From owner-acedb@net.bio.net Mon Mar 03 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!rill.news.pipex.net!pipex!warwick!bignews.shef.ac.uk!not-for-mail From: xms@dcs.shef.ac.uk (Xiao Mang Shou) Newsgroups: bionet.software.acedb Subject: aceserver Date: 4 Mar 1997 18:36:35 GMT Organization: Department of Computer Science, University of Sheffield Lines: 17 Message-ID: <5fhq3j$qag@bignews.shef.ac.uk> NNTP-Posting-Host: tiger.dcs.shef.ac.uk X-Newsreader: TIN [version 1.2 PL2] Dear netters, Can anyone tell me how to set up aceserver? I can't find aceserver binary file within the acedb package (aceclient is included). Besides, I want to set up the aceserver instead of run acedb daemon (which requires root password). The document on aceserver is oversimplified. Can anyone tell me how to get the aceserver file, any constraints on specifying port number, any files to be changed, and any other relevant information? Thank you very much. -- ----------------------------------------------------------------- Xiao Mang Shou email: X.Shou@dcs.shef.ac.uk From owner-acedb@net.bio.net Mon Mar 03 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: aceserver Date: 4 Mar 1997 20:24:45 -0000 Lines: 43 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fi0ed$lja@mserv1.dl.ac.uk> Original-To: xms@dcs.shef.ac.uk you need to recompile the server just above the w* dir which contain the source code you do ln -s wmake/makefile make aceserver ---------- to run the server setenv ACEDB ... aceserver -port 20000300 ------------ then you connect to it via aceclient -host host -port 20000300 -------- root passwd not needed for that the one thing to do is to edit wspec/server.wrm to set read/write access choose a correct place for the lock file i think the distrib says something too specific /tnp is no good becasue the client on another machine sees a different /tmp -------- you can select the time out etc on the command line --------- ask more question in case of problem jean From owner-acedb@net.bio.net Mon Mar 03 22:00:00 1997 Path: biosci!wehi.edu.au!hallowes From: hallowes@wehi.edu.au (Peter Hallowes) Newsgroups: bionet.software.acedb Subject: Editing ACeDB data from acedb application. Date: 4 Mar 1997 14:15:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <5fhq3j$qag@bignews.shef.ac.uk> NNTP-Posting-Host: net.bio.net Is there any method for editing and annotating the ACeDB database from within the acedb application, without using Ace files? ----------------------------------------- Peter Hallowes e-mail address: hallowes@wehi.edu.au Adress: 7/18 Princes Street, St Kilda Victoria, Australia 3182 ----------------------------------------- From owner-acedb@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Mazda Hewitt Newsgroups: bionet.software.acedb Subject: Re: Editing ACeDB data from acedb application. Date: Wed, 05 Mar 1997 14:57:03 +0000 Organization: John Innes Centre Lines: 12 Message-ID: <331D89BF.2781@bbsrc.ac.uk> References: <5fhq3j$qag@bignews.shef.ac.uk> NNTP-Posting-Host: jiio10.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) To: Peter Hallowes Peter Hallowes wrote: > > Is there any method for editing and annotating the > ACeDB database from within the acedb application, > without using Ace files? Yes there is, You just select the object you want to change, then using the right mouse button chose UPDATE. This will allow you to change and add new information. Mazda Hewitt From owner-acedb@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!dispatch.news.demon.net!demon!fido.news.demon.net!demon!news.unisource.nl!news.flnet.nl!usenet From: Arjen van de Linde <0vdlinde03@zeewolde.flnet.nl> Newsgroups: bionet.software.acedb Subject: Re: HELP ON INFORMATION REGARDING YEAR 2000 COMPLIANCE Date: Wed, 05 Mar 1997 19:52:31 +0100 Organization: Flevonet Message-ID: <331DC0EF.578@zeewolde.flnet.nl> References: <33133fb7.0@robby.oit.umass.edu> NNTP-Posting-Host: mdm158.lly.flnet.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Lines: 14 BONG-HACK LEE wrote: > > Dear Netters: > > I am looking for the particular software which can search all > spread sheets which I created by using LOTUS 123 and identify which ones > are all right for year 2000 or which are not O.K for year 2000. Or, any > information or idea will be appreciated. Thanks in advance! I think this should never be a problem, because in LOTUS a date is used as a number (1 Jan 1900 being number 1). Every spreadsheetprogram is using this technique and therefore the year 2000 will be just another number. Arjen van de Linde From owner-acedb@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!ix.netcom.com!news From: edwinl1@ix.netcom.com(MO & Associates) Newsgroups: bionet.software.acedb Subject: Sugestion Box/New Ideas Administrator Software Date: 6 Mar 1997 03:25:40 GMT Organization: Netcom Lines: 29 Message-ID: <5fldfk$ooi@dfw-ixnews5.ix.netcom.com> NNTP-Posting-Host: mia-fl6-17.ix.netcom.com X-NETCOM-Date: Wed Mar 05 9:25:40 PM CST 1997 THE NEW IDEAS ADMINISTRATOR Version 2.01 The best "NEW IDEAS ADMINISTRATOR" in the market. Use e-Mail (optional). Intuitive way for employees to have access to a tool in order to make suggestions to Supervisors. Can be done using computer or filling the new idea form. Can be e-mailed (optional) to his/her supervisor, director, vice-president, etc. The supervisor evaluates the idea and sends back the evaluation, asking for more info or with the final evaluation. Awards might be implemented depending the amount saved by the company. Also has different level of access, employee, supervisor, director, administrator, etc. Your Company can save millions. It can be customized for your needs. Also Help screens available. All kind of reports. Upgrades twice a year. Also help available through Internet. It's a simple but Powerful Tool for just: $139.99 Send Check or Money Order - $139.99 to: MO & Associates 666 W 81 St. 117 Hialeah, FL 33014 (The response has been so big that we need 4 to 8 weeks to process.) Satisfaction Guaranteed Ask for more info to: edwinL1@ix.netcom.com From owner-acedb@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Mazda Hewitt Newsgroups: bionet.software.acedb Subject: Jade Display writing Date: Thu, 06 Mar 1997 10:42:05 +0000 Organization: John Innes Centre Lines: 43 Message-ID: <331E9F7D.167E@bbsrc.ac.uk> NNTP-Posting-Host: jiio10.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) Hi, I have all of the documentation for jade and have it running on my acedb database, this all works fine. The problem I have is that although I can write a applet that can fetch a table form the database and display it, I don't know how to integrate a display into jade. Say I wanted to replace the Vmap display with one I have already written to display a genetic map. I need to get a array of loci objects or a table of loci names and positions. That's OK, the documentation on the AceAccessor and AceObjects is fine. But if I want the map to be brought up when a map is clicked on in jade, or highlight a specific loci, I'm stuck. I'm not sure where to alter jade to say what map to bring up when, also I'm not sure what interface is needed in my map to receive the correct object to display. There must be a way of passing what to display from one display to another. In the source code I've seen the "Implements Displayable" inheritance, is this all that is needed to interface my map into jade? public interface Displayable { public void invokeDisplay (Accessor db, Key key) ; public boolean reDisplayable() ; public String [] about () ; // Info on the display, authors, date, purpose public String nickName () ; // Name of display for human consumption } This is the Displayable interface, do I need to override the invokeDispaly method to implement the starting of my map. Is the "key" in that method the object name to be retrieved? Also, after I have brought up the display how do I display another object. Say I have a map and someone double clicks on a loci, how do I invoke the display to show a loci object? Thanks for your help. Mazda Hewitt From owner-acedb@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!news.apfel.de!fu-berlin.de!rag100.rz-berlin.mpg.DE!not-for-mail From: Ela Hunt Newsgroups: bionet.software.acedb Subject: Re: Editing ACeDB data from acedb application. Date: Thu, 06 Mar 1997 08:58:02 +0100 Organization: Max-Planck Institut fuer Molekulare Genetik Lines: 22 Message-ID: <331E790A.41C6@rag100.rz-berlin.mpg.de> References: <5fhq3j$qag@bignews.shef.ac.uk> NNTP-Posting-Host: rag100.rz-berlin.mpg.de (141.14.130.78) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Access: 16 25 816 X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) YOu can also rename objects (main menu- Add-Alias-Rename option) but overall, if you have more than 3 objects to edit, it is sometimes easier to : display the whole class by clicking on class name, then option New Keyset, then option Add-Remove, to create a list of objects to edit. Dump objects, edit and read back in Ela Peter Hallowes wrote: > > Is there any method for editing and annotating the > ACeDB database from within the acedb application, > without using Ace files? > _______________________________________________________________________________ Ela Pustulka-Hunt MA MPhil BA hunt_e@mpimg-berlin-dahlem.mpg.de Database Administrator tel. 030 - 8413-1415 Max Planck Institut fuer Molekulare Genetik, Abtl. Lehrach Ihnestrasse 73, 14195 Berlin, Germany _____________________________________________________________________________ From owner-acedb@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!warwick!bignews.shef.ac.uk!not-for-mail From: xms@dcs.shef.ac.uk (Xiao Mang Shou) Newsgroups: bionet.software.acedb Subject: webace Date: 6 Mar 1997 21:04:57 GMT Organization: Department of Computer Science, University of Sheffield Lines: 14 Message-ID: <5fnbhp$b1a@bignews.shef.ac.uk> NNTP-Posting-Host: tiger.dcs.shef.ac.uk X-Newsreader: TIN [version 1.2 PL2] Dear netter, I've managed to set up aceserver and aceclient. Now I need to put the database to the web. I wonder if there is a way to start webace without starting aceserver as inetd daemon, because I don't have root password. Can I run webace by just starting aceserver and aceclient? -- ----------------------------------------------------------------- Xiao Mang Shou email: X.Shou@dcs.shef.ac.uk From owner-acedb@net.bio.net Sun Mar 09 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!newspump.sol.net!cyclic.gsl.net!news.gsl.net!spring.edu.tw!serv.hinet.net!netnews.hinet.net!news From: "haifung" Newsgroups: bionet.software.acedb Subject: 第一次。 Date: 10 Mar 1997 16:05:23 GMT Organization: DCI HiNet Lines: 1 Message-ID: <01bc2d6d$2941e200$2f595fa8@default> NNTP-Posting-Host: 168.95.89.47 X-Newsreader: Microsoft Internet News 4.70.1155 不小心走了進來，這是我的第一次。 From owner-acedb@net.bio.net Wed Mar 12 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!rill.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-lyon1.fr!news.imag.fr!ciril.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois JEANMOUGIN) Newsgroups: bionet.software.acedb Subject: Re: aceserver/aceclient on Linux Date: 13 Mar 1997 12:18:03 GMT Organization: IGBMC Lines: 26 Message-ID: <5g8r9r$rp5@news.u-strasbg.fr> References: Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article , Staffan Bergh writes: > Hi, has anyone got the aceserver running on Linux?[...] > Before I investigate this further (i.e. to save some time :) has anyone done > this? > > Linux version 1.2.13 (Redhat 2.0 -- old, I know) Have a look at molecular linux : http://evolution.bmc.uu.se/~thomas/mol_linux/ and especially at : http://evolution.bmc.uu.se/~thomas/mol_linux/acedb/ This will help you if you switched from i386 to ELF binry format, else, perhaps you will find some help however. Francois. -- Francois Jeanmougin Service de bioinformatique / bioinformatics service IGBMC BP 163 67404 Illkirch France tel :(France) 03 88 65 32 71 / (international) (+33) 3 88 65 32 71 e-mail : jeanmougin@igbmc.u-strasbg.fr C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun (Thiefaine) From owner-acedb@net.bio.net Wed Mar 12 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news.maxwell.syr.edu!dispatch.news.demon.net!demon!newsfeed.nacamar.de!nntp.uio.no!news.kth.se!not-for-mail From: Staffan Bergh Newsgroups: bionet.software.acedb Subject: aceserver/aceclient on Linux Date: 13 Mar 1997 09:15:31 +0100 Message-ID: NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Gnus v5.3/Emacs 19.34 Lines: 15 Hi, has anyone got the aceserver running on Linux? I get errors in the rpcgen-generated code (surprise, surprise ...). The error when running rpcgen with option '-5' (that should produce SysVr4 code) is that netconfig.h is missing, the standard (option-less) invocation gives error on argument mismatches and missing functions. Some more-or-less random hacking in rpcace_sp.c gives me a server that starts, but seems to loop on client connections, slowly gobbling up more and more of the cpu until a SIGSEGV stops it. Before I investigate this further (i.e. to save some time :) has anyone done this? Linux version 1.2.13 (Redhat 2.0 -- old, I know) Cheers /staffan From owner-acedb@net.bio.net Wed Mar 12 22:00:00 1997 Path: biosci!wehi.edu.au!hallowes From: hallowes@wehi.edu.au (Peter Hallowes) Newsgroups: bionet.software.acedb Subject: Physical map clutterring Date: 13 Mar 1997 14:58:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear ACeDB community, I am implementing an ACeDB database for malaria and the problem I am facing is that positive loci of clones appear twice on the physical map; Once just below the genetic horizontal bar, in correspondence with the clone above the genetic horizontal bar. And again, attached to the bottom horiozontal bar that represents the whole contig. When the loci are close together, their second appearance has the effect of clutterring up the whole display. Is the seccond appearance of loci on the Physical Map a side effect of View : "MAP-default" Gmap Submenus Columns "Loci" 1 Point_yellow ">?Locus Positive_clone" or can I get rid of it without losing the color on the genetic map that indicates that the locus hybridises to a clone? Yours sincerely, Peter ----------------------------------------- Peter Hallowes e-mail address: hallowes@wehi.edu.au Adress: 7/18 Princes Street, St Kilda Victoria, Australia 3182 ----------------------------------------- From owner-acedb@net.bio.net Wed Mar 12 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!csulb.edu!hammer.uoregon.edu!news.uoregon.edu!news.emf.net!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: 13 Mar 1997 16:32:55 GMT Organization: Lawrence Berkeley Laboratory, Berkeley CA Lines: 1191 Approved: news-answers-request@MIT.Edu Message-ID: <5g9a7n$ci3@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.pswfs.gov Summary: Frequently Asked Questions about finding and getting started with the genome database software ACEDB. Xref: biosci bionet.software.acedb:1142 news.answers:90003 Archive-name: acedb-faq Last-modified: 13 Mar 97 Version: 1.35 ---------------------------------------------------------------------------- ACEDB FAQ ---------------------------------------------------------------------------- Curated by: Dave Matthews ---------------------------------------------------------------------------- Frequently Asked Questions about ACEDB * Q0 : What is ACEDB? * Q1 : What is the current version of ACEDB? * Q2 : What hardware/software do I need to run ACEDB? * Q3 : Where can I get ACEDB? * Q4 : What ACEDB databases exist? * Q5 : What documentation exists for ACEDB? * Q6 : What other resources are available for ACEDB? * Q7 : How should ACEDB be cited? * Q8 : Is ACEDB object-oriented? * Q9 : How does one get on/off the ACEDB announcements mailing list? * Q10 : ! When and where is the next ACEDB Workshop? * Q11 : 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 [Q4 gives contact information]. 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 circa 1990. 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 [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. 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 ACEDB? A1: (This answer refers to the software, not the C. elegans data.) Current Unix version is 4_3 (as of May 1996) and is identical to the test version test.4_3i. A Macintosh version is available as version 4.1b1. A Windows 95/NT version is available as version beta960927. To retrieve the software see Q3. To be kept informed of new releases see Q9. Return to List of Questions ---------------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. * Unix: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series 4, 5, 6 o IBM RS-6000 o PC 386/486/Pentium with Linux o NEC EWS4800 o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o 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) Return to List of Questions ---------------------------------------------------------------------------- Q3: Where can I get ACEDB? A3: Source code and Unix binaries are available in the following anonymous ftp sites: * lirmm.lirmm.fr in pub/acedb * ftp.sanger.ac.uk in pub/acedb * ncbi.nlm.nih.gov in repository/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 NEC EWS4800 binaries: * http://www.labs.nec.co.jp/freesoft/freesofte.html Windows 95/NT 3.51, from Richard Bruskiewich: * bates.biol.sfu.ca in pub/ntace * ftp.sanger.ac.uk in pub/winace * bioinformatics.weizmann.ac.il in pub/databases/acedb 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 Return to List of Questions ---------------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: In alphabetic order by Database name [Curators, please submit changes as new paragraphs] Database : AaeDB Species : Aedes aegypti (Mosquito) ACEDB_version : 3.0 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@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 Last_update : December 1994 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 Last_update : December 1996 Database : AboutDB Curator : Staffan Bergh, staffan@biochem.kth.se Subject : ACEDB itself (meta-meta-metadata) ACEDB_version: 3.0 WWW : http://www.biochem.kth.se/AboutDB.html Last_update : July 1995 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/ Last_update : August 1995 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 Last_update : 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/ Last_Update : July 1995 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/ Last_update : 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://nasc.nottm.ac.uk Last_update : Under development 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/ Last_update : 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/ Last_update : September 1995 Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edubr> 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/ Last_update : 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/ Last_update : 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 Last_updated: In development 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 : 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. Last_update : 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/ Last_update : 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 Last_updated: In development 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/ Last_update : May 1995 Database : GrainGenes Species : Wheat, barley, 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_3 (Unix), 4.1b1 (MacAce) Data_version : 1.7, December 1996 Availability : UNIX and Macintosh versions via anonymous ftp Availability : Macintosh version on CD-ROM "RiceMac / MacGrainGenes", 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 Gopher : greengenes.cit.cornell.edu Gopher : grain.jouy.inra.fr Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://wheat.pw.usda.gov/ WWW : http://grain.jouy.inra.fr Last_update : December 1996 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 WWW : http://moulon.inra.fr/acedb/igd.html 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) Last_updated: October 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 Last_update : 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/ Last_update : 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://nasc.nott.ac.uk:8400/db.html WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.shtml WWW : http://probe.nalusda.gov:8300/plant/ Last_update : 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 Last_update : 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/ Last_update : June 1995 Database : MsqDB Species : Interspecies Mosquito database ACEDB_version : 4.1 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Contact : aaedbmgr@klab.agsci.colostate.edu Last_update : March 1996 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/ Last_update : 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 Last_update : 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/ Last_update : 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 Last_update : 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/ Last_update : June 1995 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/ Last_update : 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 Last_update : 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 Last_update: In development Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu PI : Steve Tanksley 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/ Last_update : April 1996 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/ Last_update : 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 Last_update : 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 Last_update : 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 Last_update: October 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/ Last_update : 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 Last_updated: October 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 Last_update : 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/ Last_update : 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 ---------------------------------------------------------------------------- Q5: What documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Server 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. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000. Primary documents from the developers are: * acedb -- A C. elegans Database: I. Users' Guide. * acedb -- A C. elegans Database: II. Installation Guide. * acedb -- A C. elegans Database: III. Configuration Guide. * Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z. The files are in TeX (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. 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".) SampleDB, by Dave Matthews, is an ACEDB database constructed to demonstrate features of ACEDB, especially map and sequence displays. Anonymous ftp to probe.nalusda.gov:pub/acedocs/sampledb You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angistute.ps and angistute.hqx available by anonymous ftp at ncbi.nih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). URL : http://genome-www.stanford.edu/docs/aatdb_man.html. A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. URL : http://probe.nalusda.gov:8000/acedocs/overview.html. Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. Return to List of Questions ---------------------------------------------------------------------------- Q6: What other resources are available for ACEDB? A6: Perl and WWW tools The AGIS server at the National Agricultural Library provides tools for integrating version ACEDB with perl and the World-Wide Web. A WWW interface to 4.3 is available as ftp://probe.nal.usda.gov/pub/tools/webace.tar.gz. Instructions for this interface can be found at http://probe.nal.usda.gov:8000/acedocs/webace.html. (An earlier tool set is available as ftp://probe.nalusda.gov/pub/tools/acelib.tar.gz). 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/. Java Interface A Java interface to acedb is under active development. Involved people are Lincoln Stein, Jean Thierry-Mieg, Doug Bigwood, John Barnett, Sam Cartinhour. A test system can be seen at http://alpha.crbm.cnrs-mop.fr If you are interested in this approach, please contact mieg@kaa.crbm.cnrs-mop.fr X-client The 4_3 distribution contains the source code for a new version of the code called xclient. You need to recompile it (make xclient). Then, you create an empty database with the nematode models and strat xclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the montpellier server in the distrib server.wrm). The data will be saved locally and can then be viewed with a normal xace. The control of which data should be imported is very crude. In anay session, every object will be imported once. This should be rationalised, please let us know if this approach seems useful, and how it should be configured. (mieg@kaa.crbm.cnrs-mop.fr) The Developers' Archive Mike Cherry maintains an archive of tools that may be useful in curating ACEDB databases via gopher at ftp://genome-ftp.stanford.edu/pub/acedb_dev/ If you have a contribution send a message to Mike (cherry@genome.stanford.edu). The Biosci conference bionet.software.acedb There is a USENET/Biosci conference titled bionet.software.acedb created expressly for discussion of ACEDB. The best way to interact with the Biosci conferences is via a newsreader like rn, trn, tin or a WWW browser. Consult your system administrator for more information. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. All of the articles in 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. If your WWW browser is configured properly you may be able to read the newsgroup at news:biosci.software.acedb. And more The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: * http://moulon.inra.fr/acedb/acedb.html for C. elegans data * http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data * http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html A how-to manual on the Moulon server is available at http://keck.tamu.edu/cgi/staff/ace-mosaic-howto.html The Genome Computing Group, Lawrence Berkeley Laboratory, has an anonymous ftp service at machine genome.lbl.gov which contains: * flydb - LBL's Drosophila Acedb-style database * 21bdb - LBL's Human Chromosome 21 Acedb-style database * querdb - LBL's query-language extensions to Acedb * metadata - LBL's compendium of Acedb database schema variants * macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version * There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to databases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: * 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). * 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier (Jean Thierry-Mieg et al), and the Integrated Genome Database project in Heidelberg (Otto Ritter, Detlef Wolf et al). Return to List of Questions ---------------------------------------------------------------------------- Q7: How should ACEDB be cited? A7: 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 ---------------------------------------------------------------------------- Q8: Is ACEDB object-oriented? A8: From the ACEDB User's Guide: A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions ---------------------------------------------------------------------------- Q9: How can I get on/off the ACEDB announcements mailing list? A9: To get on or off the mailing list send mail to rd@sanger.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q6 for details] is on the mailing list. Return to List of Questions ---------------------------------------------------------------------------- Q10: When and where is the Next ACEDB Workshop? A10: The ACE97 Conference and Workshop will be held July 27 - August 9 in Ithaca, New York, USA. See the ACE97 Home Page for details. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/index.html. 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 ---------------------------------------------------------------------------- Q11:Who prepared this document & where is the current version? A11: This document will be 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 4 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, 1993-1996, approx. 50K 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 Thu Mar 13 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!worldnet.att.net!news.maxwell.syr.edu!news.cis.ohio-state.edu!nntp.sei.cmu.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!lchen+ From: Liren Chen Newsgroups: bionet.software.acedb Subject: Personal Search Agent Date: Fri, 14 Mar 1997 13:01:06 -0500 Organization: Doctoral student, Language Technology Institute, Carnegie Mellon, Pittsburgh, PA Lines: 4 Message-ID: <4n_N9WW00WB6Qp4HUU@andrew.cmu.edu> NNTP-Posting-Host: po7.andrew.cmu.edu Go to http://www.cs.cmu.edu/~lchen x xYou can find a personal search agent. It does improve your search efficiency. x x From owner-acedb@net.bio.net Thu Mar 13 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!worldnet.att.net!news.maxwell.syr.edu!news.cis.ohio-state.edu!nntp.sei.cmu.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!lchen+ From: Liren Chen Newsgroups: bionet.software.acedb Subject: Personal Search Agent Date: Fri, 14 Mar 1997 13:01:00 -0500 Organization: Doctoral student, Language Technology Institute, Carnegie Mellon, Pittsburgh, PA Lines: 4 Message-ID: NNTP-Posting-Host: po9.andrew.cmu.edu Go to http://www.cs.cmu.edu/~lchen x xYou can find a personal search agent. It does improve your search efficiency. x x From owner-acedb@net.bio.net Thu Mar 13 22:00:00 1997 From: (DogZ Software Center) Newsgroups: bionet.software.acedb Subject: MS Office 97 only costs US$45?! 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If you want some more details , you can go http://www.hkstar.com/~dogz now. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ DogZ Software Center From owner-acedb@net.bio.net Sun Mar 16 22:00:00 1997 Path: biosci!NATURE.BERKELEY.EDU!bosborne From: bosborne@NATURE.BERKELEY.EDU (Brian Osborne) Newsgroups: bionet.software.acedb Subject: simple 'annotation' questions... Date: 16 Mar 1997 19:30:51 -0800 Organization: Plant Gene Expression Center Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <332CBB22.7A0@nature.berkeley.edu> NNTP-Posting-Host: net.bio.net To the group, Forgive these elementary questions, I am new to acedb! I have ace files, which include genefinder predictions, as well as blastn matches, blastx matches, etc. I also have an ace file (Methods.ace), containing methods to visualize these hits. I read in both files after starting up the db - I can see that the methods have been parsed correctly by viewing them individually. But, I cannot see the blastn hits on screen, as boxes. I seem to have omitted something - how can I view the hits? And another : I have looked around the sites and found a lot of useful documentation. One thing I haven't seen is documentation on how to use genefinder and 'annotate' in acedb. Does such a document exist? Thanks for your attention to these matters, Brian O. -- Brian I. Osborne bosborne@nature.berkeley.edu Plant Gene Expression Center TEL 510 559 5924 800 Buchanan St. FAX 510 559 5678 Albany CA 94710 USA From owner-acedb@net.bio.net Sun Mar 16 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: annotate Date: 17 Mar 1997 11:31:32 -0000 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5gja2k$r29@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Brian I. Osborne is asking: One thing I haven't seen is documentation on how to use genefinder and 'annotate' in acedb. Does such a document exist? I beleive, it does not exist, i think we should produce it. jean From owner-acedb@net.bio.net Sun Mar 16 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Re: annotate Date: 17 Mar 1997 16:17:28 -0000 Lines: 4 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5gjqqo$lss@mserv1.dl.ac.uk> Original-To: mieg@kaa.crbm.cnrs-mop.fr Look at http://www.sanger.ac.uk/worm/RUNGENE.html which is Steve's guide to using genefinder in acedb. Richard From owner-acedb@net.bio.net Mon Mar 17 22:00:00 1997 Path: biosci!NATURE.BERKELEY.EDU!bosborne From: bosborne@NATURE.BERKELEY.EDU (Brian Osborne) Newsgroups: bionet.software.acedb Subject: using giface? Date: 18 Mar 1997 11:06:27 -0800 Organization: Plant Gene Expression Center Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <332EE7E8.6D4E@nature.berkeley.edu> NNTP-Posting-Host: net.bio.net To the group, I've compiled v. 4.3, and now I would like to use the giface utility to produce gif images of my ace files. Is there a description available of this utility? Thanks once again, Brian O. -- Brian I. Osborne bosborne@nature.berkeley.edu Plant Gene Expression Center TEL 510 559 5924 800 Buchanan St. FAX 510 559 5678 Albany CA 94710 USA From owner-acedb@net.bio.net Sat Mar 22 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: ACEDB data release for C.elegans Date: 23 Mar 1997 05:32:42 -0000 Lines: 121 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5h2f9q$77n@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. New ACEDB data release WG2.4-2 and WS2.4-16 for C. elegans ========================================================== With this release we are starting a new series of database updates from scratch again, rather than adding on to WS1.4-30. The new series is called WS2 (and correspondingly WG2 for the version without sequences). Because we are restarting from scratch, you must get all the updates from the series you want (WS2 or WG2), and rebuild a new database using them. Fortunately, it will be much faster reading in the sixteen new WS2 updates than thirty-some of the WS1 series. If you have a working acedb version built with the WS1 series, you must do two things: (1) 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.WS1...tar.Z or rawdata/update.WS1... files. (2) you must get a new copy of the INSTALL script, as well as all the new WS2 updates. If you do not remove the contents of the database directory, when you start up acedb it will still say "WS1" in the title bar, and will not be able to load the WS2 updates. When you have emptied it properly, it will ask if you want to reinitialise, and put WS2 in title bar. If you do not get a new copy of the INSTALL script, it will not unpack the WS2 update files. The database software has not changed. You should be using these updates in conjunction with release 4_3 of the acedb software. Reminder: there are now two versions of the C.elegans database. The WS2 update series contains everything, whereas the WG2 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. The additions since the last release are: for both types of update - a physical map update with a few changes (mid Feb) - accumulated genetic data and corrections - from CGC : bibliography, wbg subscribers and strains (February) - from Leon Avery : wbg14.5 with connections to genes etc. and for just the complete database including sequences (WS2.4-16) Data fom St Louis and Sanger Sequence databases taken in mid-Feb: - There are now 2020 (1859 before) cosmids totalling 60615799 (55996632 before) bases. - EMBL49 Sequence, dna and full embl text descriptions - We have tried to include all the missing Peptide sequences, so you do not see dashes in the blixem (multiple alignment) display. The total database sizes after adding these updates are around 390MB for the WS2 database and around 60MB for the WG2 database. 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 program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- From owner-acedb@net.bio.net Sun Mar 23 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!ix.netcom.com!enews.sgi.com!news.sgi.com!mr.net!newshub.tc.umn.edu!newsstand.tc.umn.edu!usenet From: "F.K. van Evert" Newsgroups: bionet.software.acedb Subject: ACEDB vs. RDBMS Date: Mon, 24 Mar 1997 09:28:11 -0600 Organization: Dept. of Soils, Univ. of Minnesota Lines: 15 Message-ID: <33369D8B.D66@soils.umn.edu> Reply-To: fvevert@soils.umn.edu NNTP-Posting-Host: x84-77-58.soils.openpn.umn.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) To anyone who can help: If you needed to convince someone who is currently using a standard, commercial, off-the-shelf relational DBMS, that he/she should be using ACEDB, what would you tell him? Regards, Frits F.K. van Evert University of Minnesota, Dept. of Soils St. Paul, Minnesota USA From owner-acedb@net.bio.net Mon Mar 24 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!feed1.news.erols.com!howland.erols.net!newsxfer.itd.umich.edu!yale!oitnews.harvard.edu!fas-news.harvard.edu!newspump.wustl.edu!newsreader.wustl.edu!news From: eddy@wol.wustl.edu (Sean Eddy) Newsgroups: bionet.software.acedb Subject: Re: ACEDB vs. RDBMS Date: 24 Mar 1997 17:51:27 -0600 Organization: Washington University in St. Louis, MO USA Lines: 17 Sender: eddy@wol.wustl.edu Message-ID: References: <33369D8B.D66@soils.umn.edu> NNTP-Posting-Host: wol.wustl.edu In-reply-to: "F.K. van Evert"'s message of Mon, 24 Mar 1997 09:28:11 -0600 X-Newsreader: Gnus v5.1 In article <33369D8B.D66@soils.umn.edu> "F.K. van Evert" writes: >If you needed to convince someone who is currently using a standard, >commercial, off-the-shelf relational DBMS, that he/she should be using >ACEDB, what would you tell him? `In one graphical display from your DBMS, show me the predicted gene structures, BLAST hits, PROSITE hits, tRNAs, expressed sequence tags, and repeat families on C. elegans cosmid ZK637.' (For instance.) -- - Sean Eddy, Ph.D. - Dept. of Genetics, Washington University School of Medicine - 660 S. Euclid Box 8232, St. Louis MO 63110, USA - mailto://eddy@genetics.wustl.edu http://genome.wustl.edu/eddy From owner-acedb@net.bio.net Mon Mar 24 22:00:00 1997 Path: biosci!GIBBS.OIT.UNC.EDU!groves From: groves@GIBBS.OIT.UNC.EDU ("William E. Groves") Newsgroups: bionet.software.acedb Subject: (none) Date: 25 Mar 1997 06:05:19 -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 unsubscribe From owner-acedb@net.bio.net Sun Mar 30 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!howland.erols.net!worldnet.att.net!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!sprout.nal.usda.gov!usenet From: Doug Bigwood Newsgroups: bionet.software.acedb Subject: If you are using GIG software - webace, dbrun, perlace modules ... Date: Mon, 31 Mar 1997 15:09:19 -0500 Organization: Genome Informatics Group, University of Maryland Lines: 19 Message-ID: <334019EF.6A63@gig.usda.gov> NNTP-Posting-Host: locus.gig.usda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) The Genome Informatics Group is currently preparing for a review. If you are using any of the software we have developed, or have used it in the past, please e-mail gig@gig.usda.gov to let us know. Some of the software we have developed includes WWW-acedb interfaces (webace and dbrun), perl modules for acedb (including perl client software), and gifcaptn. In your e-mail message please include: 1. a list of all of the software products from GIG that you use 2. for the web interface software a list of databases that the interface is used for and whether or not the databases are available to the public (include a URL if public) The information is needed by April 4. Please e-mail us even though you are quite sure that we know about you already. Thank you for your assistance. Doug Bigwood Manager, Genome Informatics Group From owner-acedb@net.bio.net Mon Mar 31 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Apr 1997 02:00:20 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199704011000.CAA14192@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. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net