From owner-acedb@net.bio.net Sun Aug 03 23:00:00 1997 Path: biosci!INFOWATCH.NET!info From: info@INFOWATCH.NET (Info Desk) Newsgroups: bionet.software.acedb Subject: Advertisment: Web Hosting Date: 4 Aug 1997 09:52:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <19970804152704853.BTE204@sales2.infowatch.net> NNTP-Posting-Host: net.bio.net ------------------------------- Our research indicates that the following material may interest you. This is a ONE-TIME ONLY MAILING, so you won't need to reply if this is of no interest to you (in which case we apologize for the inconvenience) ------------------------------- http://www.infowatch.net InfoWatch would like to introduce our complete Hosting and design service. FOR ONLY $29.95 PER MONTH ! · 30 MB (megabytes) of disk space · 1000 MB = 1 GB (gigabyte) of data transfer per month · 8 E-mail accounts (POP3) · Account Control Panel via the Web · Unlimited FTP updates · Site counter as well as detailed statistics · E-mail forwarding, auto responders and vacation reply Domain name registration (www.yourname.com) Register your domain with over 300 search engines Friendly customer support - in plain English! If for any reason you are not satisfied with InfoWatch's service after 60 days, we will transfer you back to your original host and pay any transfer fees. http://www.infowatch.net info@infowatch.net From owner-acedb@net.bio.net Tue Aug 12 23:00:00 1997 Path: biosci!agate!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Curator) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 13 Aug 1997 00:04:35 GMT Organization: Dept. Plant Breeding, Cornell University Lines: 1248 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <5sqtmj$cno@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.psw.fs.fed.us Summary: Frequently Asked Questions about finding and getting started with the genome database software ACEDB. URL: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html Archive-name: acedb-faq Last-modified: 11 Aug 97 Version: 1.38 ---------------------------------------------------------------------------- ACEDB FAQ ---------------------------------------------------------------------------- Curated by: Dave Matthews ---------------------------------------------------------------------------- Frequently Asked Questions about ACEDB * Q0 : What is ACEDB? * Q1 : ! What is the current version of ACEDB? * Q2 : Where can I get ACEDB? * Q3 : What hardware/software do I need to run ACEDB? * Q4 : + Can ACEDB be networked? * Q5 : ! What documentation exists for ACEDB? * Q6 : What newsgroups and mailing lists are available for ACEDB? * Q7 : + Is there a repository of software tools for ACEDB curators? * Q8 : ! When and where is the next ACEDB Workshop? * Q9 : How does ACEDB compare to commercial relational DBMS's? * Q10 : How should ACEDB be cited? * Q11 : What ACEDB databases exist? * Q12 : Who prepared this document & where is the current version? Questions marked with '+' are new, those with '!' have substantially changed answers. ---------------------------------------------------------------------------- Q0: What is ACEDB? A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning in 1989. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions ---------------------------------------------------------------------------- Q1: What is the current version of the ACEDB software? A1: The current Unix version is test.ace.4_5c, released 9 August 1997. It is to be tested for a few weeks and, if no bugs are reported, renamed ace4_5. Enhancements added during the ACE97 Workshop will be incorporated in the next release. The very latest development version is always available at ftp://ftp.sanger.ac.uk/pub/acedb_src/. This is unsupported and not to be redistributed. The Windows 95/NT version 4.5.2, 9 August 1997, corresponds to Unix test.ace.4_5c. For current information see the WinAce Web page at http://mendel.medgen.ubc.ca/rbrusk/winace.html. A Macintosh version is available as version 4.1b1, August 1995. Return to List of Questions ---------------------------------------------------------------------------- Q2: Where can I get ACEDB? A2: Source code and Unix binaries are available in the following anonymous ftp sites: * 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: * ftp.sanger.ac.uk in pub/winace * bioinformatics.weizmann.ac.il in pub/databases/acedb * Documentation: http://mendel.medgen.ubc.ca/rbrusk/winace.html MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin: (Note: The authors are not currently able to support MacAce. Latest version was 4.1b1.) * genome.lbl.gov in pub/macace * ncbi.nlm.nih.gov in repository/acedb/macace * bioinformatics.weizmann.ac.il in pub/databases/acedb Return to List of Questions ---------------------------------------------------------------------------- Q3: What hardware/software do I need to run ACEDB? A3: The software is available in binary (pre-compiled) format for a variety of machines. * Unix: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series 4, 5, 6 o IBM RS-6000 o PC 386/486/Pentium with Linux o NEC EWS4800 o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o There exist, or have existed, ports onto Alliant, Hewlett- Packard, Convex. You may have to contact the developer responsible for the port to make these real. * Windows 95/NT * Macintosh (not currently supported) The software is also available as source code, so you may be able to get it working on any machine. Return to List of Questions ---------------------------------------------------------------------------- Q4: Can ACEDB be networked? A4: ACEDB Client / Server Computing (from Doug Bigwood, aug97) There are several client/server models for ACEDB computing and several more are in development. The start of the ACEDB client/server age began with the inclusion of aceclient and aceserver in version 4.0. These are C - based and use the RPC protocol for communication. These executables can be made from the standard ACEDB distributions. Starting in version 4.5 an xaceclient is also included with ACEDB. Xaceclient provides remote read/write access to an aceserver while providing the user with the same X displays that are found in xace. To use it, you create an empty database with the appropriate models and start xaceclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the Montpellier server in the distribution server.wrm). The data will be saved locally and can then be viewed with a normal xace. A perl extension which provides aceclient functionality to Perl 5.x was developed at ACE95. The files necessary for this perl extension are now (ACEDB 4.5 and later) included in the wrpc directory of the ACEDB directory hierarchy. Documentation about how to extend perl is found at http://probe.nalusda.gov:8000/ace97/perlace/perlacecl.html. WWWAce and its successor webace were developed to provide a World Wide Web interface for ACEDB. Webace instructions can be found at http://probe.nal.usda.gov:8000/acedocs/webace.html, and http://probe.nal.usda.gov:8000/ace97/webace.html and the program itself at ftp://probe.nalusda.gov/pub/tools/webace.tar.gz. A Java-based client called Jade allows communication via sockets to an aceserver. Jade installation instructions and information on downloading can be found at http://probe.nalusda.gov:8000/ace97/Jade.installation.html. There are now development efforts underway to provide additional client/server functionality to ACEDB including a CORBA server and socket-based communications. These will likely be included in future versions of ACEDB. A new C library interface to ACEDB internals will greatly ease the development of new clients and servers that will support additional protocols. ---------------------------------------------------------------------------- Q5: What documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Library is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The WWW documentation server is part of the Agricultural Genome Information System, at http://probe.nalusda.gov:8000/acedocs/. Documents in Postscript, wordprocessor, and other non-html formats are available by ftp at ftp://probe.nalusda.gov/pub/acedocs/. Information in the ACEDB Documentation Library includes: * Primary documents from the developers Durbin & Thierry-Mieg, ca. 1992. o acedb -- A C. elegans Database: I. Users' Guide o acedb -- A C. elegans Database: II. Installation Guide o acedb -- A C. elegans Database: III. Configuration Guide o acedb -- A C. elegans Database: Syntactic Definitions for the ACEDB Data Base Manager * Tutorials, general and specific * Documentation written at the ACEDB Workshops * A repository of curator tools * A selection of models.wrm files from various databases * SampleDB, a sample database to demonstrate some ACEDB features, 1995 * This FAQ, in html format Other sources of documentation: * The ACEDB online help, a hypertext reader for the contents of the whelp directory of the ACEDB software distribution. * Contents of the wdoc, wtools, and wscripts directories. * Archives of the bionet.software.acedb newsgroup (both searchable) o http://www.bio.net/hypermail/ACEDB/, from BIOSCI o http://genome-www.stanford.edu/cgi-bin/biosci_acedb, from the Saccharomyces Genome Database site * ACEDB User's Guide in Japanese, from Tohru Sano, NEC, sano@exp.cl.nec.co.jp, http://www.cbi.or.jp/~sano/. (Postscript at http://www.labs.nec.co.jp/ . Follow the prompts to register and "download the software".) * Paper publications o Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992). AAtDB, an Arabidopsis thaliana database. Plant Molecular Biology Reporter 10: 308-309, 409-410. o Cherry, J.M. and Cartinhour, S.W. (1994). ACEDB, A tool for biological information. Pp. 347-356 in: Automated DNA Sequencing and Analysis, M. Adams, C. Fields, and C. Venter (Eds.). Academic Press. Online version: http://probe.nalusda.gov:8000/acedocs/overview.html. o Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994). Physical mapping projects and ACEDB. Pp. 111-158 in: Guide to Human Genome Computing. Bishop, M.J (Ed.). Academic Press. Return to List of Questions ---------------------------------------------------------------------------- Q6: What newsgroups and mailing lists are available for ACEDB? A6: The USENET/BIOSCI conference bionet.software.acedb is dedicated to discussions of ACEDB. The newsgroup can be accessed via a newsreader like rn or tin, a WWW browser (news:bionet.software.acedb), or e-mail. To subscribe to the e-mail version, send the message "subscribe acedb" to biosci-server@net.bio.net. Mail sent to acedb@net.bio.net will be distributed to all subscribers and to the electronic conference. Articles posted to biosci.software.acedb are archived by BIOSCI at http://www.bio.net/archives.html and by Mike Cherry at http://genome-www.stanford.edu/cgi-bin/biosci_acedb. There is also a separate mailing list for announcements of new releases of the ACEDB (worm) database as well as the ACEDB software. To get on or off this mailing list send mail to rd@sanger.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. The BIOSCI newsgroup is on this list. Return to List of Questions ---------------------------------------------------------------------------- Q7 : Is there a repository of software tools for ACEDB curators? A7: Not really, but there are several partial ones. The main tools available are for converting data from other formats to .ace format. The Agricultural Genome Information System has a growing stock of useful tools at http://probe.nalusda.gov:8000/acedocs/conversion.html. Some additional ones were contributed at the ACE97 Workshop and can be found in the Proceedings, http://probe.nalusda.gov:8000/ace97/tools/. Mike Cherry maintains an archive of tools at ftp://genome-ftp.stanford.edu/pub/acedb_dev/utilities/ For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/. Return to List of Questions ---------------------------------------------------------------------------- Q8: When and where is the next ACEDB Workshop? A8: The next ACEDB meeting is planned for summer 1998 in England. The ACE97 Conference and Workshop was held July 27 - August 9 at Cornell University, Ithaca, New York, USA. See the ACE97 Proceedings Page, http://probe.nalusda.gov:8000/ace97/proceedings.html for the results. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/. A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html. Also available online are collections of snapshots taken during the conference by Frank Eeckman and by Dave Matthews. For pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, see the online collections: * by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; * by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; * and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions ---------------------------------------------------------------------------- Q9: How does ACEDB compare to commercial relational DBMS's? A9: From Jean Thierry-Mieg, 4/97: Obviously, i have a biased opinion, but i would say that acedb is to be recommended if the following criteria are met: 1) A very complex schema, that cannot be developed at once, but will need continuous refinement in parallel with the accumulation of the data 2) The type of questions that will be asked are rather complex, with rather fuzzy answers, that one tries to refine progressively. The acedb browsing capacities are useful in this case and have no equivalent in a relational dbms ______________ I would rather recommend sybase in the following case 1) Simple schema, that can be designed from the start and does not contain too many n.n relations and does not need recursivity 2) The type of questions that will be asked is: succession of de-correlated simple questions with simple answers ____________________ Within this context, i would then list the following goodies of acedb: 1) The ace file format, which is a powerful system to prepare and exchange data between data curators. 2) The existence of an easy graphic browsing interface 3) The availability of a biology-layer, if the application is about genetics 4) Portability (any unix machine), mac (with some limitations), windows (in development) and price (ace is a freeware). This implies that you can actually redistribute the complete system, say on a CD, something impossible with sybase. 5) Ease of use, i seriously believe that ace is much easier to configure and use than sybase. _____________________ Finally one should consider the following question: concurrency. Sybase has a well designed transaction system, which will allow roll backs and refined lockings. This is essential for an application like a booking agency, with many users in simultaneous write access. Ace is much simpler minded. The graphic acedb creates a global lock allowing a single user with write access at the time, and the modifications are not echoed to the other "read access" users in real time. The non graphic client server system allows parallel downloading of data by many users, it is intended for example for collection of robots sending their independent data in parallel. This is now well tested. A graphic client system is being developed and now runs in our hands, but is not yet released. -- Therefore, if you do need real time simultaneous write access with partial locks, and roll backs, use sybase/oracle ________________ Last issue is speed and quantities of data. In principle, sybase/oracle is unlimited, whereas acedb needs to keep around 5-10% of the data in ram. But this apparent difference is misleading. On a 32 Meg machine, you can run ace with around 300.000 objects with a complex schema at high speed. With say 1M objects, you will need more memory or the performance would totally degrade because of swapping. However, this is really a lot of data. On a similar machine, your sybase oracle will work with that amount or more data only if you do not perform too many joins. This implies that you are asking simple questions from a simple schema which was indeed our first criterion to choose sybase. If you start asking complex questions and make joins, acedb is actually much more powerful. During tests run on a big dec alpha server by Otto Ritter in decembre 1995 on several million biological objects with a complex schema, acedb was about 10 times faster than sybase, both to load the data and to answer queries. I would therefore conclude that the quantity of data is not a criterion pushing one way or the other, it is the complexity of the schema that matters. Return to List of Questions ---------------------------------------------------------------------------- Q10: How should ACEDB be cited? A10: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions ---------------------------------------------------------------------------- Q11: What ACEDB databases exist? A11: In alphabetic order by Database name [Curators, please submit changes as new paragraphs. You may include html links.] A repository of many of these databases is maintained by the Agricultural Genome Information System, both for anonymous ftp at ftp://probe.nalusda.gov/pub and for WWW access via Webace at http://probe.nalusda.gov:8000/alldbs.html. Database : AaeDB Species : Aedes aegypti (yellow fever mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : AalDB Species : Aedes albopictus (Asian tiger (forest day) mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@sanger.ac.uk Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ FAQ_updated : August 1995 Database : AgaDB Species : Anopheles gambiae (malaria mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu ACeDB_version : 3.0 Subject: Contains extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe yeast); interacting loci via defined Interactions for each locus Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html FTP: ftp://keck.tamu.edu/pub/agsdb/agsdb1_0_acedb3_0_solaris2.3.tar.Z FAQ_updated : March 1994 Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : July 1995 Database : AnoDB Species : Anopheles sp. ACEDB_version : 4.5 WWW : http://konops.imbb.forth.gr/AnoDB/ Curator : Christos Louis, louis@konops.imbb.forth.gr Co-Curator : Pantelis Topalis, topalis@konops.imbb.forth.gr Contact : AnoDB-comments@konops.imbb.forth.gr Data_updated : regularly FAQ_updated : August 1997 Database : AtDB Species : Arabidopsis thaliana ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4-7 PI : J. Michael Cherry Curator : David Flanders Contact : arab-curator@genome.stanford.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : genome-ftp.stanford.edu in arabidopsis/AtDB FTP : ncbi.nlm.nih.gov in repository/AtDB WWW : http://genome-www.stanford.edu FAQ_updated : December 1996 Database : AtrDB Species : Aedes triseriatus (Eastern tree hole mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 4.1 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : September 1995 Database : BrassicaDB Species : Brassica napus (Canola/Oilseed Rape) and its parental diploid species ACEDB_version : 4.3 Description : Genetic maps of Brassica napus, QTL analyses for agronomic traits, literature references and B. napus-specific DNA sequences will be incorporated. We aim to integrate with B. napus genetic maps developed elsewhere and to produce a Java interface that will link BrassicaDB with the AAtDB (Arabidopsis thaliana) database through gene orthologies that are becoming established between these closely related plant genomes. PI : Martin Trick, Martin.Trick@bbsrc.ac.uk Curator/Developer : Mazda Hewitt, Mazda.Hewitt@bbsrc.ac.uk WWW : http://synteny.nott.ac.uk/brassica.html Data_updated : Under development FAQ_updated : August 1997 Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : August 1995 Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : September 1995 Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edu ACEDB_version : 3.0 Gopher : gopher://probe.nalusda.gov:7000/11/genome.databases/coolgenes/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : January 1996 Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 ACEDB_version : 3.0 Data_version : January 1995 (version 95.1) FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ FAQ_updated : January 1995 Database: Cruzdb Species: Trypanosoma cruzi PI: Wim Degrave ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/cruzi/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated : In development FAQ_updated : November 1996 Database : CSNDB Focus : Cell Signaling Networks Species : human Curator : Takako Igarashi, taka@nihs.go.jp Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Assistant_Curator : Masumi Yukawa, yukawa@nihs.go.jp Assistant_Curator : Shikiko Hasegawa, shasegaw@nihs.go.jp Contact : Takako Igarashi, taka@nihs.go.jp ACeDB_version : 4.1 Data : molecular data of signal molecules, molecular data of signal transductions, signal transduction pathways, domain structure and function of signal molecules, and three dimensional structures of signal molecules. Availability : CSNDB is on WWW. WWW-browser is required to attach molecular viewer RasMol (ftp: colonsay.dcs.ed.ac.uk ) for displaying three dimensional structure of protein. WWW : http://geo.nihs.go.jp/csndb.html Database : CupDB Species : Culex pipiens ACEDB_version : 4.3 WWW : currently unavailable via www Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : Cyanoace Species : Cyanobacterium synechocystis sp. strain PCC6803 Developer : Nobuyuki Miyajima, miyajima@kazusa.or.jp Comment : Converted to ACEDB from Sybase FTP : ftp://ftp.kazusa.or.jp/pub/acedb/cyanoace/ WWW : http://www.kazusa.or.jp/cyanobase/ Remark : WWW interface uses Java enhanced clickable maps. FAQ_updated : December 1996 Database : EthnobotDB (worldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database: FilDB Species: Filarial nematodes PI: Mark Blaxter ACEDB_version: 4.3 Curator: Martin Aslett Contact: Mark Blaxter, mark.blaxter@ed.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Brugia WWW: http://helios.bto.ed.ac.uk/mbx/fgn/filgen.html WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: In development FAQ_updated : November 1996 Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : May 1995 Database : GrainGenes Species : Wheat, barley, oats, sugarcane, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu Curator : Gerard R. Lazo, lazo@pw.usda.gov PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_3 (Unix), 4.1b1 (MacAce) Data_version : 1.7, December 1996 Availability : UNIX and Macintosh versions via anonymous ftp Availability : Macintosh version on CD-ROM "RiceMac / MacGrainGenes", from Dr. Baek Hie Nahm, Korea Rice Genome Research Program, Myongji University, Yongin, Korea. FTP : probe.nalusda.gov in pub/graingenes FTP : grain.jouy.inra.fr in pub/database Gopher : greengenes.cit.cornell.edu Gopher : grain.jouy.inra.fr Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://wheat.pw.usda.gov/ WWW : http://grain.jouy.inra.fr Data_updated : December 1996 FAQ_updated : December 1996 Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr Description : IGD (Integrated Genomic Database) aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : IXDB (Integrated X chromosome DataBase) Species: Homo sapiens Subject: Chromosome X Acedb_version : 4.1 Data: The YAC map constructed by the Max-Planck-Institut fuer Molekulare Genetik in Berlin, with all the attached experimental data necessary to reconstruct the map. Information on each of 9000 YAC clones mapped to the X chromosome, and constituting the YAC collection assembled with clone sets from 14 different laboratories worldwide. Latest_release:March 1996 Curator: Hugues Roest Crollius, roest@mpimg-berlin-dahlem.mpg.de Contact: Ulf Leser, leser@mpimg-berlin-dahlem.mpg.de PI: Hans Lehrach FTP: ftp.mpimg-berlin-dahlem.mpg.de in directory pub/lehrach/x-map WWW: http://www.mpimg-berlin-dahlem.mpg.de/~xteam Database: Leishdb Species: Leishmania major, L. infantum, L. peruviana, L. donovani and others PI: Jennie Blackwell PI: Al Ivens ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Leish WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/leish/leishpage.html (in development) Data_updated: October 1996 FAQ_updated : November 1996 Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie-Paule Lefranc Contact : Veronique Giudicelli, LIGM IGMM UMR CNRS 9942, BP 5051 Rte de Mende, 34000 Montpellier, giudi@ligm.crbm.cnrs-mop.fr Database : MaizeDB Species : Zea mays L. ssp. mays and related species Content : Maps, raw map data, loci, probes, genetic stocks, variations, mutant images, agronomic traits, gene products, QTL, bibliography, colleague addresses; hardlinks to sequence and germplasm databases. Latest_release : Oct 1996 Acedb_version : 4.1 Curator : Mary Polacco, maryp@teosinte.agron.missouri PI : Ed Coe, Jr., ed@teosinte.agron.missouri.edu Systems : Denis Hancock, dhancock@teosinte.agron.missouri.edu FTP : probe.nalusda.gov/pub/maizedb/macedist961001.tar.gz WWW : http://www.agron.missouri.edu WEBACE : http://probe.nalusda.gov:8300/ Contact : db_request@teosinte.agron.missouri.edu Comment : Data are periodically extracted into ACEDB format from Sybase Comment : Genera software used to maintain the Sybase database and its gateways, except for ACEDB Comment : ACEDB releases are announced on the MAIZE bulletin board; http://www.bio.net/hypermail/MAIZE/ Comment : WEBACE records are hardlinked to the Sybase server where data are curated Funding : USDA ARS Plant Genome Research Program FAQ_updated : Mar 7, 1997 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : July 1995 Database : Millet Genes Species : Pennisetum glaucum (Pearl Millet) ACEDB_version : 4.3 Curator : Matt Couchman, Matthew.Couchman@bbsrc.ac.uk PI : Katrien Devos, Katrien.Devos@bbsrc.ac.uk FTP: ftp://jiio5.jic.bbsrc.ac.uk/pub/millet WWW : http://synteny.nott.ac.uk/millet.html WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.shtml WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : March 1997 DataBase : Mousedb Species : Mus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD FAQ_updated : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : MsqDB Species : Interspecies Mosquito database ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. Curator : Staffan Bergh, staffan@biochem.kth.se Curator : Stewart Cole, stcole@pasteur.fr ACEDB_version : 4.3 Data_version : 4-22 (December 1996) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ FAQ_updated : December 1996 Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html FAQ_updated : September 1995 Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurrence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 FTP : ftp.sanger.ac.uk in pub/PomBase FAQ_updated : September 1995 Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susan McCouch ACEDB_version : 4.1 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : November 1996 Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4.6 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB WWW : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Curator : Yankai Jia, jia@genome.stanford.edu Programmer : Gail Juvik, gjuvik@genome.stanford.edu Programmer : Shuai Weng, shuai@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu FAQ_updated : September 1996 Database: SchistoDB Species: Schistosoma mansoni (plus other schistosomes) PI: David Johnston ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Schisto/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: In development FAQ_updated : November 1996 Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Sam Beer, sbeer@nightshade.cit.cornell.edu PI : none currently Release : ACEDB 4.3 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_updated : May 1997 FAQ_updated : May 1997 Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : September 1995 Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker, rcsshoe@iastate.edu Curator : David Grant, dgrant@iastate.edu Assistant_curator : Marica Imsamde, mimsande@iastate.edu Contact : David Grant, dgrant@iastate.edu ACEDB-Version : 3.7 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://macgrant.agron.iastate.edu FAQ_updated : October 1995 Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FAQ_updated : October 1994 Database: ToxoDB Species: Toxoplasma gondii PI: David Sibley PI: David Roos PI: Jim Ajioka ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Toxo/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/toxo/toxpage.html Data_updated: October 1996 FAQ_updated: November 1996 Database : TreeGenes Species : Forest trees ACEDB_version : 4.3 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ FAQ_updated : May 1996 Database: Trypbase Species: Trypanosoma brucei PI: Sara Melville ACEDB_version: 4.3 Curator: Howard Cobb Curator: Martin Aslett Contact: Sara Melville, sm160@mole.bio.cam.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/brucei WWW: http://parsun1.path.cam.ac.uk/newtryp/toppage.htm WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: October 1996 FAQ_updated: November 1996 Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html FAQ_updated : April 1994 Database : 11Db Species : Homo sapiens Subject : Physical and Genetic mapping of Human Chromosome 11 Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk) PI : Peter Little (p.little@bc.ic.ac.uk) ACEDB_version : based on 4_1 with added map displays. ACEDB_version : based on 3_6 with added map displays. Data version : 1.0 Last Update : December 1995 WWW : http://chr11.bc.ic.ac.uk FTP : ftp.cc.ic.ac.uk Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Database : 22ace Species : Homo sapiens Subject : Physical map of human chromosome 22, genomic sequencing and more ACEDB_version : 4.1 Curator : Ian Dunham, id1@sanger.ac.uk Curator : Gareth Maslen, glm@sanger.ac.uk PI : Ian Dunham FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ FAQ_updated : August 1995 Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions ---------------------------------------------------------------------------- Q12:Who prepared this document & where is the current version? A12: This document is posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The WWW version of this document is at: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html A text version is available via anonymous ftp at machine rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. Curators of ACEDB databases should take note of Question 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, 1993-1997, approx. 70K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov The GrainGenes Project is funded by the USDA ARS Plant Genome Research Program. Return to List of Questions ---------------------------------------------------------------------------- From owner-acedb@net.bio.net Wed Aug 13 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.nacamar.de!fu-berlin.de!gene.rz-berlin.mpg.DE!not-for-mail From: Ela Hunt Newsgroups: bionet.software.acedb Subject: table maker queries Date: Thu, 14 Aug 1997 09:40:28 +0200 Organization: Max-Planck Institut fuer Molekulare Genetik Lines: 64 Message-ID: <33F2B66C.41C6@rag100.rz-berlin.mpg.de> NNTP-Posting-Host: gene.rz-berlin.mpg.de (141.14.128.191) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Access: 16 25 816 X-Mailer: Mozilla 3.01 (X11; I; OSF1 V4.0 alpha) I run the following query which is OK for small data samples. If the data sample being retrieved is too big my system starts swapping and I never get anywhere. My question is: I really want out of this query only the rows where column 1 = column 5. Can the query be reformulated co that it only gets a subset of data I want? Colonne 1 Width 12 Optional Visible Class Class Cosmid From 0 Condition LLNCO* Colonne 2 Width 12 Mandatory Visible Class Class cDNA From 1 Tag Direct_selected_cDNA Condition MPI* Colonne 3 Width 12 Mandatory Visible Class Class Cosmid From 2 Tag Positive_cosmid Colonne 4 Width 12 Mandatory Visible Class Class Cosmid_restriction_fragment From 3 Tag Positive_for_cosmid_restriction_fragment_probe Colonne 5 Width 12 Mandatory Visible Class Class Cosmid From 4 Tag Positive_cosmid Condition LLNCO* Can anyone help? Ela -- _______________________________________________________________________________ Ela Pustulka-Hunt MA MPhil BA hunt_e@mpimg-berlin-dahlem.mpg.de Database Administrator tel. 030 - 8413-1415 Max Planck Institut fuer Molekulare Genetik, Abtl. Lehrach Ihnestrasse 73, 14195 Berlin, Germany _____________________________________________________________________________ From owner-acedb@net.bio.net Wed Aug 20 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!news.cis.ohio-state.edu!magnus.acs.ohio-state.edu!ts47-4.homenet.ohio-state.edu!trostyanetsky.2 From: trostyanetsky.2@pop.service.ohio-state.edu (Leonid (Larry) Trostyanetsky) Newsgroups: bionet.software.acedb Subject: RESEARCH ASSISTANT Date: Thu, 21 Aug 1997 23:44:25 GMT Organization: The Ohio State University Lines: 27 Message-ID: NNTP-Posting-Host: ts47-4.homenet.ohio-state.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] RESEARCH ASSISTANT in Bioorganic Chemistry. Undergraduate student needed to work on molecular modeling project of antitumor agent binding to DNA. Work involves the use of modeling programs such as MacroModel and Spartan on a dedicated SiliconGraphics Indigo Impact R10000. A great deal of independence is possible, and the student will be expected to bring new capabilities into the research group and to interact with other workers on this project. Requirements for this position include successful completion of Organic Chemistry (Chemistry 251/252/253) and experience with UNIX. Either research credit or work-study is possible. Please contact Professor Rob Coleman at coleman.184@osu.edu or 292-4548. Rob ------------------------------------------- Robert S. Coleman Associate Professor Department of Chemistry The Ohio State University 100 West 18th Avenue Columbus, OH 43210-1185 ------------------------------------------- (614) 292-4548 (voice) (614) 292-4647 (fax) coleman@chemistry.ohio-state.edu From owner-acedb@net.bio.net Wed Aug 20 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!news.cis.ohio-state.edu!magnus.acs.ohio-state.edu!ts47-4.homenet.ohio-state.edu!trostyanetsky.2 From: trostyanetsky.2@pop.service.ohio-state.edu (Leonid (Larry) Trostyanetsky) Newsgroups: bionet.software.acedb Subject: RESEARCH ASSISTANT Date: Thu, 21 Aug 1997 23:44:41 GMT Organization: The Ohio State University Lines: 27 Message-ID: NNTP-Posting-Host: ts47-4.homenet.ohio-state.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] RESEARCH ASSISTANT in Bioorganic Chemistry. Undergraduate student needed to work on molecular modeling project of antitumor agent binding to DNA. Work involves the use of modeling programs such as MacroModel and Spartan on a dedicated SiliconGraphics Indigo Impact R10000. A great deal of independence is possible, and the student will be expected to bring new capabilities into the research group and to interact with other workers on this project. Requirements for this position include successful completion of Organic Chemistry (Chemistry 251/252/253) and experience with UNIX. Either research credit or work-study is possible. Please contact Professor Rob Coleman at coleman.184@osu.edu or 292-4548. Rob ------------------------------------------- Robert S. Coleman Associate Professor Department of Chemistry The Ohio State University 100 West 18th Avenue Columbus, OH 43210-1185 ------------------------------------------- (614) 292-4548 (voice) (614) 292-4647 (fax) coleman@chemistry.ohio-state.edu From owner-acedb@net.bio.net Thu Aug 21 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: "*" glitch in Search: Date: 22 Aug 1997 15:47:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <9708222247.AA12891@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net In ace4_5c, typing "*matth" in the main window's Search: box doesn't auto-complete to "*matth*" and find my name, whereas it did in ace4_3. I liked it better the old way. Can we have it back? - Dave From owner-acedb@net.bio.net Thu Aug 21 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!infeed1.internetmci.com!newsfeed.internetmci.com!206.229.87.25!news-peer.sprintlink.net!news.sprintlink.net!Sprint!ais.net!newsfeed.concentric.net!news-master!news From: "Daniel Williams" Newsgroups: alt.binaries.w-software,alt.comp.software.tools,alt.med.software,amiga.software,bionet.software.acedb,bit.software,comp.software,uw.cgl.software,uw.csc.software,uw.mfcf.software Subject: Review Service Date: Thu, 21 Aug 1997 19:48:41 -0500 Organization: Concentric Internet Services Lines: 11 Message-ID: <5tinjc$dm4@chronicle.concentric.net> NNTP-Posting-Host: ts023d02.chi-il.concentric.net X-Newsreader: Microsoft Outlook Express 4.71.1008.3 X-MimeOle: Produced By Microsoft MimeOLE Engine V4.71.1008.3 Do you have software, or shareware, or freeware programs or games that u would like an official review for? D&S services / Critique reviews and critiques your games and programs. Our reviews can be sent out to sights and posted anywhere you like. When it comes to web reviews D&S is well known and well thought of. Get a professional review! for more info, email doobydo@usa.net From owner-acedb@net.bio.net Fri Aug 22 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: re: *glitch Date: 23 Aug 1997 13:11:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9708232011.AA13500@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > in 4.3 *mathh autocompleted to *mathh* > in 4.5 autocompletion does not occur if there is already a star > this is a way to allow searching for known enndings > > should we really revert to 4.3 behaviour ? In 4.3 *mathh returns just the *mathh records if any exist, and only autocompletes if none exist. That seems like useful behavior for the Search: box, though it would be inappropriate for the Query Language. - Dave From owner-acedb@net.bio.net Fri Aug 22 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: *glitch Date: 23 Aug 1997 15:34:34 +0100 Lines: 5 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5tmsdq$qmk@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk in 4.3 *mathh autocompleted to *mathh* in 4.5 autocompletion does not occur if there is already a star this is a way to allow searching for known enndings should we really revert to 4.3 behaviour ? From owner-acedb@net.bio.net Sun Aug 24 23:00:00 1997 Path: biosci!INFOWATCH.NET!info From: info@INFOWATCH.NET (Information Desk) Newsgroups: bionet.software.acedb Subject: Advertisement: Website Hosting Date: 25 Aug 1997 14:44:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <19970826061641113.NDV89@infomail.infowatch.net> NNTP-Posting-Host: net.bio.net ---------------------------------------------- Our research indicates that the following material may interest you. This is a ONE-TIME ONLY MAILING, so you won't need to reply if this is of no interest to you (in which case we apologize for the inconvenience). ---------------------------------------------- http://www.infowatch.net InfoWatch would like to introduce our complete Hosting and Promotional service. FOR ONLY $29.95 PER MONTH ! * 30 MB (megabytes) of disk space * 1000 MB = 1 GB (gigabyte) of data transfer per month * 8 E-mail accounts * Access to your account anytime via the Webs Control Panel * MS Front Page * Unlimited FTP updates * Personal CGI directory for your own scripts (or use ours) * Incredible Statistics program shows you everything * E-mail forwarding, auto responders, and vacation reply * Domain name registration (www.yourname.com) * Register your domain with over 350 search engines * Friendly customer support If for any reason you are not satisfied with InfoWatch's service after 60 days, we will transfer you back to your original host and pay any transfer fees. http://www.infowatch.net info@infowatch.net From owner-acedb@net.bio.net Sun Aug 24 23:00:00 1997 Path: biosci!dkfz-heidelberg.de!A.Kuehl From: A.Kuehl@dkfz-heidelberg.de (Anja Kuehl) Newsgroups: bionet.software.acedb Subject: Running ACEDB on a HP-UX (Convex)-Machine Date: 25 Aug 1997 02:07:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net We have installed the source code of ACEDB for HP-UX-machines on our Convex. During the compilation we had some difficulties but after changing the makefile (e.g. deleting the chrono.o file) we were able to run xace and tace on our machine. The only thing that does not work is the Query language. We don't get any result when we use it. Has anybody made the same experiences? Anja Kuehl From owner-acedb@net.bio.net Mon Aug 25 23:00:00 1997 Path: biosci!CORNELL.EDU!mab8 From: mab8@CORNELL.EDU (Marci Blinstrub) Newsgroups: bionet.software.acedb Subject: truncated locus names in ace 4.5 Date: 26 Aug 1997 09:33:41 -0700 Organization: Cornell University Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <3403055E.B1AE1D54@cornell.edu> NNTP-Posting-Host: net.bio.net I have noticed in both the WinAce release and ACeDb version 4.5 that some of the names of the marker loci on the gmap display are truncated. No matter how big I make the window, they still remain this way. Is there any way to force the display to show the full names? I don't remember ever seeing anything like this in version 4.3. From owner-acedb@net.bio.net Mon Aug 25 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!feed1.news.erols.com!infeed1.internetmci.com!newsfeed.internetmci.com!194.72.7.126!news-peer.bt.net!btnet!nntp.news.xara.net!xara.net!nntp2.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: convex Date: 26 Aug 1997 15:11:28 +0100 Lines: 22 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5tuo6g$qft@mserv1.dl.ac.uk> Original-To: net@kaa.crbm.cnrs-mop.fr please, which source code did you install normally you should just have had to edit wmake/CONVEX_DEF did you do that. can you send me that file in w1/chrono.c there is a protection: #if !(defined(SOLARIS) || defined(MACINTOSH) || defined(IBM) || defined(WIN32) || defined(HP) || defined(CONVEX)) #define CHRONO #endif i just added CONVEX do you have data in the system ? try tace acedb>Find Author acedb>Query COUNT Paper > 3 // to find authors woith more than 3 papers etc From owner-acedb@net.bio.net Mon Aug 25 23:00:00 1997 Path: biosci!NIGHTSHADE.CIT.CORNELL.EDU!noelyap From: noelyap@NIGHTSHADE.CIT.CORNELL.EDU ("N. Yap") Newsgroups: bionet.software.acedb Subject: LongText and hypertext Date: 26 Aug 1997 12:06:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <9708261906.AA18190@nightshade.cit.cornell.edu> NNTP-Posting-Host: net.bio.net I have been experimenting with the hypertext feature in ?LongText objects. It appears that only whole words can be activated as links, is this correct? What are valid characters? I have so far found that only alphanumerics, underscore, and hyphens are allowed. Would it be possible to include other characters like slash and colon? Thanks, Noel -- Immanuel V. Yap E-MAIL: noelyap@nightshade.cit.cornell.edu Curator, RiceBlastDB ivy1@cornell.edu Plant Breeding Dept. OFFICE: (607) 255-3103 320 Bradfield Hall HOME: (607) 257-3463 Cornell University (607) 266-9398 Ithaca NY 14853 From owner-acedb@net.bio.net Mon Aug 25 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Richard Durbin Newsgroups: bionet.software.acedb Subject: re: truncated locus names in ace 4.5 Date: 26 Aug 1997 18:07:57 +0100 Lines: 8 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5tv2hd$ae9@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Aha. This is a feature, not a bug. In order to not push loci too far out of position, their names are truncated as necessary (down to a single character) as you zoom out. After considerable discussion amongst users of the working version over the last year (at the Sanger Centre and elsewhere) the consensus was that this was an improvement. Richard From owner-acedb@net.bio.net Mon Aug 25 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: re: truncated locus names in ace 4.5 Date: 26 Aug 1997 09:38:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <9708261638.AA16884@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > some of the names of the marker loci on the gmap display are truncated. Yes, I noticed the same thing. In one case locus "adh" is truncated cleanly to "ad". The only way you'd know it's really adh from the map display is by zooming in. - Dave From owner-acedb@net.bio.net Tue Aug 26 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!sbeer From: sbeer@GREENGENES.CIT.CORNELL.EDU ("Sam Beer") Newsgroups: bionet.software.acedb Subject: tree displays in 4.5 Date: 27 Aug 1997 09:13:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9708271612.AA18770@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net In the tree displays in ACEDB 4.5, fields in vector tags are separated by 2 spaces, instead of a tab (as in 4.3). This sometimes gives the tree a "ragged" appearance, compared to the former tree display. Can alternative separator characters be specified by curators using 4.5? Thanks, Sam Beer Curator, SolGenes From owner-acedb@net.bio.net Tue Aug 26 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: re-vote? locus name truncation on Gmap Date: 27 Aug 1997 06:39:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9708271339.AA18535@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Richard said, > In order to not push loci too far out of > position, their names are truncated as necessary (down to a single > character) as you zoom out. After considerable discussion amongst users of > the working version over the last year (at the Sanger Centre and elsewhere) > the consensus was that this was an improvement. I don't know if I agree. I think I'd prefer to have them bumped to a new position, and in cases of extreme crowding for some to disappear altogether, rather than displaying them under incorrect names. At least, could clicking once on the locus cause its full name be shown on the map? And would it be possible to shade the truncated names grey or otherwise decorate them to indicate they're not whole? - Dave From owner-acedb@net.bio.net Tue Aug 26 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: fwd: Hardware/system requirements for ACEDB Date: 27 Aug 1997 15:57:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <9708272257.AA19574@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Hi Savita, I'm forwarding your question along to more knowledgable folks. - Dave > Date: Wed, 27 Aug 1997 17:39:25 -0500 > From: Savita Kini > To: acedbfaq@s27w007.pswfs.gov > Subject: Hardware/system requirements for ACEDB > > Hi > > I have installed ACEDB 4.3 on a SunSparc10 with Solaris 2.5.1 as the > operating system and it also has CDE installed which also hogs lot of > memory. It would be great if u could give me some details on possible > requirements for swap space/RAM etc for installing and running ACEDB > without any memory problems. I have been facing the problem recently > that when I run xace twice(say opening two databases simultaneously for > comparison etc) then my swap space get totally filled. > > Awaiting ur reply. > > Thanks > Savita Kini > -- > ________________________________________________________________________ > Savita Kini Residence:4302 College Main #332 > Graduate Research Assistant Bryan, TX -77801 > USDA ARS > Cotton Research Lab > Phone:(o)-(409)-260-9328/862-4869 > Agronomy Road, > College Station,TX-77843 (H)-(409)-268-8038 > http://ee.tamu.edu/~kini > ________________________________________________________________________ From owner-acedb@net.bio.net Wed Aug 27 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!csulb.edu!logbridge.uoregon.edu!feta.direct.ca!newsfeed.direct.ca!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: tree in 4.5 Date: 28 Aug 1997 09:38:21 +0100 Lines: 5 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5u3ddt$guc@mserv1.dl.ac.uk> Original-To: net@kaa.crbm.cnrs-mop.fr i see, we should revert to tabs also, there is a choice of tree layout now more horizontal or more vertical which is available from preferences, although it does not seem to work for me (i never tested that myself, but i was told it works) From owner-acedb@net.bio.net Wed Aug 27 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!206.229.87.50!news-pull.sprintlink.net!news-in-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: abbreviations Date: 28 Aug 1997 10:24:52 +0100 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5u3g54$jvu@mserv1.dl.ac.uk> Original-To: net@kaa.crbm.cnrs-mop.fr one of the problem of not abbreviating was that the porint out were unusabel the present system has 4 levels full name 3 letters abbrev 1 letter abbrev gone as soon as abbreviation starts , names already touch each other and when they go away the display if full crowded also when you touch a gene its full descriptor goes in the top blue report line From owner-acedb@net.bio.net Wed Aug 27 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!206.229.87.50!news-pull.sprintlink.net!news-in-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: memory Date: 28 Aug 1997 10:21:45 +0100 Lines: 4 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5u3fv9$jti@mserv1.dl.ac.uk> Original-To: net@kaa.crbm.cnrs-mop.fr the problem with xace is that if you open it twice, you use twice the RAM space doubl;es i suppose the sapce to run the full worm database is around 30 Meg but this depends on machines From owner-acedb@net.bio.net Wed Aug 27 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: re: abbreviations Date: 28 Aug 1997 08:09:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <9708281509.AA20716@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Jean says, > the present system has 4 levels > > full name > 3 letters abbrev > 1 letter abbrev > gone I don't think levels 3 and 1 are very useful for our (Cornell) databases, since on the one hand our locus names are highly degenerate in the first three characters, and on the worse hand we have a number of 1-character gene names with which these abbreviations could be confused. Would it be possible to replace the locus name with a graphic, a little circle or something, instead of the abbreviated name? That would be preferable to me. Maybe this could be made a choice via the map's View object? > also when you touch a gene its full descriptor goes in the top blue report > line Oh, I didn't notice that. - Dave From owner-acedb@net.bio.net Wed Aug 27 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Richard Durbin Newsgroups: bionet.software.acedb Subject: Hardware/system requirements for ACEDB Date: 28 Aug 1997 10:47:36 +0100 Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5u3hfo$lmi@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk The amount of memory you require for ACEDB depends very much on how big the database is (i.e. the disk space used by the database/ subdirectory). Our rule of thumb is that one typically uses 5-10Mb plus up to 10% of the disk space size of the database. So with a 200Mb database perhaps 25Mb memory, and with a 500Mb database (e.g. the C.elegans one) up to 50-60Mb. In fact for short sessions less memory is used -- it is only when all classes are explored, or for example when parsing big files that these sorts of amounts of memory get used. Richard From owner-acedb@net.bio.net Wed Aug 27 23:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: re: tree in 4.5 Date: 28 Aug 1997 11:58:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9708281858.AA21022@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Jean says, > also, there is a choice of tree layout now > more horizontal or more vertical which > is available from preferences, although it does not seem to work for me > (i never tested that myself, but i was told it works) Aha, I just made it work. Looks like the default is more horizontal. If you de-select "HORIZONTAL_TREE" in the Preferences window and then click Done or Save, nothing at all seems to happen in the current xace session. (Should it?) However if you click Save and start a new xace session, you'll see what more vertical looks like. I don't think either of these is as good as the 4_3-style tabbed layout, but it could be a matter of preference. - Dave From owner-acedb@net.bio.net Thu Aug 28 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!xfer.kren.nm.kr!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!cs.utexas.edu!news.tamu.edu!not-for-mail From: scartinh@coyote.tamu.edu Newsgroups: bionet.software.acedb Subject: Re: re-vote? locus name truncation on Gmap Date: 29 Aug 1997 12:59:18 -0500 Organization: Texas A&M University, College Station, Texas Lines: 26 Message-ID: References: <9708271339.AA18535@greengenes.cit.cornell.edu> NNTP-Posting-Host: coyote.tamu.edu NNTP-Posting-Date: 29 Aug 1997 17:56:29 GMT X-Newsreader: Gnus v5.3/Emacs 19.34 matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") writes: > > Richard said, > > > In order to not push loci too far out of > > position, their names are truncated as necessary (down to a single > > character) as you zoom out. After considerable discussion amongst users of > > the working version over the last year (at the Sanger Centre and elsewhere) > > the consensus was that this was an improvement. > > I don't know if I agree. I think I'd prefer to have them bumped to a new > position, and in cases of extreme crowding for some to disappear altogether, > rather than displaying them under incorrect names. > > At least, could clicking once on the locus cause its full name be shown on > the map? And would it be possible to shade the truncated names grey or > otherwise decorate them to indicate they're not whole? > > - Dave > > Could we make name truncation an option? Sam From owner-acedb@net.bio.net Fri Aug 29 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!news.oru.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!infeed1.internetmci.com!newsfeed.internetmci.com!195.99.66.215!news-feed1.eu.concert.net!news.worldonline.nl!not-for-mail From: "The Ghost" Newsgroups: bionet.software.acedb Subject: LQQK FOR THE NEW SOFTWARE LIST// Date: 30 Aug 1997 21:12:12 GMT Organization: World Online Lines: 8 Message-ID: <01bcb589$647ea660$7582f1c3@deghost> NNTP-Posting-Host: ldn1-p117.worldonline.nl X-Newsreader: Microsoft Internet News 4.70.1155 VISIT MY HOMEPAGE FOR THE NEW CD-ROM LIST CRAZY BITES THE LEGACY WINFILES WINZIP XFILES AND MUTCH MORE http://home.worldonline.nl/~deghost From owner-acedb@net.bio.net Fri Aug 29 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!csulb.edu!logbridge.uoregon.edu!infeed1.internetmci.com!newsfeed.internetmci.com!192.220.251.22!netnews.nwnet.net!news-hub.interserv.net!news.interserv.com!email-now9.com From: "SPECIAL !!!" special@email-now9.com Newsgroups: bionet.software.acedb Subject: „„„„„„„>> 9 0 % O F F <<„„„„„„„ Date: Sat, 30 Aug 1997 07:17:32 -0700 Organization: TUV Lines: 6 Message-ID: <300897071732@email-now9.com> NNTP-Posting-Host: hd63-085.hil.compuserve.com <<<<<<< COMPUTER SOFTWARE / HARDWARE >>>>>>> >>> UP TO 90 % OFF <<< http://www.quantcom.com/auctionfirst/ <<<><>><><>=>===>><= From owner-acedb@net.bio.net Sun Aug 31 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!cam-news-feed3.bbnplanet.com!news.bbnplanet.com!zylum.nettrip.net!not-for-mail From: Nick@tzcc.com (Nick Dinielli (The Fatman)) Newsgroups: bionet.software.acedb Subject: For additional software support visit: http://www.tzcc.com Date: Mon, 01 Sep 1997 02:48:34 GMT Organization: NetTrip, Inc. Lines: 2 Message-ID: <32fa6e14.6967817@news.carroll.com> Reply-To: Nick@tzcc.com NNTP-Posting-Host: nj-tc1-080.nettrip.net Mime-Version: 1.0 Content-Type: text/plain X-Newsreader: Forte Agent 1.0/32.390MH For additional software support visit: http://www.tzcc.com From owner-acedb@net.bio.net Sun Aug 31 23:00:00 1997 Path: biosci!agate!howland.erols.net!infeed1.internetmci.com!newsfeed.internetmci.com!192.220.251.22!netnews.nwnet.net!news-hub.interserv.net!news.interserv.com!email-now7.com From: "SPECIAL !!!" special@email-now7.com Newsgroups: bionet.software.acedb Subject: <<>> COMPUTER SOFTWARE / HARDWARE <<>> Date: Sun, 31 Aug 1997 20:30:28 -0700 Organization: STU Lines: 5 Message-ID: <310897203028@email-now7.com> NNTP-Posting-Host: hdn105-167.hil.compuserve.com <<<<<<< COMPUTER SOFTWARE / HARDWARE >>>>>>> >>> UP TO 90 % OFF <<< http://www.quantcom.com/auctionfirst/ <<<><>><><><=<<<==>< From owner-acedb@net.bio.net Sun Aug 31 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Sep 1997 02:00:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199709010900.CAA22932@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. From owner-acedb@net.bio.net Sun Aug 31 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!newsxfer3.itd.umich.edu!infeed1.internetmci.com!newsfeed.internetmci.com!192.220.251.22!netnews.nwnet.net!news-hub.interserv.net!news.interserv.com!discount-software8.com From: "DISCOUNTS !" software@discount-software8.com Newsgroups: bionet.software.acedb Subject: +++ C O M P U T E R A U C T I O N +++ Date: Mon, 01 Sep 1997 11:16:47 -0700 Organization: EFGH Lines: 5 Message-ID: <010997111647@discount-software8.com> NNTP-Posting-Host: ad20-035.compuserve.com <<<<<<< COMPUTER SOFTWARE / HARDWARE >>>>>>> >>> UP TO 90 % OFF <<< http://www.quantcom.com/auctionfirst/ =>>=>==>=>=><>>><<=>