From owner-acedb@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!nntp.uio.no!news.apfel.de!fu-berlin.de!news-ber1.dfn.de!news-lei1.dfn.de!news-nue1.dfn.de!news-mue1.dfn.de!news-stu1.dfn.de!news.belwue.de!News.Uni-Marburg.DE!not-for-mail From: Michael Otto Newsgroups: bionet.software.acedb Subject: webace / wwwace Date: Tue, 04 Feb 1997 15:02:08 +0100 Organization: MZ fuer Humangenetik Lines: 13 Message-ID: <32F74160.96C@Mailer.Uni-Marburg.DE> Reply-To: otto@Mailer.Uni-Marburg.DE NNTP-Posting-Host: pc2010.humangenetik.humanmedizin.uni-marburg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (WinNT; I) Hi outhere, is there anyone who is running webace or wwwace (different programs) on a SUN under SunOS 4.1.x ? I tried to compile them.. but I'll get alway errors. ACEDB system is complete and can be compiled, but when I follow the changes in the wwwace documentation, I'll fail. thanks in advance -- Michael Otto -- From owner-acedb@net.bio.net Sun Feb 09 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!lll-winken.llnl.gov!fnnews.fnal.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Curator) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Date: 10 Feb 1997 19:19:11 GMT Organization: Lawrence Berkeley Laboratory, Berkeley CA Lines: 1224 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <5dnsbf$nj9@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.pswfs.gov Summary: Frequently Asked Questions about finding and getting started with the genome database software ACEDB. Archive-name: acedb-faq Last-modified: 10 Feb 97 Version: 1.34 Xref: biosci bionet.software.acedb:1103 news.answers:87172 ---------------------------------------------------------------------------- ACEDB FAQ ---------------------------------------------------------------------------- Curated by: Dave Matthews ---------------------------------------------------------------------------- Frequently Asked Questions about ACEDB * Q0 : What is ACEDB? * Q1 : What is the current version of ACEDB? * Q2 : What hardware/software do I need to run ACEDB? * Q3 : Where can I get ACEDB? * Q4 : What ACEDB databases exist? * Q5 : What documentation exists for ACEDB? * Q6 : What other resources are available for ACEDB? * Q7 : How should ACEDB be cited? * Q8 : Is ACEDB object-oriented? * Q9 : How does one get on/off the ACEDB announcements mailing list? * Q10 : When and where is the next ACEDB Workshop? * Q11 : Who prepared this document & where is the current version? Questions marked with '+' are new, those with '!' have substantially changed answers. ---------------------------------------------------------------------------- Q0: What is ACEDB? A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [Q4 gives contact information]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions ---------------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: (This answer refers to the software, not the C. elegans data.) Current Unix version is 4_3 (as of May 1996) and is identical to the test version test.4_3i. A Macintosh version is available as version 4.1b1. A Windows 95/NT version is available as version beta960927. To retrieve the software see Q3. To be kept informed of new releases see Q9. Return to List of Questions ---------------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. * Unix: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series 4, 5, 6 o IBM RS-6000 o PC 386/486/Pentium with Linux o NEC EWS4800 o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o There exist, or have existed, ports onto Alliant, Hewlett- Packard, Convex. You may have to contact the developer responsible for the port to make these real. * Windows 95/NT * Macintosh: [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a 17" color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. Return to List of Questions ---------------------------------------------------------------------------- Q3: Where can I get ACEDB? A3: Source code and Unix binaries are available in the following anonymous ftp sites: * lirmm.lirmm.fr in pub/acedb * ftp.sanger.ac.uk in pub/acedb * ncbi.nlm.nih.gov in repository/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb Linux binaries in ELF and a.out format, from Jeff Bryer: * ncbi.nlm.nih.gov in repository/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb NEC EWS4800 binaries: * http://www.labs.nec.co.jp/freesoft/freesofte.html Windows 95/NT 3.51, from Richard Bruskiewich: * bates.biol.sfu.ca in pub/ntace * ftp.sanger.ac.uk in pub/winace * bioinformatics.weizmann.ac.il in pub/databases/acedb MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin: * genome.lbl.gov in pub/macace * ncbi.nlm.nih.gov in repository/acedb/macace * bioinformatics.weizmann.ac.il in pub/databases/acedb Return to List of Questions ---------------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: In alphabetic order by Database name [Curators, please submit changes as new paragraphs] Database : AaeDB Species : Aedes aegypti (Mosquito) ACEDB_version : 3.0 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Last_update : December 1994 Database : AtDB Species : Arabidopsis thaliana Current version : 3-5 PI : J. Michael Cherry Curator : David Flanders Contact : arab-curator@genome.stanford.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : genome-ftp.stanford.edu in arabidopsis/aatdb FTP : ncbi.nlm.nih.gov in repository/aatdb FTP : probe.nalusda.gov in pub/aatdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://genome-www.stanford.edu WWW : http://probe.nalusda.gov:8300/plant/ Last_update : August 1995 Database : AboutDB Curator : Staffan Bergh, staffan@biochem.kth.se Subject : ACEDB itself (meta-meta-metadata) ACEDB_version: 3.0 WWW : http://www.biochem.kth.se/AboutDB.html Last_update : July 1995 Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@sanger.ac.uk Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ Last_update : August 1995 Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu ACeDB_version : 3.0 Subject: Contains extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe yeast); interacting loci via defined Interactions for each locus Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html FTP: ftp://keck.tamu.edu/pub/agsdb/agsdb1_0_acedb3_0_solaris2.3.tar.Z Last_update : March 1994 Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_Update : July 1995 Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 4.1 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : September 1995 Database : BrassicaDB Species : Brassica napus (Canola/Oilseed Rape) and its parental diploid species ACEDB_version : 4.3 Description : Genetic maps of Brassica napus, QTL analyses for agronomic traits, literature references and B. napus-specific DNA sequences will be incorporated. We aim to integrate with B. napus genetic maps developed elsewhere and to produce a Java interface that will link BrassicaDB with the AAtDB (Arabidopsis thaliana) database through gene orthologies that are becoming established between these closely related plant genomes. PI : Martin Trick, Martin.Trick@bbsrc.ac.uk Curator/Developer : Mazda Hewitt, Mazda.Hewitt@bbsrc.ac.uk WWW : http://nasc.nottm.ac.uk Last_update : Under development Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : August 1995 Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : September 1995 Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edubr> ACEDB_version : 3.0 Gopher : gopher://probe.nalusda.gov:7000/11/genome.databases/coolgenes/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : January 1996 Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 ACEDB_version : 3.0 Data_version : January 1995 (version 95.1) FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ Last_update : January 1995 Database: Cruzdb Species: Trypanosoma cruzi PI: Wim Degrave ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/cruzi/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Last_updated: In development Database : CSNDB Focus : Cell Signaling Networks Species : human Curator : Takako Igarashi, taka@nihs.go.jp Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Assistant_Curator : Masumi Yukawa, yukawa@nihs.go.jp Assistant_Curator : Shikiko Hasegawa, shasegaw@nihs.go.jp Contact : Takako Igarashi, taka@nihs.go.jp ACeDB_version : 4.1 Data : molecular data of signal molecules, molecular data of signal transductions, signal transduction pathways, domain structure and function of signal molecules, and three dimensional structures of signal molecules. Availability : CSNDB is on WWW. WWW-browser is required to attach molecular viewer RasMol (ftp: colonsay.dcs.ed.ac.uk ) for displaying three dimensional structure of protein. WWW : http://geo.nihs.go.jp/csndb.html Database : Cyanoace Species : Cyanobacterium synechocystis sp. strain PCC6803 Developer : Nobuyuki Miyajima, miyajima@kazusa.or.jp Comment : Converted to ACEDB from Sybase FTP : ftp://ftp.kazusa.or.jp/pub/acedb/cyanoace/ WWW : http://www.kazusa.or.jp/cyanobase/ Remark : WWW interface uses Java enhanced clickable maps. Last_update : December 1996 Database : EthnobotDB (worldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : June 1995 Database: FilDB Species: Filarial nematodes PI: Mark Blaxter ACEDB_version: 4.3 Curator: Martin Aslett Contact: Mark Blaxter, mark.blaxter@ed.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Brugia WWW: http://helios.bto.ed.ac.uk/mbx/fgn/filgen.html WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Last_updated: In development Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : May 1995 Database : GrainGenes Species : Wheat, barley, oats, sugarcane, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu Curator : Gerard R. Lazo, lazo@pw.usda.gov PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_3 (Unix), 4.1b1 (MacAce) Data_version : 1.7, December 1996 Availability : UNIX and Macintosh versions via anonymous ftp Availability : Macintosh version on CD-ROM "RiceMac / MacGrainGenes", from Dr. Baek Hie Nahm, Korea Rice Genome Research Program, Myongji University, Yongin, Korea. FTP : probe.nalusda.gov in pub/graingenes FTP : grain.jouy.inra.fr in pub/database Gopher : greengenes.cit.cornell.edu Gopher : grain.jouy.inra.fr Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://wheat.pw.usda.gov/ WWW : http://grain.jouy.inra.fr Last_update : December 1996 Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr WWW : http://moulon.inra.fr/acedb/igd.html Description : IGD (Integrated Genomic Database) aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : IXDB (Integrated X chromosome DataBase) Species: Homo sapiens Subject: Chromosome X Acedb_version : 4.1 Data: The YAC map constructed by the Max-Planck-Institut fuer Molekulare Genetik in Berlin, with all the attached experimental data necessary to reconstruct the map. Information on each of 9000 YAC clones mapped to the X chromosome, and constituting the YAC collection assembled with clone sets from 14 different laboratories worldwide. Latest_release:March 1996 Curator: Hugues Roest Crollius, roest@mpimg-berlin-dahlem.mpg.de Contact: Ulf Leser, leser@mpimg-berlin-dahlem.mpg.de PI: Hans Lehrach FTP: ftp.mpimg-berlin-dahlem.mpg.de in directory pub/lehrach/x-map WWW: http://www.mpimg-berlin-dahlem.mpg.de/~xteam Database: Leishdb Species: Leishmania major, L. infantum, L. peruviana, L. donovani and others PI: Jennie Blackwell PI: Al Ivens ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Leish WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/leish/leishpage.html (in development) Last_updated: October 1996 Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie-Paule Lefranc Contact : Veronique Giudicelli, LIGM IGMM UMR CNRS 9942, BP 5051 Rte de Mende, 34000 Montpellier, giudi@ligm.crbm.cnrs-mop.fr Database : MaizeDB Species : Zea mays L. ssp. mays and related species Latest_release : April 1995 Acedb_version : 3.3 Comment : MaizeDB is a periodically extracted ACeDB front end for the Maize Genome Database, MaizeDB, a SYBASE database, implemented using Genera software, developed by Stan Letovsky. Comment : Genera provides (1) up-to-the-minute form internet access to SYBASE databases, both for query (WWW and APT) and data entry (APT only); (2) database design alterations by systems administrators; (3) gopher file extraction. Comment: MaizeDB uses WWW record-to-record hard-links to 16 external databases for (1) annotated sequences: GenBank, dbEST, GenoBase, PIR, SwissProt, Prosite, ENZYME; (2) other species genome information: AAtDB(Arabidopsis), RiceGenes, GrainGenes, SaachDB (yeast), CGSC(E. coli), XLocus, RiceGenes, GrainGenes (3) germplasm: GRIN. Data : Over 100,000 records include: 6513 mapped loci (located to chromosome or better) including 1081 mapped genes and 1937 mapped probed sites (gene candidates); 2448 probes; 2460 map scores; 1551 gel patterns (Probe/Enzyme/Stock); 8777 stocks; 18,100 Variations (alleles, DNA polymorphisms, rearrangements, etc); 596 phenotypes; 317 traits; 715 gene products; 6158 bibliographic references; 2200 researchers with addresses. FTP : probe.nalusda.gov in pub/maizedb Gopher : gopher.agron.missouri.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: corncob WWW : http://www.agron.missouri.edu/top.html WWW : http://probe.nalusda.gov:8300/plant/ WWW Genera information : http://gdbdoc.gdb.org/letovsky/genera/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe, ed@teosinte.agron.missouri.edu Curator : Mary Polacco, maryp@teosinte.agron.missouri.edu Assoc Curator : Pat Byrne, byrne@teosinte.agron.missouri.edu QTL data Assoc Curator : Georgia Davis, gdavis@teosinte.agron.missouri.edu Map data Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic Stock data Assoc Curator : Christiane Fauron, FAURON@GENE1.med.utah.edu Mitochondrion genome Assoc Curator : Carolyn Wetzel, cmwetzel@iastate.edu Chloroplast genome Assoc Curator : Steve Rodermel, S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome Design : Stan Letovsky, letovsky@gdb.org Design : Mary Berlyn, mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock, dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 11 April 1995 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : July 1995 Database : Millet Genes Species : Pennisetum Glaucum (Pearl Millet) ACEDB_version : 4.3 Curator : Matt Couchman, Matthew.Couchman@bbsrc.ac.uk PI : Katrien Devos, Katrien.Devos@bbsrc.ac.uk FTP: ftp://jiio5.jic.bbsrc.ac.uk/pub/millet WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.html WWW : http://probe.nalusda.gov:8300/plant/ Last_update : December 1996 DataBase : Mousedb Species : Mus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD Last_update : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : June 1995 Database : MsqDB Species : Interspecies Mosquito database ACEDB_version : 4.1 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Contact : aaedbmgr@klab.agsci.colostate.edu Last_update : March 1996 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. Curator : Staffan Bergh, staffan@biochem.kth.se Curator : Stewart Cole, stcole@pasteur.fr ACEDB_version : 4.3 Data_version : 4-22 (December 1996) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ Last_update : December 1996 Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au Curator : Gail Juvik, gjuvik@nalusda.gov - ACEDB version ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html Last_update : September 1995 Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurrence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : June 1995 Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 FTP : ftp.sanger.ac.uk in pub/PomBase Last_update : September 1995 Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Last_update : June 1995 Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susan McCouch ACEDB_version : 4.1 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : November 1996 Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4.6 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB WWW : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Curator : Yankai Jia, jia@genome.stanford.edu Programmer : Gail Juvik, gjuvik@genome.stanford.edu Programmer : Shuai Weng, shuai@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Last_update : September 1996 Database: SchistoDB Species: Schistosoma mansoni (plus other schistosomes) PI: David Johnston ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Schisto/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Last_update: In development Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu PI : Steve Tanksley Release : ACEDB 4.3 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : April 1996 Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Last_update : September 1995 Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker, rcsshoe@iastate.edu Curator : David Grant, dgrant@iastate.edu Assistant_curator : Marica Imsamde, mimsande@iastate.edu Contact : David Grant, dgrant@iastate.edu ACEDB-Version : 3.7 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://macgrant.agron.iastate.edu Last_update : October 1995 Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Last_update : October 1994 Database: ToxoDB Species: Toxoplasma gondii PI: David Sibley PI: David Roos PI: Jim Ajioka ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Toxo/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/toxo/toxpage.html Last_update: October 1996 Database : TreeGenes Species : Forest trees ACEDB_version : 4.3 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ Last_update : May 1996 Database: Trypbase Species: Trypanosoma brucei PI: Sara Melville ACEDB_version: 4.3 Curator: Howard Cobb Curator: Martin Aslett Contact: Sara Melville, sm160@mole.bio.cam.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/brucei WWW: http://parsun1.path.cam.ac.uk/newtryp/toppage.htm WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Last_updated: October 1996 Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Last_update : April 1994 Database : 11Db Species : Homo sapiens Subject : Physical and Genetic mapping of Human Chromosome 11 Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk) PI : Peter Little (p.little@bc.ic.ac.uk) ACEDB_version : based on 4_1 with added map displays. ACEDB_version : based on 3_6 with added map displays. Data version : 1.0 Last Update : December 1995 WWW : http://chr11.bc.ic.ac.uk FTP : ftp.cc.ic.ac.uk Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Database : 22ace Species : Homo sapiens Subject : Physical map of human chromosome 22, genomic sequencing and more ACEDB_version : 4.1 Curator : Ian Dunham, id1@sanger.ac.uk Curator : Gareth Maslen, glm@sanger.ac.uk PI : Ian Dunham FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ Last_update : August 1995 Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions ---------------------------------------------------------------------------- Q5: What documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000. Primary documents from the developers are: * acedb -- A C. elegans Database: I. Users' Guide. * acedb -- A C. elegans Database: II. Installation Guide. * acedb -- A C. elegans Database: III. Configuration Guide. * Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z. The files are in TeX (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. ACEDB User's Guide in Japanese, from Tohru Sano, NEC, sano@exp.cl.nec.co.jp http://www.cbi.or.jp/~sano/ . (Postscript at http://www.labs.nec.co.jp/ . Follow the prompts to register and "download the software".) SampleDB, by Dave Matthews, is an ACEDB database constructed to demonstrate features of ACEDB, especially map and sequence displays. Anonymous ftp to probe.nalusda.gov:pub/acedocs/sampledb You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angistute.ps and angistute.hqx available by anonymous ftp at ncbi.nih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). URL : http://genome-www.stanford.edu/docs/aatdb_man.html. A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. URL : http://probe.nalusda.gov:8000/acedocs/overview.html. Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. Return to List of Questions ---------------------------------------------------------------------------- Q6: What other resources are available for ACEDB? A6: Perl and WWW tools The AGIS server at the National Agricultural Library provides tools for integrating version ACEDB with perl and the World-Wide Web. A WWW interface to 4.3 is available as ftp://probe.nal.usda.gov/pub/tools/webace.tar.gz. Instructions for this interface can be found at http://probe.nal.usda.gov:8000/acedocs/webace.html. (An earlier tool set is available as ftp://probe.nalusda.gov/pub/tools/acelib.tar.gz). For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/. Java Interface A Java interface to acedb is under active development. Involved people are Lincoln Stein, Jean Thierry-Mieg, Doug Bigwood, John Barnett, Sam Cartinhour. A test system can be seen at http://alpha.crbm.cnrs-mop.fr If you are interested in this approach, please contact mieg@kaa.crbm.cnrs-mop.fr X-client The 4_3 distribution contains the source code for a new version of the code called xclient. You need to recompile it (make xclient). Then, you create an empty database with the nematode models and strat xclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the montpellier server in the distrib server.wrm). The data will be saved locally and can then be viewed with a normal xace. The control of which data should be imported is very crude. In anay session, every object will be imported once. This should be rationalised, please let us know if this approach seems useful, and how it should be configured. (mieg@kaa.crbm.cnrs-mop.fr) The Developers' Archive Mike Cherry maintains an archive of tools that may be useful in curating ACEDB databases via gopher at ftp://genome-ftp.stanford.edu/pub/acedb_dev/ If you have a contribution send a message to Mike (cherry@genome.stanford.edu). The Biosci conference bionet.software.acedb There is a USENET/Biosci conference titled bionet.software.acedb created expressly for discussion of ACEDB. The best way to interact with the Biosci conferences is via a newsreader like rn, trn, tin or a WWW browser. Consult your system administrator for more information. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. All of the articles in biosci.software.acedb are archived by Biosci at http://www.bio.net/archives.html and by Mike Cherry at http://genome-www.stanford.edu/cgi-bin/biosci_acedb. If your WWW browser is configured properly you may be able to read the newsgroup at news:biosci.software.acedb. And more The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: * http://moulon.inra.fr/acedb/acedb.html for C. elegans data * http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data * http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html A how-to manual on the Moulon server is available at http://keck.tamu.edu/cgi/staff/ace-mosaic-howto.html The Genome Computing Group, Lawrence Berkeley Laboratory, has an anonymous ftp service at machine genome.lbl.gov which contains: * flydb - LBL's Drosophila Acedb-style database * 21bdb - LBL's Human Chromosome 21 Acedb-style database * querdb - LBL's query-language extensions to Acedb * metadata - LBL's compendium of Acedb database schema variants * macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version * There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to databases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: * 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). * 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier (Jean Thierry-Mieg et al), and the Integrated Genome Database project in Heidelberg (Otto Ritter, Detlef Wolf et al). Return to List of Questions ---------------------------------------------------------------------------- Q7: How should ACEDB be cited? A7: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions ---------------------------------------------------------------------------- Q8: Is ACEDB object-oriented? A8: From the ACEDB User's Guide: A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions ---------------------------------------------------------------------------- Q9: How can I get on/off the ACEDB announcements mailing list? A9: To get on or off the mailing list send mail to rd@sanger.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q6 for details] is on the mailing list. Return to List of Questions ---------------------------------------------------------------------------- Q10: When and where is the Next ACEDB Workshop? A10: A workshop is being planned for July 27 - August 9, 1997 in Ithaca, New York, USA. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/index.html. A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html. Also available online are collections of snapshots taken during the conference by Frank Eeckman and by Dave Matthews. For pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, see the online collections: * by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; * by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; * and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions ---------------------------------------------------------------------------- Q11:Who prepared this document & where is the current version? A11: This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The WWW version of this document is at: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html A text version is available via anonymous ftp at machine rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov This FAQ was created and maintained from 1993 - 1996 by Bradley K. Sherman. Major contributions in getting it off the ground were made by Mike Cherry, John McCarthy, and Doug Bigwood. Other contributors include: * Lisa Lorenzen * David Matthews * Edie Paul * Donn Davy * Eric De Mund * Sam Cartinhour It is currently maintained by Dave Matthews. Please cite as: Matthews, D.E., and B.K. Sherman, ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993-1996, approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov The GrainGenes Project is funded by the USDA ARS Plant Genome Research Program. Return to List of Questions ---------------------------------------------------------------------------- From owner-acedb@net.bio.net Mon Feb 10 22:00:00 1997 Path: biosci!KAA.CRBM.CNRS-MOP.FR!mieg From: mieg@KAA.CRBM.CNRS-MOP.FR (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: (none) Date: 11 Feb 1997 09:20:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: <9702111723.AA04277@beta.crbm.cnrs-mop.fr> NNTP-Posting-Host: net.bio.net Madame, monsieur, I found your email on the last acedb FAQ as I have to fill a report on what I do, which fortunatelly is not too often at cnrs, would you be kind enough to email me a short reply describing 1) Have you used, for how long, and do you still use acedb if no, you are done but please do not say no just to alleviate your work ! if yes, please answer some of the folowing questions # Questions about the code 2) On what machine 3) Do you care for: unix version on some other platform mac version pc windows version graphic client version server/client technology java visualisation 4) Do you crash often, loose data ever ? 5) Which are the bad or missing displays that should be improved # Questions about your own data 6) If not confidential: the subject 7) How many objects in the data base, see class command from tace 8) How many different ace databases you run 9) Do you distribute, how many users do you have ? 10) Did you ever produce a cd 11) Do you have/care for/need a web interface to your data # Plans for the future 12) Do you intend to switch to something else, if yes what/why ? or to keep using acedb ? # Wish list !! your most desired new feature, you never know !! it might be granted Thank you for your collaboration Danielle et Jean and i ll copy all your answers to Richard, so he won't have to ask again. From owner-acedb@net.bio.net Thu Feb 13 22:00:00 1997 Path: biosci!AAAS.ORG!WYEE From: WYEE@AAAS.ORG (WYEE) Newsgroups: bionet.software.acedb Subject: Bioinformatics Job Skills: Next Wave Special Issue Date: 14 Feb 1997 08:24:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: <00025777.1205@aaas.org> NNTP-Posting-Host: net.bio.net Please forward to interested members of your scientific community. BIOINFORMATICS SKILLS SPECIAL NEXT WAVE ISSUE Bioinformatics is arguably the "next big thing" to hit biology and computer science. The Next Wave site (www.nextwave.org) is following up last year's general bioinformatics New Niche feature with a special issue on bioinformatics skills. We look at the skills that are in highest demand, career directions, and the future of this emerging field. --- What Hiring Managers Want: Bioinformatics group leaders at Bayer, Myriad Genetics, TIGR, and Wyeth-Ayerst Research discuss the skills they value most. --- Hot Skill Sets: Eight people with diverse industry and academia backgrounds discuss which skills they've needed most and how they acquired them. Career tips from bioinformatics researchers at SmithKline Beecham, Millenium Pharmaceuticals, Mercator Genetics, the Keck Center for Computational Biology, and more. --- Past, Present, and Future: An overview on the field from a Canadian scientist and start-up company consultant. --- Virtual Education: Bioinformatics skill-building classes and tools accessible on and off the Web. --- What's Next: Predictions for the post-genomic era. Experts offer their educated guesses. The URL for Science's Next Wave is www.nextwave.org We encourage you and your peers and colleagues to visit the Next Wave site. Science's Next Wave is a Web site published by Science magazine and the American Association for the Advancement of Science (AAAS). If you would not like to receive e-mail notices about future Next Wave features which present career information for scientists, please let us know. The Editors of Science's Next Wave E-mail: nextwave@aaas.org From owner-acedb@net.bio.net Sat Feb 15 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Dr Mark Watson Newsgroups: alt.comp.databases,bionet.molbio.proteins.fluorescent,bionet.software.acedb,comp.database,comp.databases,comp.databases.xbase.misc,bionet.software,sci.med.informatics,sci.stat.math,sci.stat.edu,sci.stat.consult Subject: qestionnaire data analysis Date: 16 Feb 1997 10:53:05 -0800 Organization: The University of Western Australia Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <3302A0A0.56E2@cyllene.uwa.edu.au> Reply-To: mwatson@cyllene.uwa.edu.au NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molbio.proteins.fluorescent:946 bionet.software.acedb:1107 comp.databases:44694 comp.databases.xbase.misc:11633 bionet.software:17901 sci.med.informatics:8466 sci.stat.math:13749 sci.stat.edu:12463 sci.stat.consult:23525 Dear netters I am about to begin data entry/ data analysis (statistical) from a medical questionnaire. The questionnaire consists of both open ended and closed ended questions. I need to 1) enter the data from the questionnaires and 2) Perform statistical type analyses of this data. I have no previous experience in this area but have access to SPSS. I would like to know if this is the most appropriate package to use or if there are better / easier ways of doing it. All suggestions will be appreciated Please reply to my e-mail account _____________________________________________________________ Hassan Vally BSc(Hons) PhD Student Dept of Medicine Ph (09) 346 3464 QEII Medical Centre Fax (09) 346 2816 4th Floor, G Block email hvally@cyllene.uwa.edu.au Verdun St Nedlands, 6907 Perth, Western Australia From owner-acedb@net.bio.net Sat Feb 15 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Doug Bigwood Newsgroups: bionet.software.acedb,bionet.software Subject: ACEDB 1997 Conference Announcement (ACE97) Date: 16 Feb 1997 10:54:49 -0800 Organization: Genome Informatics Group, University of Maryland Lines: 81 Sender: daemon@net.bio.net Distribution: world Message-ID: <3304900C.2CF8@gig.usda.gov> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software.acedb:1108 bionet.software:17902 This is the first announcement regarding the ACEDB 1997 Conference (ACE97). Not all of the details have been worked out, but here are facts as they are known now. *************************************************************************** NOTE: If you are planning on attending please send a message to Doug Bigwood so that we can plan accordingly. Thank you. *************************************************************************** Location: Cornell University, Ithaca, New York, USA Dates: July 27 through August 9 Major Sponsors: USDA Plant Genome Initiative (ARS/NAL) and Cornell University Format: Similar to ACE95, but the program is not set (Formal Conference: 2-3 days of presentations, 1-2 days of tutorials - Workshop: remainder). A future announcement will cover the details for submitting papers for presentation. Workshop topics will also be solicited. Costs: Registration Fee: As low as possible (hopefully not more than $100 for the full 2 weeks and $50 for the formal conference). Credit cards will be accepted. Housing (dormitory): $18/night single, $15/night double (per person) - hotels are available close to campus for those wishing more luxurious accommodations. Meals: A meal plan is available for a campus cafeteria (costs to be announced), several eating establishments are available close by. We are looking into having a continental breakfast served in the dormitory each day (this would add a small cost). There will be a morning and afternoon coffee break each day. Registration Deadline: June 13 (registration *will* be limited, but hopefully the limit will allow us to accommodate all who wish to attend). Registration forms will be available soon. Organizers: Dave Matthews, Cornell University Doug Bigwood, Genome Informatics Group, University of Maryland Future Announcements: More information will be posted on the bionet.software.acedb newsgroup as it becomes available. The most up-to-date information regarding the conference will be available at: http://probe.nalusda.gov:8000/ace97.html Miscellaneous Information: Richard Durbin and Jean Thierry-Mieg will attend. A well equipped computer facility close to the dormitory will be utilized (see http://www.cadif.cornell.edu) A barbeque (for conference attendees) and a banquet (for workshop attendees) are planned. The weekend of Aug. 2-3 will be free. There will be absolutely *no* peacocks present. From owner-acedb@net.bio.net Mon Feb 17 22:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: questions about Macace Date: 18 Feb 1997 10:38:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: <9702181838.AA15673@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Greetings Pierre and Louis-Marie! > Date: Tue, 18 Feb 1997 17:19:17 +0100 > To: "Dave Matthews" > From: raboin@cirad.fr (Louis Marie Raboin) > Subject: Re: questions about Macace > > Greetings from Montpellier, Dave ! > > We are making a lot of progress with our Acedb database on banana molecular > data. > We 've got it on UNIX as well as on Mac. We 've got a few questions about > the latter. First Macace requires more than 30 Megabytes RAM to run. That > is a lot for the average capability of our macs. We would like to know > wether it is possible to lower this memory requirement and how to go about > it. I believe you can run in only 16 MB (including virtual memory) as long as you aren't loading data, but you need 32 MB to load. So I suppose you could do all your loading on your biggest Mac and then copy the folder "database" to the other ones. > The other point is Macace Tablemaker which doesn't seem to work. We 've > got no choice in the selector keyset. We checked on the RiceMac CDROM and > it's the same. Maybe this has been fixed in later versions (We've got > Macace 4.1). Yes, Tablemaker seems to be completely nonfunctional in Macace 4.1b1, which is the latest version as far I know. > We wonder if you 're working with this Mac platform. Anyway we > welcome any information. We 're asking you because we couldn't contact > Frank Eeckman. Maybe you know his new Email address. No I don't. You might try Cyrus Harmon, sly@fly2.berkeley.edu, or Richard Durbin, rd@sanger.ac.uk. > Thanks a lot. > > best regards, > Pierre and Louis-Marie, > > ---------------------------------------------------------------------------- > Louis Marie Raboin > CIRAD-AGETROP > 2477, av du val de Montferrand - BP 5035 > 34032 Montpellier cedex 1 FRANCE > tel: 04/67/61/56/31 > raboin@cirad.fr > ---------------------------------------------------------------------------- You're welcome, I hope this is a little help. I'll cc this to the acedb newsgroup, maybe you can get more informed answers from other folks. best, - Dave From owner-acedb@net.bio.net Mon Feb 17 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsxfer3.itd.umich.edu!rill.news.pipex.net!pipex!warwick!bignews.shef.ac.uk!not-for-mail From: xms@dcs.shef.ac.uk (Xiao Mang Shou) Newsgroups: bionet.software.acedb Subject: Questions on setting up a new database Date: 18 Feb 1997 22:07:09 GMT Organization: Department of Computer Science, University of Sheffield Lines: 18 Message-ID: <5ed96d$heu@bignews.shef.ac.uk> NNTP-Posting-Host: tiger.dcs.shef.ac.uk X-Newsreader: TIN [version 1.2 PL2] Dear Netter, I'm new to the ACEDB package. I want to use ACEDB to create my own database. I have tried to set up a test database by creating models.wrm, classes.wrm, tags.wrm files under wspec/. I have also created a *.ace file under rawdata/. But every time I started acedb, it caused core dump. If any of you knows what's going wrong, would you please let me know? I've tried both with and without the system's original files under the database dir. Both ways caused core dump. -- ----------------------------------------------------------------- Xiao Mang Shou email: X.Shou@dcs.shef.ac.uk From owner-acedb@net.bio.net Tue Feb 18 22:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Mazda Hewitt Newsgroups: bionet.software.acedb Subject: Re: Questions on setting up a new database Date: Wed, 19 Feb 1997 10:13:03 +0000 Organization: John Innes Centre Lines: 18 Message-ID: <330AD22F.2781@bbsrc.ac.uk> References: <5ed96d$heu@bignews.shef.ac.uk> NNTP-Posting-Host: jiio10.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V3.2 alpha) To: Xiao Mang Shou hmm, I need a little bit more information to figure it out straight away, what system are you running acedb on? Did you get a precompiled version, or did you compile it for yourself? What version of acedb are you using? usually all you need to do is to download the binary release for your system, create an acedb directory, move the binary release into the acedb directory, untar the file, create a database directory in the acedb directory, add your user name to passwd.wrm in the wspec directory, then in the acedb directory type bin/xace . then that should work. Mazda From owner-acedb@net.bio.net Wed Feb 19 22:00:00 1997 Path: biosci!ioks.uio.no!peter.kierulf From: peter.kierulf@ioks.uio.no (KIERULF Peter) Newsgroups: bionet.software.acedb Subject: m-RNA standard- quantitation Date: 20 Feb 1997 02:58:15 -0800 Organization: Ullev=?iso-8859-1?Q?=E5l Sykehus Oslo?= Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <330C2E58.25F3@ioks.uio.no> Reply-To: peter.kierulf@ioks.uio.no NNTP-Posting-Host: net.bio.net Hi there, Any one have any good suggestion to preparation og m-RNA stand with poly-a tail (20-40 aaa-s) for PAI 2 (Plasminogen activator inhibitor 2)?. Thanks for you advices Peter Kierulf Clinical Chemistry Dep. Ulleval University Hospital N-0407 OSLO, NORWAY Telephone: +47 22 11 94 86 Telefax: +47 22 11 81 89 _-----------------------------------Mobil telphone: 922.85111 E-mail (RFC Formate): peter.kierulf@ioks.uio.no E-mai. (SA Formate): /G=peter/S=kierulf/OU=ioks/O=uio/PRMD=uninett/C=no From owner-acedb@net.bio.net Wed Feb 19 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!newsxfer3.itd.umich.edu!rill.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-lyon1.fr!newsserver.cilea.it!sirio.cineca.it!galileo.polito.it!usenet From: "Andrea Lionetti" Newsgroups: bionet.software.acedb Subject: software SQL*NET Date: 20 Feb 1997 07:46:58 GMT Organization: DELGROSSO S.p.A. Lines: 8 Message-ID: <01bc1f01$bc7f77f0$a30374c2@delgrosso> NNTP-Posting-Host: delgrosso.torino.alpcom.it X-Newsreader: Microsoft Internet News 4.70.1157 Gentile lettore, mi č utile sapere se sul mercato ci sono altri software che mettono in connessione il server con database ORACLE con il PC-ACCESS. Ciao. -- Andrea Lionetti Nichelino - TO - Italy E-Mail: delgrosso@clean.it http:\\www.clean.it From owner-acedb@net.bio.net Wed Feb 19 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!rill.news.pipex.net!pipex!warwick!bignews.shef.ac.uk!not-for-mail From: xms@dcs.shef.ac.uk (Xiao Mang Shou) Newsgroups: bionet.software.acedb Subject: RE: Setting up a new database Date: 20 Feb 1997 17:26:58 GMT Organization: Department of Computer Science, University of Sheffield Lines: 24 Message-ID: <5ei1h2$pgn@bignews.shef.ac.uk> NNTP-Posting-Host: tiger.dcs.shef.ac.uk X-Newsreader: TIN [version 1.2 PL2] Thanks those who have replied to my previous message. I am using acedb43 on sun4. In order to set up my own database, I first cleared all files under database dir, deleted models.wrm file under wspec dir. Then I created my own models.wrm file and a *.ace file under rawdata/. The problem is after I started acedb, the main window still listed classes like Map, Author, Sequence, Clone, etc. The class I defined in the models.wrm was not shown in the main window, but it was there when clicking Class menu. After I read the *.ace file, the Class I defined was still not shown in the main window. I would like to know why the main window always displays Map, Author etc. classes even though I already deleted the default models.wrm? How can I let the system display classes that only defined in models.wrm? Also I found even I made changes to models.wrm, acedb would always load the previous one. I can only delete all files under database/ in order to reflush the changes in models.wrm. Is that right? -- ----------------------------------------------------------------- Xiao Mang Shou email: X.Shou@dcs.shef.ac.uk From owner-acedb@net.bio.net Thu Feb 20 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!rill.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!rain.fr!news.remcomp.fr!invivo!eWattel.lille From: eWattel.lille@invivo.remcomp.fr (Eric Wattel) Reply-To: eWattel.lille@invivo.remcomp.fr Newsgroups: bionet.software.acedb Distribution: world Subject: DNA bending and DNA-protein interaction Date: 21 Feb 1997 10:37:13 GMT Message-ID: <154791837.1999873@invivo.remcomp.fr> Organization: inVivo Lines: 8 We would like to test bending proprieties and possible protein - DNA interaction of short DNA sequences (~35 pieces of 50-2500 pb) using an appropriate software. Mac or PC software would be welcome. Thanks in advance end ******************************************************************** Sent by inVivo. The BBS of Life Sciences, Paris, France, info@invivo.edu http://www.invivo.net/ From owner-acedb@net.bio.net Mon Feb 24 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!newspump.sol.net!mindspring!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-feed5.bbnplanet.com!umass.edu!robby.oit.umass.edu!emily.oit.umass.edu!not-for-mail From: bonghack@emily.oit.umass.edu (BONG-HACK LEE) Newsgroups: bionet.software.acedb Subject: HELP ON INFORMATION REGARDING YEAR 2000 COMPLIANCE Date: 25 Feb 97 19:38:31 GMT Organization: University of Massachusetts, Amherst Lines: 6 Message-ID: <33133fb7.0@robby.oit.umass.edu> NNTP-Posting-Host: robby.oit.umass.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Dear Netters: I am looking for the particular software which can search all spread sheets which I created by using LOTUS 123 and identify which ones are all right for year 2000 or which are not O.K for year 2000. Or, any information or idea will be appreciated. Thanks in advance! From owner-acedb@net.bio.net Mon Feb 24 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!news-peer.gsl.net!news.gsl.net!news-tokyo.gsl.net!news.gsl.net!ruby.hknet.com!usenet From: "PLAM" Newsgroups: bionet.software.acedb Subject: ACE Date: 25 Feb 1997 07:08:35 GMT Organization: ASMG Lines: 4 Message-ID: <01bc22ef$bea8e880$24f143ca@hknet> NNTP-Posting-Host: mp018.hknet.com X-Newsreader: Microsoft Internet News 4.70.1155 Hi hello, Is there anybody who has ACE certification information or know how to be a ACE. Kindly to contact me. Thanks a lot! From owner-acedb@net.bio.net Wed Feb 26 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!insync!uunet!in3.uu.net!198.151.175.33!news.xensei.com!news From: chi@healthtech.com (Cambridge Healthtech Institute) Newsgroups: bionet.software.acedb Subject: Cambridge Healthtech Institute’s MOLECULAR EVOLUTION Date: Thu, 27 Feb 1997 18:15:22 GMT Organization: Cambridge Healthtech Institute Lines: 129 Message-ID: <5f4iqh$qqc@xensei3.xensei.com> Reply-To: chi@healthtech.com NNTP-Posting-Host: chi.xensei.com X-Newsreader: Forte Free Agent 1.0.82 Cambridge Healthtech Institute’s MOLECULAR EVOLUTION April 24-25, 1997 Copley Plaza, Boston, Massachusetts Co-sponsored by: Canji, Inc., Pharmacia Biotech, and PharmaGenics A large number of biomedical applications involve the search for compounds with improved activity or performance. The application of molecular evolution is proving to be extremely well suited for this purpose, particular for identification of nucleic acids or peptides. Genetics makes it possible to employ sequential rounds of screening and selection, followed by further mutation, to allow for the generation of compounds adapted for a desired target or under specific conditions. Phage display and other related techniques have been used extensively for this purpose. Examples of the development of antibodies, mutated proteins, and a range of research, selection, and therapeutic applications are covered in detail. Learn how leaders in this field are taking advantage of the power of this technology and how you might benefit from making greater use of it by attending this timely event. NUCLEIC ACID EVOLUTION In Vivo and In Vitro Applications of Nucleic Acid Ligands Dr. Daniel W. Drolet, NeXstar Pharmaceuticals (confirmed) Mirror-Image RNA Ligands Dr. Jens P. Furste, Freie Universitst Berlin (confirmed) Aptamer Evolution: Prospects for Diagnostics and Therapeutics Dr. Andrew D. Ellington, Indiana University (confirmed) Ribozymes from Random Sequences: Dr. David Bartel, Whitehead Institute and Massachusetts Institute of Technology (confirmed) ENGINEERING PROTEINS AND ANTIBODIES Exploiting the Diversity of Large Human Antibody Libraries Dr. John McCafferty, Cambridge Antibody Technology Ltd. (confirmed) Molecular Evolution of Proteins, Pathways and Viruses by DNA Shuffling Dr. Willem Stemmer, Maxygen, Inc. (confirmed) In Vitro Selection of Peptides Acting on NMDA Glutamate Receptors Dr. Min Li, John Hopkins School of Medicine (confirmed) Synthesis Based Molecular Design of Antibodies and Proteins: Dr. William D. Huse, Ixsys, Inc. (confirmed) Dr. Manuel Baca, Genentech, Inc. (confirmed) RESEARCH AND SELECTION USING PHAGE DISLAY Cloning Novel Genes with Phage-Displayed Peptide Ligands Dr. Brian Kay, University of North Carolina at Chapel Hill (confirmed) Adenovirus Expression Systems in Conjunction with Autofluorescent Proteins: Potential Use in the Screening of Peptide Libraries Dr. Luc Peloquin, Quantum Biotechnologies Inc. (confirmed) Functional Epitope Mapping by Negative Selection of Phage-Displayed Randomized Protein Libraries Dr. Laurent Jespers, Flanders Interuniversity Institute for Biotechnology (confirmed) Automated Affinity Based Screening Using Serial Column Chromatography Interfaced with Mass Spectrometry Dr. Satish Jindal, ChemGenics Pharmaceuticals (confirmed) Use of Combinatorially Generated Phage Displayed Ligands to Develop Engineered Microprotein Ligands for Large Scale Biotherapeutic Purification Dr. John Maclennan, Dyax Corporation (confirmed) Identification of Optimal Ligands for Protein Domains Using Oriented Peptide Libraries Dr. Zhou (Sonny) Songyang, Harvard Medical School (confirmed) THERAPEUTIC DEVELOPMENTS USING PHAGE DISPLAY Identification of Amino Acids Critical for the Activity of a Peptide Mimetic of Erythropoietin and Discription of a Minimal Functional Epitope Dr. Dana Johnson, R.W. Johnson Pharmaceutical Research Institute (confirmed) Combinatorial Methods and Directed Evolution Applied to Staphylococcal a-hemolysin, a Pore-Forming Protein Dr. Hagan Bayley, Worcester Foundation for Biomedical Research (confirmed) Human Protein Display: A New System for Discovering Drug Binding Targets Dr. Allan Peng, GeneMax, Inc. (confirmed) Novel Approaches for Targeting Tumors and Inhibiting Metastasis Dr. Renata Pasqualini, La Jolla Cancer Research Center, The Burnham Institute (confirmed) Sampling Peptide Space for Cell-Targeting Peptides Dr. Stephen A. Johnston, University of Texas, Southwestern Medical Center, (confirmed) Cloning Using Phage Display Dr. Bob Shopes, Tera Biotechnology Corporation (confirmed) Establishing Site Directed Assays Using Phage Displayed Libraries of Peptides and Antibodies Dr. Arthur J. Blume, DGI BioTechnologies, L.L.C. (confirmed) From the rapid progess of combinatorial chemistry and genetics an interest has been generated in the selection of random peptides from target proteins and in investigating ligand-receptor interactions. Some challenges that will be examined are the screening of combinatorial libraries for selecting high-affinity ligands against target molecules, following the sequential cycles of random mutagenesis and screening to direct the evolution of enzymes, and developing new techniques such as phage display for optimum peptide /receptor binding. The expectation that from the selection and use of phage display, proteins for therapeutics and drug discovery may be developed. Advance registration March 7, 1997 poster deadline March 21, 1997 For registration and hotel information, please contact: Cambridge Healthtech Institute 1037 Chestnut Street Newton Upper Falls, MA 02164 USA Phone: 617-630-1300 Fax: 617-630-1325 e-mail: chi@healthtech.com http://www.healthtech.com/conferences/ ______________________________ Cambridge Healthtech Institute 1037 Chestnut Street Newton Upper Falls, MA 02164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tel: 617.630.1300 fax: 617.630.1325 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ inquiries@healthtech.com World Wide Web http://www.healthtech.com/conferences From owner-acedb@net.bio.net Wed Feb 26 22:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Mazda Hewitt Newsgroups: bionet.software.acedb Subject: Setting up JADE Date: Thu, 27 Feb 1997 15:27:59 +0000 Organization: John Innes Centre Lines: 28 Message-ID: <3315A7FF.41C6@bbsrc.ac.uk> NNTP-Posting-Host: jiio10.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) Hello all, I've been setting up the jade distribution on my DEC alpha. I've compiled up the beta of 4.4 and implemented the server and the x-client. I've added the jade model and parsed tables.ace and meta.jave.ace. This worked ok. The aceclient attaches to the server and can access the data as normal. Jade will start but it gives me an error: Jade global init Graphics sun.awt.motif.X11Graphics[0,0] Jade global init 2 Jade global init Graphics sun.awt.motif.X11Graphics[0,0] Thread running 2 Jade global init Graphics sun.awt.motif.X11Graphics[0,0] Jade global init 2 Jade global init Graphics sun.awt.motif.X11Graphics[0,0] Thread running finished Jade global init Graphics sun.awt.motif.X11Graphics[0,0] Jade global init Graphics sun.awt.motif.X11Graphics[0,0] Jade global init Graphics sun.awt.motif.X11Graphics[0,0] Jade global init Graphics sun.awt.motif.X11Graphics[0,0] JadeSelector construct JadeSelector init find_one failed on Jade:default I wonder if you can help. Mazda From owner-acedb@net.bio.net Wed Feb 26 22:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: correction: data containing " -C" Date: 27 Feb 1997 13:08:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9702272108.AA02849@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > Is there any way to escape " -C" in a .ace file, so values containing this > string can be loaded, instead of being treated as a comment? Sorry, badly-put question. I meant values that _begin_ with -C. Like Locus : x Probe -Cde123 Dave From owner-acedb@net.bio.net Wed Feb 26 22:00:00 1997 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: data containing " -C" Date: 27 Feb 1997 12:59:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <9702272058.AA02825@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Is there any way to escape " -C" in a .ace file, so values containing this string can be loaded, instead of being treated as a comment? - Dave From owner-acedb@net.bio.net Fri Feb 28 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Mar 1997 02:00:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199703011000.CAA02976@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net