perhaps 25Mb memory, and with a 500Mb database (e.g. the C. elegans one) up to 50-60Mb. In fact for short sessions less memory is used -- it is only when all classes are explored, or for example when parsing big files that these amounts of memory get used. Return to List of Questions _________________________________________________________________ Q4: Can ACEDB be networked? A4: ACEDB Client / Server Computing (from Doug Bigwood, aug97) There are several client/server models for ACEDB computing and several more are in development. The start of the ACEDB client/server age began with the inclusion of aceclient and aceserver in version 4.0. These are C - based and use the RPC protocol for communication. These executables can be made from the standard ACEDB distributions. Starting in version 4.5 an xaceclient is also included with ACEDB. Xaceclient provides remote read/write access to an aceserver while providing the user with the same X displays that are found in xace. To use it, you create an empty database with the appropriate models and start xaceclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the Montpellier server in the distribution server.wrm). The data will be saved locally and can then be viewed with a normal xace. A perl extension which provides aceclient functionality to Perl 5.x was developed at ACE95. The files necessary for this perl extension are now (ACEDB 4.5 and later) included in the wrpc directory of the ACEDB directory hierarchy. Documentation about how to extend perl is found at http://probe.nalusda.gov:8000/ace97/perlace/perlacecl.html. WWWAce and its successor webace were developed to provide a World Wide Web interface for ACEDB. Webace instructions can be found at http://probe.nal.usda.gov:8000/acedocs/webace.html, and http://probe.nal.usda.gov:8000/ace97/webace.html and the program itself at ftp://probe.nalusda.gov/pub/tools/webace.tar.gz. A Java-based client called Jade allows communication via sockets to an aceserver. Jade installation instructions and information on downloading can be found at http://probe.nalusda.gov:8000/ace97/Jade.installation.html. There are now development efforts underway to provide additional client/server functionality to ACEDB including a CORBA server and socket-based communications. These will likely be included in future versions of ACEDB. A new C library interface to ACEDB internals will greatly ease the development of new clients and servers that will support additional protocols. _________________________________________________________________ Q5: What documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Library is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The WWW documentation server is part of the Agricultural Genome Information System, at http://probe.nalusda.gov:8000/acedocs/. Documents in Postscript, wordprocessor, and other non-html formats are available by ftp at ftp://probe.nalusda.gov/pub/acedocs/. Information in the ACEDB Documentation Library includes: * Primary documents from the developers Durbin & Thierry-Mieg, ca. 1992. + acedb -- A C. elegans Database: I. Users' Guide + acedb -- A C. elegans Database: II. Installation Guide + acedb -- A C. elegans Database: III. Configuration Guide + acedb -- A C. elegans Database: Syntactic Definitions for the ACEDB Data Base Manager * Tutorials, general and specific * Documentation written at the ACEDB Workshops * A repository of curator tools * A selection of models.wrm files from various databases * SampleDB, a sample database to demonstrate some ACEDB features, 1995 * This FAQ, in html format Other sources of documentation: * The ACEDB online help, a hypertext reader for the contents of the whelp directory of the ACEDB software distribution. * Contents of the wdoc, wtools, and wscripts directories. * Archives of the bionet.software.acedb newsgroup (both searchable) + http://www.bio.net/hypermail/ACEDB/, from BIOSCI + http://genome-www.stanford.edu/cgi-bin/biosci_acedb, from the Saccharomyces Genome Database site * ACEDB User's Guide in Japanese, from Tohru Sano, NEC, sano@exp.cl.nec.co.jp, http://www.cbi.or.jp/~sano/. (Postscript at http://www.labs.nec.co.jp/ . Follow the prompts to register and "download the software".) * Paper publications + Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992). AAtDB, an Arabidopsis thaliana database. Plant Molecular Biology Reporter 10: 308-309, 409-410. + Cherry, J.M. and Cartinhour, S.W. (1994). ACEDB, A tool for biological information. Pp. 347-356 in: Automated DNA Sequencing and Analysis, M. Adams, C. Fields, and C. Venter (Eds.). Academic Press. Online version: http://probe.nalusda.gov:8000/acedocs/overview.html. + Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994). Physical mapping projects and ACEDB. Pp. 111-158 in: Guide to Human Genome Computing. Bishop, M.J (Ed.). Academic Press. Return to List of Questions _________________________________________________________________ Q6: What newsgroups and mailing lists are available for ACEDB? A6: The USENET/BIOSCI conference bionet.software.acedb is dedicated to discussions of ACEDB. The newsgroup can be accessed via a newsreader like rn or tin, a WWW browser (news:bionet.software.acedb), or e-mail. To subscribe to the e-mail version, send the message "subscribe acedb" to biosci-server@net.bio.net. Mail sent to acedb@net.bio.net will be distributed to all subscribers and to the electronic conference. Articles posted to biosci.software.acedb are archived by BIOSCI at http://www.bio.net/archives.html and by Mike Cherry at http://genome-www.stanford.edu/cgi-bin/biosci_acedb. There is also a separate mailing list for announcements of new releases of the ACEDB (worm) database as well as the ACEDB software. To get on or off this mailing list send mail to rd@sanger.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. The BIOSCI newsgroup is on this list. Return to List of Questions _________________________________________________________________ Q7 : Is there a repository of software tools for ACEDB curators? A7: Not really, but there are several partial ones. The main tools available are for converting data from other formats to .ace format. The Agricultural Genome Information System has a growing stock of useful tools at http://probe.nalusda.gov:8000/acedocs/conversion.html. Some additional ones were contributed at the ACE97 Workshop and can be found in the Proceedings, http://probe.nalusda.gov:8000/ace97/tools/. Mike Cherry maintains an archive of tools at ftp://genome-ftp.stanford.edu/pub/acedb_dev/utilities/ For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/. New! Pascal Hingamp has created a tool for mirroring remote databases to your own machine. UPace is a flexibly configurable, well documented Perl script intended to be adaptable to any ACEDB database available by ftp, with updating as often as you like. ftp://ftp.hgmp.mrc.ac.uk/pub/phingamp/ Return to List of Questions _________________________________________________________________ Q8: When and where is the next ACEDB Workshop? A8: The next ACEDB meeting is planned for summer 1998 in England. The ACE97 Conference and Workshop was held July 27 - August 9 at Cornell University, Ithaca, New York, USA. See the ACE97 Proceedings Page, http://probe.nalusda.gov:8000/ace97/proceedings.html for the results. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/. A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html. Also available online are collections of snapshots taken during the conference by Frank Eeckman and by Dave Matthews. For pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, see the online collections: * by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; * by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; * and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions _________________________________________________________________ Q9: How does ACEDB compare to commercial relational DBMS's? A9: From Jean Thierry-Mieg, 4/97: Obviously, i have a biased opinion, but i would say that acedb is to be recommended if the following criteria are met: 1) A very complex schema, that cannot be developed at once, but will need continuous refinement in parallel with the accumulation of the data 2) The type of questions that will be asked are rather complex, with rather fuzzy answers, that one tries to refine progressively. The acedb browsing capacities are useful in this case and have no equivalent in a relational dbms ______________ I would rather recommend sybase in the following case 1) Simple schema, that can be designed from the start and does not contain too many n.n relations and does not need recursivity 2) The type of questions that will be asked is: succession of de-correlated simple questions with simple answers ____________________ Within this context, i would then list the following goodies of acedb: 1) The ace file format, which is a powerful system to prepare and exchange data between data curators. 2) The existence of an easy graphic browsing interface 3) The availability of a biology-layer, if the application is about genetics 4) Portability (any unix machine), mac (with some limitations), windows (in development) and price (ace is a freeware). This implies that you can actually redistribute the complete system, say on a CD, something impossible with sybase. 5) Ease of use, i seriously believe that ace is much easier to configure and use than sybase. _____________________ Finally one should consider the following question: concurrency. Sybase has a well designed transaction system, which will allow roll backs and refined lockings. This is essential for an application like a booking agency, with many users in simultaneous write access. Ace is much simpler minded. The graphic acedb creates a global lock allowing a single user with write access at the time, and the modifications are not echoed to the other "read access" users in real time. The non graphic client server system allows parallel downloading of data by many users, it is intended for example for collection of robots sending their independent data in parallel. This is now well tested. A graphic client system is being developed and now runs in our hands, but is not yet released. -- Therefore, if you do need real time simultaneous write access with partial locks, and roll backs, use sybase/oracle ________________ Last issue is speed and quantities of data. In principle, sybase/oracle is unlimited, whereas acedb needs to keep around 5-10% of the data in ram. But this apparent difference is misleading. On a 32 Meg machine, you can run ace with around 300.000 objects with a complex schema at high speed. With say 1M objects, you will need more memory or the performance would totally degrade because of swapping. However, this is really a lot of data. On a similar machine, your sybase oracle will work with that amount or more data only if you do not perform too many joins. This implies that you are asking simple questions from a simple schema which was indeed our first criterion to choose sybase. If you start asking complex questions and make joins, acedb is actually much more powerful. During tests run on a big dec alpha server by Otto Ritter in decembre 1995 on several million biological objects with a complex schema, acedb was about 10 times faster than sybase, both to load the data and to answer queries. I would therefore conclude that the quantity of data is not a criterion pushing one way or the other, it is the complexity of the schema that matters. Return to List of Questions _________________________________________________________________ Q10: How should ACEDB be cited? A10: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions _________________________________________________________________ Q11: What ACEDB databases exist? A11: In alphabetic order by Database name [Curators, please submit changes as new paragraphs. You may include html links.] A repository of many of these databases is maintained by the Agricultural Genome Information System, both for anonymous ftp at ftp://probe.nalusda.gov/pub and for WWW access via Webace at http://probe.nalusda.gov:8000/alldbs.html. Database : AaeDB Species : Aedes aegypti (yellow fever mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : AalDB Species : Aedes albopictus (Asian tiger (forest day) mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@sanger.ac.uk Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ FAQ_updated : August 1995 Database : aCHEdb Species : wide range of species Subject : alpha/beta fold family of proteins database ESTHER. Sequences phylogenetically related to cholinesterases (alpha/beta hydrolase, carboxylesterases, lipases, adhesion molecules.) Comment : Converted to ACEDB from the original ESTHER database. ACEDB_version : UNIX 4.5, MacAce 4.0b4 Data_version : August 1997 Curator : Xavier Cousin - cousin@ensam.inra.fr Curator : Thierry Hotelier - hotelier@ensam.inra.fr Curator : Arnaud Chatonnet - chatonne@ensam.inra.fr Contact : chedb@ensam.inra.fr Availability: Unix and Macintosh versions via anonymous ftp FTP: ftp://ftp.toulouse.inra.fr in pub/esther WWW : http://www.ensam.inra.fr/cholinesterase FAQ_updated : September 1997 Database : AgaDB Species : Anopheles gambiae (malaria mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu ACeDB_version : 3.0 Subject: Contains extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe yeast); interacting loci via defined Interactions for each locus Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html FTP: ftp://keck.tamu.edu/pub/agsdb/agsdb1_0_acedb3_0_solaris2.3.tar.Z FAQ_updated : March 1994 Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : July 1995 Database : AnoDB Species : Anopheles sp. ACEDB_version : 4.5 WWW : http://konops.imbb.forth.gr/AnoDB/ Curator : Christos Louis, louis@konops.imbb.forth.gr Co-Curator : Pantelis Topalis, topalis@konops.imbb.forth.gr Contact : AnoDB-comments@konops.imbb.forth.gr Data_updated : regularly FAQ_updated : August 1997 Database : AtDB Species : Arabidopsis thaliana ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4-7 PI : J. Michael Cherry Curator : David Flanders Contact : arab-curator@genome.stanford.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : genome-ftp.stanford.edu in arabidopsis/AtDB FTP : ncbi.nlm.nih.gov in repository/AtDB WWW : http://genome-www.stanford.edu FAQ_updated : December 1996 Database : AtrDB Species : Aedes triseriatus (Eastern tree hole mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 4.1 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : September 1995 Database : BrassicaDB Species : Brassica napus (Canola/Oilseed Rape) and its parental diploid species ACEDB_version : 4.3 Description : Genetic maps of Brassica napus, QTL analyses for agronomic traits, literature references and B. napus-specific DNA sequences will be incorporated. We aim to integrate with B. napus genetic maps developed elsewhere and to produce a Java interface that will link BrassicaDB with the AAtDB (Arabidopsis thaliana) database through gene orthologies that are becoming established between these closely related plant genomes. PI : Martin Trick, Martin.Trick@bbsrc.ac.uk Curator/Developer : Mazda Hewitt, Mazda.Hewitt@bbsrc.ac.uk WWW : http://synteny.nott.ac.uk/brassica.html Data_updated : Under development FAQ_updated : August 1997 Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : August 1995 Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : September 1995 Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edu ACEDB_version : 3.0 Gopher : gopher://probe.nalusda.gov:7000/11/genome.databases/coolgenes/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : January 1996 Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 ACEDB_version : 3.0 Data_version : January 1995 (version 95.1) FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ FAQ_updated : January 1995 Database: Cruzdb Species: Trypanosoma cruzi PI: Wim Degrave ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/cruzi/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated : In development FAQ_updated : November 1996 Database : CSNDB Focus : Cell Signaling Networks Species : human Curator : Takako Igarashi, taka@nihs.go.jp Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Assistant_Curator : Masumi Yukawa, yukawa@nihs.go.jp Assistant_Curator : Shikiko Hasegawa, shasegaw@nihs.go.jp Contact : Takako Igarashi, taka@nihs.go.jp ACeDB_version : 4.1 Data : molecular data of signal molecules, molecular data of signal transductions, signal transduction pathways, domain structure and function of signal molecules, and three dimensional structures of signal molecules. Availability : CSNDB is on WWW. WWW-browser is required to attach molecular viewer RasMol (ftp: colonsay.dcs.ed.ac.uk ) for displaying three dimensional structure of protein. WWW : http://geo.nihs.go.jp/csndb.html Database : CupDB Species : Culex pipiens ACEDB_version : 4.3 WWW : currently unavailable via www Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : Cyanoace Species : Cyanobacterium synechocystis sp. strain PCC6803 Developer : Nobuyuki Miyajima, miyajima@kazusa.or.jp Comment : Converted to ACEDB from Sybase FTP : ftp://ftp.kazusa.or.jp/pub/acedb/cyanoace/ WWW : http://www.kazusa.or.jp/cyanobase/ Remark : WWW interface uses Java enhanced clickable maps. FAQ_updated : December 1996 Database : EthnobotDB (worldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database: FilDB Species: Filarial nematodes PI: Mark Blaxter ACEDB_version: 4.3 Curator: Martin Aslett Contact: Mark Blaxter, mark.blaxter@ed.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Brugia WWW: http://helios.bto.ed.ac.uk/mbx/fgn/filgen.html WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: In development FAQ_updated : November 1996 Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : May 1995 Database : GrainGenes Species : Wheat, barley, rye, oats, sugarcane, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu Curator : Gerard R. Lazo, lazo@pw.usda.gov PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_5 (Unix), 4.1b1 (MacAce) Data_version : 1.8, December 1997 Availability : UNIX, Windows, Macintosh versions via anonymous ftp Availability : Windows, Macintosh versions on CD-ROM from Dr. Baek Hie Nahm, Korea Rice Genome Research Program, Myongji University, Yongin, Korea. FTP : probe.nalusda.gov in pub/graingenes FTP : grain.jouy.inra.fr in pub/database WWW : http://probe.nalusda.gov:8000/alldbs.html WWW : http://wheat.pw.usda.gov/ WWW : http://grain.jouy.inra.fr Gopher : greengenes.cit.cornell.edu Gopher : grain.jouy.inra.fr Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ FAQ_updated : December 1997 Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr Description : IGD (Integrated Genomic Database) aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : IXDB (Integrated X chromosome DataBase) Species: Homo sapiens Subject: Chromosome X Acedb_version : 4.1 Data: The YAC map constructed by the Max-Planck-Institut fuer Molekulare Genetik in Berlin, with all the attached experimental data necessary to reconstruct the map. Information on each of 9000 YAC clones mapped to the X chromosome, and constituting the YAC collection assembled with clone sets from 14 different laboratories worldwide. Latest_release:March 1996 Curator: Hugues Roest Crollius, roest@mpimg-berlin-dahlem.mpg.de Contact: Ulf Leser, leser@mpimg-berlin-dahlem.mpg.de PI: Hans Lehrach FTP: ftp.mpimg-berlin-dahlem.mpg.de in directory pub/lehrach/x-map WWW: http://www.mpimg-berlin-dahlem.mpg.de/~xteam Database: Leishdb Species: Leishmania major, L. infantum, L. peruviana, L. donovani and others PI: Jennie Blackwell PI: Al Ivens ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Leish WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/leish/leishpage.html (in development) Data_updated: October 1996 FAQ_updated : November 1996 Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie-Paule Lefranc Contact : Veronique Giudicelli, LIGM IGMM UMR CNRS 9942, BP 5051 Rte de Mende, 34000 Montpellier, giudi@ligm.crbm.cnrs-mop.fr Database : MaizeDB Species : Zea mays L. ssp. mays and related species Content : Maps, raw map data, loci, probes, genetic stocks, variations, mutant images, agronomic traits, gene products, QTL, bibliography, colleague addresses; hardlinks to sequence and germplasm databases. Latest_release : Oct 1996 Acedb_version : 4.1 Curator : Mary Polacco, maryp@teosinte.agron.missouri PI : Ed Coe, Jr., ed@teosinte.agron.missouri.edu Systems : Denis Hancock, dhancock@teosinte.agron.missouri.edu FTP : probe.nalusda.gov/pub/maizedb/macedist961001.tar.gz WWW : http://www.agron.missouri.edu WEBACE : http://probe.nalusda.gov:8300/ Contact : db_request@teosinte.agron.missouri.edu Comment : Data are periodically extracted into ACEDB format from Sybase Comment : Genera software used to maintain the Sybase database and its gateways, except for ACEDB Comment : ACEDB releases are announced on the MAIZE bulletin board; http://www.bio.net/hypermail/MAIZE/ Comment : WEBACE records are hardlinked to the Sybase server where data are curated Funding : USDA ARS Plant Genome Research Program FAQ_updated : Mar 7, 1997 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : July 1995 Database : Millet Genes Species : Pennisetum glaucum (Pearl Millet) ACEDB_version : 4.3 Curator : Matt Couchman, Matthew.Couchman@bbsrc.ac.uk PI : Katrien Devos, Katrien.Devos@bbsrc.ac.uk FTP: ftp://jiio5.jic.bbsrc.ac.uk/pub/millet WWW : http://synteny.nott.ac.uk/millet.html WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.shtml WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : March 1997 DataBase : Mousedb Species : Mus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD FAQ_updated : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : MsqDB Species : Interspecies Mosquito database ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. Curator : Staffan Bergh, staffan@biochem.kth.se Curator : Stewart Cole, stcole@pasteur.fr ACEDB_version : 4.3 Data_version : 4-22 (December 1996) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ FAQ_updated : December 1996 Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html FAQ_updated : September 1995 Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurrence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 FTP : ftp.sanger.ac.uk in pub/PomBase FAQ_updated : September 1995 Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : Receptor Database Species : all Curator : Kotoko Nakata, nakata@nihs.go.jp Co-Curator : Takako Igarashi, taka@nihs.go.jp Co-Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Contact : Kotoko Nakata, nakata@nihs.go.jp ACeDB_version : 4.1 WWW : http://impact.nihs.go.jp/RDB.html Data_updated : regularly FAQ_updated : October 1997 Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susan McCouch ACEDB_version : 4.1 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : November 1996 Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4.6 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB WWW : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Curator : Yankai Jia, jia@genome.stanford.edu Programmer : Gail Juvik, gjuvik@genome.stanford.edu Programmer : Shuai Weng, shuai@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu FAQ_updated : September 1996 Database: SchistoDB Species: Schistosoma mansoni (plus other schistosomes) PI: David Johnston ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Schisto/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: In development FAQ_updated : November 1996 Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Sam Beer, sbeer@nightshade.cit.cornell.edu PI : none currently Release : ACEDB 4.3 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_updated : May 1997 FAQ_updated : May 1997 Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : September 1995 Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker, rcsshoe@iastate.edu Curator : David Grant, dgrant@iastate.edu Assistant_curator : Marica Imsamde, mimsande@iastate.edu Contact : David Grant, dgrant@iastate.edu ACEDB-Version : 3.7 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://macgrant.agron.iastate.edu FAQ_updated : October 1995 Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FAQ_updated : October 1994 Database: ToxoDB Species: Toxoplasma gondii PI: David Sibley PI: David Roos PI: Jim Ajioka ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Toxo/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/toxo/toxpage.html Data_updated: October 1996 FAQ_updated: November 1996 Database : TreeGenes Species : Forest trees ACEDB_version : 4.3 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ FAQ_updated : May 1996 Database: Trypbase Species: Trypanosoma brucei PI: Sara Melville ACEDB_version: 4.3 Curator: Howard Cobb Curator: Martin Aslett Contact: Sara Melville, sm160@mole.bio.cam.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/brucei WWW: http://parsun1.path.cam.ac.uk/newtryp/toppage.htm WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: October 1996 FAQ_updated: November 1996 Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html FAQ_updated : April 1994 Database : 11Db Species : Homo sapiens Subject : Physical and Genetic mapping of Human Chromosome 11 Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk) PI : Peter Little (p.little@bc.ic.ac.uk) ACEDB_version : based on 4_1 with added map displays. ACEDB_version : based on 3_6 with added map displays. Data version : 1.0 Last Update : December 1995 WWW : http://chr11.bc.ic.ac.uk FTP : ftp.cc.ic.ac.uk Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Database : 22ace Species : Homo sapiens Subject : Physical map of human chromosome 22, genomic sequencing and more ACEDB_version : 4.1 Curator : Ian Dunham, id1@sanger.ac.uk Curator : Gareth Maslen, glm@sanger.ac.uk PI : Ian Dunham FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ FAQ_updated : August 1995 Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions _________________________________________________________________ Q12:Who prepared this document & where is the current version? A12: This document is posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The WWW version of this document is at: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html A text version is available via anonymous ftp at machine rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. Curators of ACEDB databases should take note of Question "What ACEDB databases exist?", and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov This FAQ was created and maintained from 1993 - 1996 by Bradley K. Sherman. Major contributions in getting it off the ground were made by Mike Cherry, John McCarthy, and Doug Bigwood. Other contributors include: * Lisa Lorenzen * David Matthews * Edie Paul * Donn Davy * Eric De Mund * Sam Cartinhour It is currently maintained by Dave Matthews. Please cite as: Matthews, D.E., and B.K. Sherman, ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993-1998, approx. 70K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov The GrainGenes Project is funded by the USDA ARS Plant Genome Research Program. Return to List of Questions _________________________________________________________________ From owner-acedb@net.bio.net Sat Feb 21 22:00:00 1998 From: "Qwertskie" Newsgroups: alt.binaries.w-software,alt.comp.software.financial,alt.comp.software.tools,alt.fan.dean-stark.software.tester,alt.geo-software,alt.med.software,amiga.software,at.tuwien.software,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet. Subject: !VERY CHEAP PC SOFTWARE Date: Sun, 22 Feb 1998 06:30:04 -0000 Lines: 15 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: usr54-cro.cableinet.co.uk X-NNTP-Posting-Host: usr54-cro.cableinet.co.uk Message-ID: <34efc58c.0@ispc-news.cableinet.net> Organization: "Cable Internet (post doesn't reflect views of Cable Internet)" X-NNTP-Posting-Host: 194.117.152.68 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!nntprelay.mathworks.com!uknet!cableinet-uk!news.cableinet.co.uk!ispc-news.cableinet.net!usr54-cro.cableinet.co.uk Xref: biosci bionet.software:20553 bionet.software.acedb:1626 bionet.software.gcg:3007 For the very latest in PC Software Direct to you... E-Mail: dgbl@cyberdude.com Mobile: +44 07 970 305 002 Operating Systems; MS DOS, Windows, Office; WP's, Speadsheets, Databases, Presentation, DTP, Utilities, Virus Killers, Graphic, Music Applications... ALL LASTEST TITLES 101% Error Free & Virus Free From owner-acedb@net.bio.net Sat Feb 21 22:00:00 1998 From: "Qwertskie" Newsgroups: alt.binaries.w-software,alt.comp.software.financial,alt.comp.software.tools,alt.fan.dean-stark.software.tester,alt.geo-software,alt.med.software,amiga.software,at.tuwien.software,bionet.software,bionet.software.acedb Subject: !VERY CHEAP PC SOFTWARE Date: Sun, 22 Feb 1998 06:31:25 -0000 Lines: 16 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: usr54-cro.cableinet.co.uk X-NNTP-Posting-Host: usr54-cro.cableinet.co.uk Message-ID: <34efc60c.0@ispc-news.cableinet.net> Organization: "Cable Internet (post doesn't reflect views of Cable Internet)" X-NNTP-Posting-Host: 194.117.152.68 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!newsfeed2.uk.ibm.net!ibm.net!news-lond.gip.net!news.gsl.net!gip.net!uknet!cableinet-uk!news.cableinet.co.uk!ispc-news.cableinet.net!usr54-cro.cableinet.co.uk Xref: biosci bionet.software:20554 bionet.software.acedb:1627 !VERY CHEAP PC SOFTWARE For the very latest in PC Software Direct to you... E-Mail: dgbl@cyberdude.com Mobile: +44 07 970 305 002 Operating Systems; MS DOS, Windows, Office; WP's, Speadsheets, Databases, Presentation, DTP, Utilities, Virus Killers, Graphic, Music Applications... ALL LASTEST TITLES 101% Error Free & Virus Free From owner-acedb@net.bio.net Sat Feb 21 22:00:00 1998 From: "Qwertskie" Newsgroups: alt.binaries.w-software,alt.comp.software.financial,alt.comp.software.tools,alt.fan.dean-stark.software.tester,alt.geo-software,alt.med.software,amiga.software,at.tuwien.software,bionet.software,bionet.software.acedb Subject: !VERY CHEAP PC SOFTWARE Date: Sun, 22 Feb 1998 06:31:25 -0000 Lines: 16 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: usr54-cro.cableinet.co.uk X-NNTP-Posting-Host: usr54-cro.cableinet.co.uk Message-ID: <34efc5de.0@ispc-news.cableinet.net> Organization: "Cable Internet (post doesn't reflect views of Cable Internet)" X-NNTP-Posting-Host: 194.117.152.68 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!europa.clark.net!152.158.16.55!newsfeed2.uk.ibm.net!ibm.net!news-lond.gip.net!news.gsl.net!gip.net!uknet!cableinet-uk!news.cableinet.co.uk!ispc-news.cableinet.net!usr54-cro.cableinet.co.uk Xref: biosci bionet.software:20555 bionet.software.acedb:1628 !VERY CHEAP PC SOFTWARE For the very latest in PC Software Direct to you... E-Mail: dgbl@cyberdude.com Mobile: +44 07 970 305 002 Operating Systems; MS DOS, Windows, Office; WP's, Speadsheets, Databases, Presentation, DTP, Utilities, Virus Killers, Graphic, Music Applications... ALL LASTEST TITLES 101% Error Free & Virus Free From owner-acedb@net.bio.net Sun Feb 22 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!oleane!jussieu.fr!ext.jussieu.fr!mac2-info.sb-roscoff.fr!user From: crepinau@sb-roscoff.fr (Crepineau florent) Newsgroups: bionet.software.acedb Subject: NEWBIE : .ace format from Phrap and ACEDB? Date: 23 Feb 1998 12:48:32 GMT Organization: Station biologique de Roscoff Lines: 16 Message-ID: NNTP-Posting-Host: mac2-info.sb-roscoff.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear ACEDB users, I am looking for a contig assembler (I asked you a while ago about TIGR assembler and ACEDB). I can not use Acembly because it doe not recognize my SCF format (don't ask me why, I don't know). So I looked for the package Phred/Phrap/Consed. It is very powerful and Phrap produce a .ace file. Does anybody know if this .ace file is compatible with ACEDB? (I have looked in the FAQ and in the archive and could not find the answer) Thank you in advance. Florent Crepineau / Station Biologique de Roscoff crepinau@sb-roscoff.fr From owner-acedb@net.bio.net Tue Feb 24 22:00:00 1998 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Genome Informaticist position at Cornell Date: 25 Feb 1998 09:17:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <9802251715.AA11727@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net GENOME INFORMATICIST The Plant Genetic Resources Unit, USDA-ARS, has an opening at Cornell University, Ithaca, New York, for a Genome Informaticist to develop improved means of access to plant genome data. The incumbent will be responsible for envisioning, engineering and implementing interactions among Internet and other publicly available biological data sources to enhance their information content, usefulness and accessibility to scientists working on genetic improvement of crop plants. Particular emphasis will be placed on developing software interfaces and graphical presentations to facilitate data exploration, visualization, and expert analysis. Incumbent will provide local expertise, advice and collaboration to scientists with bioinformatics problems such as processing and organizing their laboratory data, accessing public data, and analyzing/interpreting these data. Incumbent is expected to interact locally with other informatics components of the campus-wide Cornell Genomics Initiative, and to provide national and international leadership in improvement of plant genome databases and specialized software for application to crop enhancement. Candidates must be U.S. citizens and have knowledge of plant molecular biology, genetics and plant physiology, as well as skill in molecular biological and molecular genetic techniques. A Ph.D. is desirable. Salary is $46,254 - $71,503. Application procedures and additional information can be found at http://www.ars.usda.gov/afm/hrd/vacancy/x8n-8086.htm, or call Sharon Maio at (607) 255-5487. Applications must be marked ARS-X8N-8086 and postmarked by March 23, 1998. USDA-ARS IS AN EQUAL OPPORTUNITY EMPLOYER. From owner-acedb@net.bio.net Tue Feb 24 22:00:00 1998 Path: biosci!UCSD.EDU!dsmith From: dsmith@UCSD.EDU (Doug Smith) Newsgroups: bionet.software.acedb Subject: (none) Date: 25 Feb 1998 08:46:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802251645.IAA01224@biomail.ucsd.edu> NNTP-Posting-Host: net.bio.net subscribe Doug Smith, Professor of Biology .... dsmith@ucsd.edu Department of Biology, 0116; UCSD; La Jolla CA 92093 phone: 619-534-2620 FAX: 619-534-7108 http://www-biology.ucsd.edu/others/dsmith/dnasys.html From owner-acedb@net.bio.net Wed Feb 25 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: Extend database? Date: 26 Feb 1998 22:59:36 -0000 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6d4s4o$rho@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, acedbg@sanger.ac.uk !! FATAL ERROR 0: !! can't Extend DataBase. You need to add partitions This means: the file wspec/database.wrm does not have enough definition lines possibly since you allready are full you also have to add lines, but not edit the existing lines, to $ACEDB/database.map in the future, acedb will disconsider this info, but in the present code, the file is too short PLease Ian, can you edit it everywhere i ll modify disknew.c to 1) disregard this limit 2) automatically extend the file forthe sake of earlier versions of the code From owner-acedb@net.bio.net Thu Feb 26 22:00:00 1998 Path: biosci!wehi.edu.au!hallowes From: hallowes@wehi.edu.au (Peter Hallowes) Newsgroups: bionet.software.acedb Subject: (none) Date: 26 Feb 1998 19:49:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net help From owner-acedb@net.bio.net Thu Feb 26 22:00:00 1998 Path: biosci!INEXCHANGE.NET!info From: info@INEXCHANGE.NET (Info Desk) Newsgroups: bionet.software.acedb Subject: Advertisement: Website Hosting Date: 27 Feb 1998 15:57:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <19980227235106070.AFH147@out.inexchange.net> NNTP-Posting-Host: net.bio.net http://www.inexchange.net info@inexchange.net InExchange would like to introduce our complete Hosting and Promotional service. FOR ONLY $19.95 PER MONTH ! * 20 MB (megabytes) of disk space * 750 MB of data transfer per month * 5 E-mail accounts * INTERNATIONAL Hosting * Access to your account anytime via the Web Control Panel * Full MS Front Page support * Unlimited FTP updates * Personal CGI directory for your own scripts (or use ours) * The best statistics analyzer in the industry * E-mail forwarding, auto responders and vacation reply * Domain name registration (www.yourname.com) * FREE registration of your domain with over 250 search engines * Real Audio/Video support * Inquire about our $16.95 plan * Other plans also include: Shopping cart application and database access/utilities Cold Fusion Hosting CyberCash, iBill and VersaNet ready Instant on-line credit card processing For additional details, please refer to our website: http://inexchange.net info@inexchange.net From owner-acedb@net.bio.net Thu Feb 26 22:00:00 1998 Path: biosci!wehi.edu.au!hallowes From: hallowes@wehi.edu.au (Peter Hallowes) Newsgroups: bionet.software.acedb Subject: (none) Date: 26 Feb 1998 20:08:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net help From owner-acedb@net.bio.net Sat Feb 28 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Mar 1998 02:00:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199803011000.CAA20743@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. 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. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms.