From owner-acedb@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!is.bbsrc.ac.uk!news From: Mazda Hewitt Newsgroups: bionet.software.acedb Subject: Re: Trouble with installing ACEDB on Linux Date: Mon, 02 Dec 1996 10:19:02 +0000 Organization: John Innes Centre Lines: 22 Message-ID: <32A2AD16.446B@bbsrc.ac.uk> References: <328B3BEC.37C7@uia.ua.ac.be> 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 3.0Gold (X11; I; OSF1 V3.2 alpha) To: Nerogenetics Laboratory OK, I can't diagnose your problem with your install script, but this should work: from you ACEDB directory, the one with the ./bin and ./database subdirectories type ./bin/xace . or try form the directory above your database directory type /path/to/xace . this should solve your~: >ACEDB="/usr/local/acedb_43" but the program still could not find the >database ??? Mazda From owner-acedb@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: ACEDB data updates for C.elegans Date: 3 Dec 1996 19:45:00 -0000 Lines: 105 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <581vvs$p6h@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. ACEDB data updates WG1.4-7 and WS1.4-21 to 4-26 for C. elegans ============================================================== ****** IMPORTANT NOTICE: you must get a new copy of INSTALL ******** Versions of the INSTALL script from before December 1996 will not unpackage these update files correctly. ******************************************************************** You should be using these updates in conjunction with previous WS1 and WG1 releases, and version 4_3 of the acedb software. Reminder: there are now two versions of the C.elegans database. The WS1 update series contains everything, whereas WG1 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. The additions since WG1.4-6 and WS1.4-20 are: for both types of update - a physical map update with a few changes (mid Nov) - accumulated genetic data including a substantial number of new gene_classes and loci, also some mapping data - from CGC: bibliography, strains and subscribers (late Oct) - from Leon Avery: wbg14.4 with connections to genes etc. and for the first time connections to Cells and Cell_groups (any comments ??) and for just the complete database including sequences (WS1.4-16) Data fom St Louis and Sanger Sequence databases taken in mid-Nov: - There are now 1777 (1714 before) cosmids totalling 53695369 (51655842 before) bases. The total database sizes after adding these updates are around 480Mb for the WS1 database (we said it would grow!) and around 65Mb for the WG1 database. It will take a long time to read in the WS1 updates, particularly WS1.4-22 to 4-24. All six updates took us several hours. 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 Tue Dec 03 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!news.cerf.net!news1.ni.net!news From: member@haha.com (member) Newsgroups: bionet.software.acedb Subject: **** http://206.103.186.160 **** Date: Wed, 04 Dec 1996 06:28:32 GMT Organization: Network Intensive Lines: 1 Sender: BatMan Message-ID: <32a81a0f.3583838@news.ni.net> Reply-To: member@haha.com NNTP-Posting-Host: yyuen.newgeneration.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent .99f/32.299 From owner-acedb@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!news.ox.ac.uk!is.bbsrc.ac.uk!news From: Jo Dicks Newsgroups: bionet.software.acedb Subject: POSITION OFFERED Date: Thu, 05 Dec 1996 15:18:12 +0000 Organization: John Innes Centre Lines: 47 Message-ID: <32A6E7B4.DCC@bbsrc.ac.uk> Reply-To: jo.dicks@bbsrc.ac.uk NNTP-Posting-Host: pc0659.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0Gold (WinNT; I) COMPUTER PROGRAMMER/COMPUTATIONAL BIOLOGIST A new post is available at the John Innes Centre in Norwich, UK. The post will involve the development of novel software for the display of comparative plant genome data. Much of the new software will be written for the World Wide Web in Java, although current expertise in this is not essential. The successful applicant will have the opportunity to work under his/her own initiative and should be strongly motivated. The post involves linking data from several organisms. Consequently, the post-holder will be expected to co-ordinate the integration of the separate plant databases that are part of the UK Crop Plant Bioinformatics Network. This Network is a new initiative funded by the Biotechnology and Biological Sciences Research Council (BBSRC). One aim of the Network is to develop bioinformatics as a research tool. Accordingly, the successful applicant will be given the opportunity to design and implement software using novel computer tools and languages. Communication with other bioinformatics groups in the UK and worldwide will also be a priority of the project. QUALIFICATIONS Applicants should have a first degree in computer science or in biology. A postgraduate qualification, particularly in some form of bioinformatics, would be helpful. Some experience of computer programming is essential. Ability in one or more of Java, C++, C and Perl programming would be an advantage, as would familiarity with UNIX, WWW and the ACEDB database. SALARY The appointment will be for a fixed term of three years within Pay Band 6 within the salary range £13,951 to £24,174 per annum. The John Innes Centre is an Equal Opportunities Employer and operates a non-contributory superannuation scheme. HOW TO APPLY Application forms may be obtained by writing to the Personnel Officer, John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH quoting reference BIONET2. Alternatively forms may be requested by email from the Personnel Officer at "JICPERS@BBSRC.AC.UK". Completed applications should be postmarked on or before 31st December 1996. The John Innes Centre is a Registered Charity (No. 511709), grant aided by the Biotechnology and Biological Sciences Research Council. From owner-acedb@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: ACEDB data release fixed Date: 6 Dec 1996 00:23:02 -0000 Lines: 45 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <587p16$1c4@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk As a number of people have pointed out, the ACEDB data release made earlier this week had a problem for updates WS1.4-21 to 4-25. When the INSTALL script unpackaged the update files, they were misnamed, having names xxx.W1.xx instead of xxx.WS1.xxx. This has now been fixed at all ftp locations (NCBI, Sanger, Montpellier). During this process update WS1.4-25 was missing for a time - this is also now back. The data have not changed. If you have successfully changed the names and loaded the original versions, you do not need to do anything. If you got the bugged versions, but were not able to load them, you can either delete what you have and get them again, or with less effort you can rename the incorrect files in rawdata as follows: cd rawdata mv update.W1.4-21 update.WS1.4-21 mv update.W1.4-22 update.WS1.4-22 mv update.W1.4-23 update.WS1.4-23 mv update.W1.4-24 update.WS1.4-24 mv update.W1.4-25 update.WS1.4-25 They should then read in fine. I apologise for the error, and thank Jean for fixing at Montpellier and NCBI, and various people for finding the problem themselves and posting the fix to newsgroups. Richard Durbin PS Adding protein and sequence updates has become extremely slow. We have been working on speeding this up in a future version of the software. Meanwhile, you can speed things up a lot yourself if you can put the rawdata directory and the database directory on different physical disks. To do this, make one of the two directories (e.g. rawdata/) a symbolic link to a directory on another disk, before you INSTALL the updates. The Unix commands to do this would be: mkdir 'dir_on_another_disk'/rawdata ln -s 'dir_on_another_disk'/rawdata rawdata source INSTALL Or, if you have already run INSTALL, but not read the updates in, move the contents of rawdata/ to the directory on the other disk, rmdir rawdata, and make the symbolic link as above. From owner-acedb@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: jattwood@hgmp.mrc.ac.uk (Mr J. Attwood) Newsgroups: bionet.software.acedb Subject: Warning in database/log.wrm Date: 5 Dec 1996 17:08:37 -0000 Lines: 18 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <586vil$emf@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Hi, I've just discovered a number of messages like the following in my database/log.wrm file:- Class 109: object rhpanel:Genebridge4 has 1647 > 1000 celLs, please edit the models This is a consequence of an object being XREFed by a large number of its components and is both outside my control and an inherent part of the model. Is it serious and, if so, what way could I edit the model to work around the difficulty. The Genebridge4 RH panel is being used by more and more labs to type their markers, so the number of XREFS is bound to increase with time. Thanks in advance, John Attwood, MRC Human Biochemical Genetics Unit, London, UK From owner-acedb@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!news-stkh.gsl.net!news.gsl.net!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: multiple XREF Date: 6 Dec 1996 10:26:08 -0000 Lines: 68 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <588sc0$rk9@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk acedb will support arbitrarilly large number of XREF but the performance degrades, hence the warning: Class 109: object rhpanel:Genebridge4 has 1647 > 1000 celLs, please edit the models you do not have to do anything at this stage but the system is slower and opening lots of large objects, like in table maker, may use large amounts of memory we have the same problem with the homologies of the nematode sequencing project and are planning, in a future release, to change the managing of the objects aiming to speed up the handling of large objects The one case where you really should change your model is the case where you have a class using a ?Text like in the following example: ?Foo Bar ?Text and then i have 50000 foo objects, named foo1 to foo50000 and all of them contain the SAME text value. example Foo foo1 Bar hello Foo foo2 Bar hello Foo foo3 Bar hello etc. 50000 times then the text object hello will contain 50000 XREF and this is bad THis model can be fixed in 2 ways, either declare the model as ?Foo Bar Text then hello is pure text, is not xrefed, takes no memory, the drawbaxk is that searching the Foo who contain Hello is no slower alternativelly, declare hello as a tag ?Foo Bar Hello World the difference with the previious method is that now we have a controlled vocabulary, Bar can only evaluate to Hello or World ____ In both cases, one can define a subclass Class HelloFoo Is_a_subclass_of Foo Filter "Bar = Hello" // case Text Filter Hello // case Hello is a tag this ensures immediate access to all the helloFoo at no cost _____ Conclusion large number of Xref are bad bud not lethal. it is worth thinking about them and keep them around only if they are really useful From owner-acedb@net.bio.net Sun Dec 08 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!news.mathworks.com!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: 9 Dec 1996 17:11:56 GMT Organization: Lawrence Berkeley Laboratory, Berkeley CA Lines: 1217 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <58hh8s$8e@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:1049 news.answers:81990 Archive-name: acedb-faq Last-modified: 9 Dec 96 Version: 1.32 ---------------------------------------------------------------------------- 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: [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a 17" color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. 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 MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin: * genome.lbl.gov in pub/macace * ncbi.nlm.nih.gov in repository/acedb/macace 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) Last_update : December 1994 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 Database : AAtDB Species : Arabidopsis thaliana Current version : 3-5 Last_update : August 1995 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/aatdb FTP : ncbi.nlm.nih.gov in repository/aatdb FTP : probe.nalusda.gov in pub/aatdb Gopher : genome-gopher.stanford.edu/11/Arabidopsis Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://genome-www.stanford.edu WWW : http://probe.nalusda.gov:8300/plant/ Database : AboutDB Curator : Staffan Bergh, staffan@biochem.kth.se Subject : ACEDB itself (meta-meta-metadata) ACEDB_version: 3.0 Last_update : July 1995 WWW : http://www.biochem.kth.se/AboutDB.html 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 Last_update : August 1995 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/ 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 Last_update : March 1994 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 Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 Last_Update : July 1995 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 4.1 Last_updated : September 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ 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 Last_update : Under development WWW : http://nasc.nottm.ac.uk Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Last_update : August 1995 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/ Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Last_update : September 1995 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/ Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edubr> ACEDB_version : 3.0 Last_update : January 1996 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/ 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 Last_update : January 1995 (version 95.1) ACEDB_version : 3.0 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/ Database: Cruzdb Species: Trypanosoma cruzi PI: Wim Degrave Last_updated: In development 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 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 Last_update : December 1996 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. Database : EthnobotDB (worldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Last_update : June 1995 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/ Database: FilDB Species: Filarial nematodes PI: Mark Blaxter Last_updated: In development 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 Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Last_update : May 1995 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/ Database : GrainGenes Species : Wheat, barley, oats, sugarcane, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_3 Data_version : 1.6 Last_update : April 1996 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/graingenes Gopher : greengenes.cit.cornell.edu/ 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/graingenes.html 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 Last_updated: October 1996 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) 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 Latest_release : April 1995 Acedb_version : 3.3 Comment : MaizeDB is a periodically extracted ACeDB front end for the Maize Genome Database, MaizeDB, a SYBASE database, implemented using Genera software, developed by Stan Letovsky. Comment : Genera provides (1) up-to-the-minute form internet access to SYBASE databases, both for query (WWW and APT) and data entry (APT only); (2) database design alterations by systems administrators; (3) gopher file extraction. Comment: MaizeDB uses WWW record-to-record hard-links to 16 external databases for (1) annotated sequences: GenBank, dbEST, GenoBase, PIR, SwissProt, Prosite, ENZYME; (2) other species genome information: AAtDB(Arabidopsis), RiceGenes, GrainGenes, SaachDB (yeast), CGSC(E. coli), XLocus, RiceGenes, GrainGenes (3) germplasm: GRIN. Data : Over 100,000 records include: 6513 mapped loci (located to chromosome or better) including 1081 mapped genes and 1937 mapped probed sites (gene candidates); 2448 probes; 2460 map scores; 1551 gel patterns (Probe/Enzyme/Stock); 8777 stocks; 18,100 Variations (alleles, DNA polymorphisms, rearrangements, etc); 596 phenotypes; 317 traits; 715 gene products; 6158 bibliographic references; 2200 researchers with addresses. FTP : probe.nalusda.gov in pub/maizedb Gopher : gopher.agron.missouri.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: corncob WWW : http://www.agron.missouri.edu/top.html WWW : http://probe.nalusda.gov:8300/plant/ WWW Genera information : http://gdbdoc.gdb.org/letovsky/genera/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe, ed@teosinte.agron.missouri.edu Curator : Mary Polacco, maryp@teosinte.agron.missouri.edu Assoc Curator : Pat Byrne, byrne@teosinte.agron.missouri.edu QTL data Assoc Curator : Georgia Davis, gdavis@teosinte.agron.missouri.edu Map data Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic Stock data Assoc Curator : Christiane Fauron, FAURON@GENE1.med.utah.edu Mitochondrion genome Assoc Curator : Carolyn Wetzel, cmwetzel@iastate.edu Chloroplast genome Assoc Curator : Steve Rodermel, S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome Design : Stan Letovsky, letovsky@gdb.org Design : Mary Berlyn, mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock, dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 11 April 1995 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 Last_update : July 1995 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/ 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://jiio5.jic.bbsrc.ac.uk:8000/index.html WWW : http://probe.nalusda.gov:8300/plant/ 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_vertion : 4.0 Last_update : June 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : MsqDB Species : Interspecies Mosquito database Last_update : March 1996 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 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 Last_update : November 1995 ACEDB_version : 4.1 Data_version : 4-9 (November 1995) 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/ 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 Curator : Gail Juvik, gjuvik@nalusda.gov - ACEDB version ACEDB_vertion : 4.0 Last_update : September 1995 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 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 Last_update : June 1995 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/ 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 Last_update : September 1995 FTP : ftp.sanger.ac.uk in pub/PomBase 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 Last_update : June 1995 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/ Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susan McCouch ACEDB_version : 4.1 Last_update : November 1996 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/ Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 2.0, MacAce 2.0b4 Last_update : September 1995 Data_version : 2.4.12 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 : genome-gopher.stanford.edu 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 : Rita Schmidt, bleb@genome.stanford.edu Curator : Barbara Dunn, bdunn@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Programmer : Karen Davis, karen@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Database: SchistoDB Species: Schistosoma mansoni (plus other schistosomes) PI: David Johnston Last_updated: In development 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 Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu PI : Steve Tanksley Release : ACEDB 4.3 Last_update : April 1996 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/ 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 Last_update : September 1995 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/ Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker Curator : David Grant, dgrant@iastate.edu Assistant_curator : Marica Imsamde, mimsande@mendel.agron.iastate.edu Contact : David Grant, dgrant@iastate.edu ACEDB-Version : 3.7 Last_update : October 1995 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://mendel.agron.iastate.edu:8000/main.html 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 Last_update : October 1994 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 Database: ToxoDB Species: Toxoplasma gondii PI: David Sibley PI: David Roos PI: Jim Ajioka Last_update: October 1996 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 Database : TreeGenes Species : Forest trees ACEDB_version : 4.3 Last_update : May 1996 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/ Database: Trypbase Species: Trypanosoma brucei PI: Sara Melville Last_updated: October 1996 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 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 Last_update : April 1994 FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html 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 Last_update : August 1995 FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu Last_update : September 1993 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 Hohru Sano, NEC, sano@exp.cl.nec.co.jp http://www.cbi.or.jp/~sano/ . (Postscript at http://www.labs.nec.co.jp/ .) [True? Someone please confirm, I don't see it there. - Dave] 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 gopher://genome-gopher.stanford.edu:70/11/ftp 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: An attempt is being made to organize a workshop summer 1997 in Ithaca, New York, USA. 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 Tue Dec 10 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Macace C.elegans updates Date: 11 Dec 1996 18:48:16 -0000 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <58mvlg$fu7@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk New ftp versions of macace are now available including the recent updates up to WS1.4-26 and WG1.4-7. These have been provided by Richard Feichtinger from Martinsried (thank you very much Richard). They are available in the "macace" folder at the Sanger and NCBI ftp sites: ftp://ncbi.nlm.nih.gov/repository/acedb/macace/ and ftp://ftp.sanger.ac.uk/pub/acedb/macace Richard From owner-acedb@net.bio.net Thu Dec 12 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!worldnet.att.net!uunet!in3.uu.net!136.142.185.26!newsfeed.pitt.edu!news.duq.edu!newsgate.duke.edu!cgc.botany.duke.edu!user From: chlamy@acpub.duke.edu (Elizabeth Harris) Newsgroups: bionet.software.acedb Subject: MacAce 2.0b4 and System 7.5.5 Date: 12 Dec 1996 14:35:31 GMT Organization: Duke University Lines: 14 Message-ID: NNTP-Posting-Host: cgc.botany.duke.edu Since upgrading my PowerPC 8100 to System 7.5.5 I have been unable to save revisions in MacAce 2.0b4. Trying to do so produces an immediate type 11 error and requires restarting the computer. Is this a known bug, and is there a way to overcome it? I gave up on attempts to upgrade to MacAce 4.1 last summer, after a frustrating week of multiple error messages, system crashes, funny colors on my screen, and lack of documentation on how to get it up and running, i.e. I don't consider trying to repeat this upgrade process to be an answer to my present problem. -- Elizabeth Harris chlamy@acpub.duke.edu From owner-acedb@net.bio.net Thu Dec 12 22:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!news.sprintlink.net!news-peer.sprintlink.net!worldnet.att.net!uunet!in1.uu.net!205.228.200.21!telepath!usenet From: hombre Newsgroups: bionet.software.acedb Subject: Re: ACEDB Genome Database Software FAQ Date: Fri, 13 Dec 1996 00:04:19 -0600 Organization: Telepath Lines: 682 Message-ID: <32B0F1E3.DF6@telepath.com> References: <58hh8s$8e@overload.lbl.gov> Reply-To: mail.telepath.com NNTP-Posting-Host: zoom4196.telepath.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) ACEDB FAQ Curator wrote: > > Archive-name: acedb-faq > Last-modified: 9 Dec 96 > Version: 1.32 > > ---------------------------------------------------------------------------- > > 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: > [Contributed by Frank Eeckman] Macace is distributed as a > self-extracting archive that contains the application, the wspec files, > and a fully up to date database. macace 3.0 is available with an > updated 21bdb database. Please send all questions/bug reports to > eeckman@llnl.gov A native powerPC version is available as well. Macace > needs a macintosh with > 16 MBytes of RAM, and a 17" color monitor is > preferred. System 7 or greater is required. For the multimedia > extensions Quicktime 1.0 is required. Please add your name to our > mailing list by sending email to eeckman@llnl.gov. It is our belief > that for cost savings a powerPC mac will beat the advertised > linux-intel combination. Macace is fully compatible with xace, but > includes some multimedia extensions (picture and movie support) not > found in the unix versions. > > 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 > > MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin: > > * genome.lbl.gov in pub/macace > * ncbi.nlm.nih.gov in repository/acedb/macace > > 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) > Last_update : December 1994 > 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 > > Database : AAtDB > Species : Arabidopsis thaliana > Current version : 3-5 > Last_update : August 1995 > 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/aatdb > FTP : ncbi.nlm.nih.gov in repository/aatdb > FTP : probe.nalusda.gov in pub/aatdb > Gopher : genome-gopher.stanford.edu/11/Arabidopsis > Gopher : probe.nalusda.gov:7000/11/genome.databases/ > WWW : http://genome-www.stanford.edu > WWW : http://probe.nalusda.gov:8300/plant/ > > Database : AboutDB > Curator : Staffan Bergh, staffan@biochem.kth.se > Subject : ACEDB itself (meta-meta-metadata) > ACEDB_version: 3.0 > Last_update : July 1995 > WWW : http://www.biochem.kth.se/AboutDB.html > > 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 > Last_update : August 1995 > 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/ > > 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 > Last_update : March 1994 > 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 > > Database : Alfagenes > Species : Medicago sativa (alfalfa) > Curator : D. Z. Skinner, dzolek@ksu.ksu.edu > Telephone : (913) 532-7247 > ACEDB_version : 3.0 > Last_Update : July 1995 > FTP : probe.nalusda.gov in pub/alfagenes > Gopher : probe.nalusda.gov:7000/11/genome.databases/ > WWW : http://probe.nalusda.gov:8300/plant/ > > Database : BeanGenes > Species : Phaseolus and Vigna > Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu > ACEDB_version : 4.1 > Last_updated : September 1995 > Gopher : probe.nalusda.gov:7000/11/genome.databases/ > WWW : http://probe.nalusda.gov:8300/plant/ > > 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 > Last_update : Under development > WWW : http://nasc.nottm.ac.uk > > Database : ChlamyDB > Species : Chlamydomonas > Curator : Elizabeth Harris > Contact : chlamy@acpub.duke.edu > ACEDB_version : 3.0 > Data_version : 1.2 > Last_update : August 1995 > 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/ > > Database : CIMMYT (Wheat International Nursery Data) > Species : Triticum spp. > ACEDB_version : 4.0 > Last_update : September 1995 > 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/ > > Database : CoolGenes > Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba > Curator : Fred Muehlbauer, muehlbau@wsu.edubr> ACEDB_version : 3.0 > Last_update : January 1996 > 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/ > > 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 > Last_update : January 1995 (version 95.1) > ACEDB_version : 3.0 > 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/ > > Database: Cruzdb > Species: Trypanosoma cruzi > PI: Wim Degrave > Last_updated: In development > 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 > > 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 > Last_update : December 1996 > 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. > > Database : EthnobotDB (worldwide plant uses) > Species : wide range of plant species > ACEDB_version : 4.0 > Last_update : June 1995 > 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/ > > Database: FilDB > Species: Filarial nematodes > PI: Mark Blaxter > Last_updated: In development > 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 > > Database : FoodplantDB (Native American Food Plants) > Species : Over 1,100 plant species > ACEDB_version : 4.0 > Last_update : May 1995 > 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/ > > Database : GrainGenes > Species : Wheat, barley, oats, sugarcane, relatives > Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu > PI : Olin D. Anderson, oandersn@pw.usda.gov > ACEDB_version : 4_3 > Data_version : 1.6 > Last_update : April 1996 > Availability : Macintosh and UNIX versions via anonymous ftp > FTP : probe.nalusda.gov in pub/graingenes > Gopher : greengenes.cit.cornell.edu/ > 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/graingenes.html > > 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 > Last_updated: October 1996 > 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) > > 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 > Latest_release : April 1995 > Acedb_version : 3.3 > Comment : MaizeDB is a periodically extracted ACeDB front end for the Maize > Genome Database, MaizeDB, a SYBASE database, implemented using Genera > software, developed by Stan Letovsky. > Comment : Genera provides (1) up-to-the-minute form internet access to > SYBASE databases, both for query (WWW and APT) and data entry (APT only); > (2) database design alterations by systems administrators; (3) gopher file > extraction. > Comment: MaizeDB uses WWW record-to-record hard-links to 16 external > databases for (1) annotated sequences: GenBank, dbEST, GenoBase, PIR, > SwissProt, Prosite, ENZYME; (2) other species genome information: > AAtDB(Arabidopsis), RiceGenes, GrainGenes, SaachDB (yeast), CGSC(E. coli), > XLocus, RiceGenes, GrainGenes (3) germplasm: GRIN. > Data : Over 100,000 records include: 6513 mapped loci (located to chromosome > or better) including 1081 mapped genes and 1937 mapped probed sites (gene > candidates); 2448 probes; 2460 map scores; 1551 gel patterns > (Probe/Enzyme/Stock); 8777 stocks; 18,100 Variations (alleles, DNA > polymorphisms, rearrangements, etc); 596 phenotypes; 317 traits; 715 gene > products; 6158 bibliographic references; 2200 researchers with addresses. > FTP : probe.nalusda.gov in pub/maizedb > Gopher : gopher.agron.missouri.edu > Gopher : probe.nalusda.gov:7000/11/genome.databases/ > Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: > corncob > WWW : http://www.agron.missouri.edu/top.html > WWW : http://probe.nalusda.gov:8300/plant/ > WWW Genera information : http://gdbdoc.gdb.org/letovsky/genera/genera.html > Funding : MaizeDB USDA/ARS to E. Coe > Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn > Curator/PI : Ed Coe, ed@teosinte.agron.missouri.edu > Curator : Mary Polacco, maryp@teosinte.agron.missouri.edu > Assoc Curator : Pat Byrne, byrne@teosinte.agron.missouri.edu QTL data > Assoc Curator : Georgia Davis, gdavis@teosinte.agron.missouri.edu Map data > Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic > Stock data > Assoc Curator : Christiane Fauron, FAURON@GENE1.med.utah.edu Mitochondrion > genome > Assoc Curator : Carolyn Wetzel, cmwetzel@iastate.edu Chloroplast genome > Assoc Curator : Steve Rodermel, S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome > Design : Stan Letovsky, letovsky@gdb.org > Design : Mary Berlyn, mary@fetalpig.biology.yale.edu > Systems Manager : Denis Hancock, dhancock@teosinte.agron.missouri.edu > Contact : db_request@teosinte.agron.missouri.edu > Last_update : 11 April 1995 > > 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 > Last_update : July 1995 > 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/ > > 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://jiio5.jic.bbsrc.ac.uk:8000/index.html > WWW : http://probe.nalusda.gov:8300/plant/ > > 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_vertion : 4.0 > Last_update : June 1995 > Gopher : probe.nalusda.gov:7000/11/genome.databases/ > WWW : http://probe.nalusda.gov:8300/related/ > > Database : MsqDB > Species : Interspecies Mosquito database > Last_update : March 1996 > 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 > > 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 > Last_update : November 1995 > ACEDB_version : 4.1 > Data_version : 4-9 (November 1995) > 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/ > > 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 > Curator : Gail Juvik, gjuvik@nalusda.gov - ACEDB version > ACEDB_vertion : 4.0 > Last_update : September 1995 > 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 > > 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 > Last_update : June 1995 > 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/ > > 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 > Last_update : September 1995 > FTP : ftp.sanger.ac.uk in pub/PomBase > > 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 > Last_update : June 1995 > 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/ > > Database : RiceGenes > Species : Oryza sativa > Curator : Edie Paul, epaul@nightshade.cit.cornell.edu > PI : Susan McCouch > ACEDB_version : 4.1 > Last_update : November 1996 > 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/ > > Database : SacchDB > Species : Saccharomyces cerevisiae > Subject : Budding (common baker's) Yeast Genome > ACEDB_version : UNIX 2.0, MacAce 2.0b4 > Last_update : September 1995 > Data_version : 2.4.12 > 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 : genome-gopher.stanford.edu > 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@geno From owner-acedb@net.bio.net Sun Dec 15 22:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!news-stkh.gsl.net!news.gsl.net!eru.mt.luth.se!news.kth.se!not-for-mail From: Staffan Bergh Newsgroups: bionet.microbiology,bionet.software.acedb,sci.med Subject: MycDB.4-22 Followup-To: bionet.microbiology Date: 16 Dec 1996 08:36:23 +0100 Lines: 119 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 Xref: biosci bionet.microbiology:8151 bionet.software.acedb:1057 sci.med:144564 MycDB 4-22 Stockholm & Paris December 13, 1996 The 22nd release of the Mycobacterium database, MycDB, is now available. MycDB is funded by the WHO and the Fondation Raoul Follereau and is maintained jointly by the Unite de Genetique Moleculaire Bacterienne at the Institut Pasteur in Paris, France and the Department of Biochemistry at The Royal Institute of Technology in Stockholm, Sweden. MycDB is available free of charge via Internet network transfer. A complete description of the procedure to retrieve and install the software and database is available through the Internet (see MycDB.Retrieval). MycDB is also available through the WorldWideWeb servers at the Royal Institute of Technology (URL: http://www.biochem.kth.se/MycDB.html) and (through the good offices of the Genome Informatics Group at the National Agricultural Library) on the Agricultural Genome Information Server, AGIS, in Beltsville, Maryland, USA (WorldWideWeb - URL: http://probe.nalusda.gov:8300/other/index.html or gopher - URL: gopher://probe.nalusda.gov:7000/11/genome.databases/mycdb/). Be aware that it may take some time for the update to reach NAL. MycDB uses the excellent database software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg (CNRS, France). The ACEDB software allows the user to browse information by simply pointing and clicking with the workstation mouse. A variety of powerful query methods are also available. However, our experience is that most users choose the mouse interface to find the information they are interested in. As far as possible all information is connected to other information in the database. The database software presents the information in separate windows that allow many parts of the database to be viewed at one time. There are also many paths to any piece of information, allowing the user to easily navigate the connections between the various types of information. New in release 4-22: * Due to the amount of new data, this update comes as 9 files, update.myc.4-14.tar.Z to update.myc.4-22.tar.Z. * There is now a Windows 95/Windows NT version of the software. See the file MycDB.Retrieval for more info. * No model changes were made, but the method of keeping the database up-to-date has changed somewhat. Due to this some errors may have crept in, and the size of the update is somewhat inflated (but see below for the major reason for the size of this update). Please bear with us while we weed them out, the new curation scheme is intended to speed up the work with the database, and should shortly lead to more frequent updates. * The amount of sequence data is now: 17237 Sequence objects, of which 1236 contain nucleotide sequences (DNA objects). Of these, 330 come from the M. tuberculosis/M. bovis cluster (total 2,414,443 nt), 78 from M. leprae (total 2,420,756 nt) and 53 from M. smegmatis (total 96,572 nt). Total amount of sequence is 5,281,466 nt, an increase of 84.4% since last release. The largest contigous sequence is more than 201 kbp (MD0103). The great increase is due both to the M. tuberculosis sequencing efforts of Bart Barrell and his group at the Sanger Centre, and the group of Doug Smith at Genome Therapeutics (increase in M. tuberculosis sequences is 260%!), and to improved searching strategy for EMBL/GenBank. The coverage of EMBL/GenBank is current up to November 15. There are 5928 Peptide sequences, most of which are blastx hits from SwissProt. As earlier announced these will in the future move to a class of their own, with a special display. * There are 456 new Papers, from MedLine and from Sequence records, current up to November 5. The naming scheme for paper objects have changed, so that most papers now have names formed from their MedLine UID's (MEDLINE_xxxxxxxx). * The Colleague class has seen a substantial update, with the inclusion of the entire attendance list from this summer's Mycobact'96 conference in Stockholm. For information on earlier releases, see MycDB.4-13.Release.txt. The database currently requires a Unix workstation running X-Windows, a Macintosh or a PC running Windows 95 or Windows NT. A variety of precompiled versions of the ACEDB database software are available through anonymous ftp. See the file MycDB.Retrieval.txt for more info. If you have any questions, problems or comments please contact us, via e-mail, fax, mail or telephone. If you are impatient and are already familiar with internet/ftp, all relevant information can be found at * the WWW server at the Department of Biochemistry, KTH: http://www.biochem.kth.se/MycDB.html * the ftp server at the Department of Biochemistry, KTH: ftp.biochem.kth.se (130.237.52.64) in pub/MycDB * the ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in pub/MycDB * the mirror site at the Weizmann Institute in Israel (thanks Jaime!): bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb * or the mirror site at the Microbiology Dept., University of British Columbia in Canada (thanks Yossef!): cod.microbiology.ubc.ca (137.82.165.101) in pub/MycDB The file MycDB.Retrieval.txt describes in more detail the database system requirements, network retrieval procedures for obtaining the database and methods of obtaining future updates. For more information contact Staffan Bergh or Stewart Cole. Staffan Bergh Biochemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden Email: staffan@biochem.kth.se Fax: (46 8) 24 54 52 Voice: (46 8) 790 9230 Stewart Cole Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris Cedex 15, France Email: stcole@pasteur.fr Fax: (33 1) 45.68.85.93 Voice: (33 1) 45.68.84.46 ---------------------------------------------------------------------------- /staffan Last modified: Fri Dec 13 16:08:12 1996 From owner-acedb@net.bio.net Mon Dec 16 22:00:00 1996 Path: biosci!cgi.nsk.su!kuznecov From: kuznecov@cgi.nsk.su (Kuznecov S.B.) Newsgroups: bionet.software.acedb Subject: Where I can get the mapping information? Date: 16 Dec 1996 22:34:14 -0800 Organization: Institute of Cytology & Genetics Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net If somebody knows, please send me the Web addresses of sites where I can get the most updated information about the number of genes and genetic markers mapped in the mammalian spicies (the best variant: the names of animals and the number of markers mapped in each of them by 1996). My e-mail address: kuznecov@cgi.nsk.su Yours sincerely, Denis M. Larkin Institute of Cytology and Genetics Novosibirsk 630090 Russia From owner-acedb@net.bio.net Tue Dec 17 22:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!tin!jhinshel From: "Mr. J Hinshelwood" Newsgroups: bionet.software.acedb Subject: gel analysis Date: Wed, 18 Dec 1996 17:18:23 +0000 Organization: MRC Human Genome Resource Centre Lines: 4 Message-ID: NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: jhinshel@tin Does anyone know of freeware for analysis of gels for unix or pc.eg densitometry etc From owner-acedb@net.bio.net Mon Dec 23 22:00:00 1996 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!news.ibm.net.il!news.biu.ac.il!news.tau.ac.il!usenet From: yoav_ab@netvision.net.il (yoav abrahami) Newsgroups: bionet.software.acedb Subject: looking for beaker Date: Tue, 24 Dec 1996 18:32:17 GMT Organization: Tel-Aviv University Computation Center Lines: 8 Message-ID: <32c021a3.13250197@news.tau.ac.il> NNTP-Posting-Host: slip-303.tau.ac.il X-Newsreader: Forte Free Agent 1.1/32.230 Hello there! Maybe someone has a version of the sottware "Beaker" for PC?( not for mac!!!) I will be greatfull if someone can send me a copy or even information on a ftp site i can download it from. my e-mail is: yoav_ab@netvision.net.il thanx, yoav. (israel) From owner-acedb@net.bio.net Thu Dec 26 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!news.ibm.net.il!news.biu.ac.il!news.tau.ac.il!usenet From: yoav_ab@netvision.net.il (yoav abrahami) Newsgroups: bionet.software.acedb Subject: looking for beaker Date: Tue, 24 Dec 1996 18:32:17 GMT Organization: Tel-Aviv University Computation Center Lines: 8 Message-ID: <32c021a3.13250197@news.tau.ac.il> NNTP-Posting-Host: slip-303.tau.ac.il X-Newsreader: Forte Free Agent 1.1/32.230 Hello there! Maybe someone has a version of the sottware "Beaker" for PC?( not for mac!!!) I will be greatfull if someone can send me a copy or even information on a ftp site i can download it from. my e-mail is: yoav_ab@netvision.net.il thanx, yoav. (israel) From owner-acedb@net.bio.net Fri Dec 27 22:00:00 1996 Path: biosci!rutgers!igor.rutgers.edu!newsserver.jvnc.net!news.merck.com!cam-news-feed1.bbnplanet.com!delphi.com!news-feed.iguide.com!news.uoregon.edu!tezcat!feed1.news.erols.com!worldnet.att.net!uunet!in3.uu.net!192.215.247.55!news1.ni.net!news From: polo@haha.com (polo) Newsgroups: bionet.software.acedb Subject: *** http://206.103.186.160 *** Date: Wed, 18 Dec 1996 06:12:53 GMT Organization: Network Intensive Lines: 1 Sender: BatMan Message-ID: <32b7a03a.675301@news.ni.net> Reply-To: polo@haha.com NNTP-Posting-Host: yyuen.newgeneration.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent .99f/32.299 From owner-acedb@net.bio.net Fri Dec 27 22:00:00 1996 Path: biosci!rutgers!igor.rutgers.edu!newsserver.jvnc.net!news.merck.com!cam-news-feed1.bbnplanet.com!delphi.com!news-feed.iguide.com!news.uoregon.edu!tezcat!feed1.news.erols.com!howland.erols.net!worldnet.att.net!uunet!in3.uu.net!192.215.247.55!news1.ni.net!news From: polo@haha.com (polo) Newsgroups: bionet.software.acedb Subject: download free software *** http://206.103.186.160 *** Date: Wed, 18 Dec 1996 06:12:52 GMT Organization: Network Intensive Lines: 1 Sender: BatMan Message-ID: <32b6a02d.662707@news.ni.net> Reply-To: polo@haha.com NNTP-Posting-Host: yyuen.newgeneration.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent .99f/32.299 From owner-acedb@net.bio.net Fri Dec 27 22:00:00 1996 Path: biosci!rutgers!igor.rutgers.edu!newsserver.jvnc.net!news.merck.com!cam-news-feed1.bbnplanet.com!delphi.com!news-feed.iguide.com!news.uoregon.edu!tezcat!feed1.news.erols.com!howland.erols.net!usc!news.cerf.net!news1.ni.net!news From: polo@haha.com (polo) Newsgroups: bionet.software.acedb Subject: ***** http://206.103.186.160 ***** Date: Wed, 18 Dec 1996 06:04:01 GMT Organization: Network Intensive Lines: 1 Sender: BatMan Message-ID: <32bb8950.496162@news.ni.net> Reply-To: polo@haha.com NNTP-Posting-Host: yyuen.newgeneration.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit From owner-acedb@net.bio.net Tue Dec 31 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Jan 1997 02:00:42 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701011000.CAA00965@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