From owner-acedb@net.bio.net Fri Dec 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!EU.net!peer-news.britain.eu.net!warwick!bham!bhamcs!news.ox.ac.uk!news From: Ewan Birney Newsgroups: bionet.software.acedb Subject: manual editing Date: Sat, 02 Dec 1995 12:16:08 +0100 Organization: Oxford University Lines: 26 Message-ID: <30C03578.41C6@molbiol.ox.ac.uk> NNTP-Posting-Host: nmro.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b3 (X11; I; IRIX 5.3 IP22) I have a small ACeDB database that I am playing around with: Most of the data is inputted automatically from database searching routines but there is a fair amount of "manual" editing required - things which have to be removed/ renamed/altered and comments added (as objects themselves rather than comments to the tags). I was wondering what the best way of doing this was - At the moment I am making little .ace files with -D 's in to remove the data, but it would be good to have some more automated systems (running through - WWW? Tcl?) which one could imagine either writting the .ace files themselves (probably using tace to get at the ACeDB data to display to the user ) and then the user loading those .ace files into tace/xace or perhaps running the "input" side of it from the WWW CGI bin - but then, that requires giving hte WWW "user" permissions on the ACeDB database which I don't particularly like. How do other people handle this? DO you have any advice for this sort of manual editing... thanks alot ewan From owner-acedb@net.bio.net Mon Dec 04 22:00:00 1995 Path: biosci!MH1.LBL.GOV!mccarthy From: mccarthy@MH1.LBL.GOV (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Software to create #map_location data from MapMaker output Date: 5 Dec 1995 15:13:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <199512052312.PAA13474@mh1.lbl.gov> Reply-To: JLMcCarthy@lbl.gov NNTP-Posting-Host: net.bio.net BNL's Cotton Genome Project is building genetic linkage maps using MapMaker. The project wants store and display gmap location information for each marker using ACEDB. We hope that perhaps someone else has already written some software to do at least part of our task of extracting the data from MapMaker output files and getting it into ACEDB via .ace files. The specific way the project is using MapMaker is as follows: 1. For each chromosome/linkage group/chromosome arm map, find a set of "Landmark Loci" with threshold LOD scores of at least 3. a. Denote these as Main_Marker for the map in ACEDB. b. Compute Position for each Locus from cumulative inter-marker distances 2. Use MapMaker's "pairwise" command to produce a table of distances and LOD scores for each of the other markers with each of the framework markers for that chromosome/linkage group/chromosome arm. 3. Use data from #3 to compute map locations for non-framework loci, using distances from markers with maximum LOD scores and using some kind of inverse of the LOD score for Error (horizontal gmap placement) in ACEDB. If anyone knows of software that already does something like this, please send me email. Even if you don't know of anything that creates .ace files, perhaps you might suggest where we might inquire to see whether someone has done something to simply extract map positions and errors from MapMaker output. I'll be glad to post my findings, if any, back to the newsgroup. Thanks, -John +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720-9000, U.S.A. | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Tue Dec 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!newsfeed.ACO.net!fuw.edu.pl!news.nask.org.pl!gemini.coi.pw.edu.pl!ien1!syrobak From: syrobak@ien1 (Sylwester Robak) Newsgroups: bionet.software.acedb Subject: Re: ACEDB Genome Database Software FAQ Date: 5 Dec 1995 17:38:07 GMT Organization: Warsaw University of Technology Lines: 1139 Message-ID: <4a201v$net@gemini.coi.pw.edu.pl> References: <49kql5$5vf@overload.lbl.gov> NNTP-Posting-Host: ien1.ien.pw.edu.pl X-Newsreader: TIN [version 1.2 PL2] ACEDB FAQ Pseudouser (acedbfaq@s27w007.pswfs.gov) wrote: : Archive-name: acedb-faq : Last-modified: 11/30/95 : Version: 1.26 : ACEDB FAQ : ********* : Curated by: Bradley K. Sherman : Frequently Asked Questions about ACEDB : ++++++++++++++++++++++++++++++++++++++ : o Q0 : What is ACEDB? : o -------------------- : o Q1 : What is the current version of ACEDB? : o ------------------------------------------- : o Q2 : What hardware/software do I need to run ACEDB? : o ---------------------------------------------------- : o Q3 : Where can I get ACEDB? : o ---------------------------- : o Q4 : What ACEDB databases exist? : o --------------------------------- : o Q5 : What documentation exists for ACEDB? : o ------------------------------------------ : o Q6 : What other resources are available for ACEDB? : o --------------------------------------------------- : o Q7 : How should ACEDB be cited? : o -------------------------------- : o Q8 : Is ACEDB object-oriented? : o ------------------------------- : o Q9 : How doe one get on/off the ACEDB announcements mailing list? : o ------------------------------------------------------------------ : o Q10 : When and where is the next ACEDB Workshop? : o ------------------------------------------------- : o Q11 : Who prepared this document & where is the current version? : o ----------------------------------------------------------------- : 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 version is 4_1 (as of 10 August 1995). : A test (beta) version of ACEDB 4.0b4 (5/95) is available. : A Macintosh version is available as version 2.0b4. : 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. : o Unix and X11: : o Sun/SunOS 4.x : o Sun/Solaris : o DEC DECstation3100, 5100 etc. : o DEC Alpha/OSF-1 : o Silicon Graphics Iris series : o PC 386/486/Pentium with Linux (free Unix) Jeff Bryer, : jbryer@darwin.mbb.sfu.ca and Ken Clark provide a linux version of 4.1 and : a complete C. elegans data set at trog.mbb.sfu.ca in /pub/acedb as : bin.linux.4_1.tar.Z. : o There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM : R6000, Convex. You may have to contact the developer responsible for the : port to make these real. : o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: : patrick@wbar.uta.edu email: phil@decster.uta.edu : o Macintosh: : o [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. : o ACEDB for The NEC EWS4800 is available via anonymous ftp at ftp.nec.co.jp : (192.135.93.2) in /pub/packages/acedb/ace2. Contact Tohru Sano Fundamental : Research Laboratories NEC Corporation Tsukuba, 305, JAPAN, e-mail: : sano@exp.cl.nec.co.jp, FAX: +81-298-56-6136, VOICE: +81-298-50-1507 : (Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems : SPARCstation II, and users can interact using Macintoshes and PC-clones by using : X11 implementations for the personal computers and a LAN. --bks) : X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install : new fonts on your machine be sure to run bldfamily(1) so that they are : available. : Return to List of Questions : Q3: Where can I get ACEDB? : ++++++++++++++++++++++++++ : A3: : +++ : The standard ACEDB source and binaries are available in the following public : access accounts (anonymous ftp sites) accessible via Internet: : o lirmm.lirmm.fr in pub/acedb : o cele.mrc-lmb.cam.ac.uk in pub/acedb : o ncbi.nlm.nih.gov in repository/acedb : o bioinformatics.weizmann.ac.il in pub/databases/acedb. : MacAce is available from: : o genome.lbl.gov in pub/macace : o cele.mrc-lmb.cam.ac.uk in pub/acedb/macace : Linux; ACEDB version 4.1 (and earlier versions) for Linux 2-10: : o trog.mbb.sfu.ca /pub/acedb as bin.linux.4_1.tar.Z. : ACEDB for The NEC EWS4800: : o ftp.nec.co.jp in /pub/packages/acedb/ace2. : Return to List of Questions : Q4: What ACEDB databases exist? : +++++++++++++++++++++++++++++++ : A4: : +++ : In alphabetic order by Database name : ------------------------------------ : [Curators, please submit changes as new paragraphs] : Database : AaeDB : Species : Aedes aegypti (Mosquito) : Last_update : December 1994 : ACEDB_version : 3.0 : WWW : http://klab.agsci.colostate.edu/ : Curator : Dennis Knudson, dknudson@lamar.colostate.edu : Curator : Martin Ferguson, martinf@lamar.colostate.edu : Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu : Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu : Contact : aaedbmgr@klab.agsci.colostate.edu : Database : AAtDB : Species : Arabidopsis thaliana : Current version : 3-5 : Last_update : August 1995 : Curator : John Morris : Contact : curator@frodo.mgh.harvard.edu : Availability : UNIX and Macintosh versions via anonymous ftp : FTP : Macintosh version - weeds.mgh.harvard.edu in aatdb/MacAAtDB : FTP : UNIX version - weeds.mgh.harvard.edu in aatdb/aatdb.3x : FTP : probe.nalusda.gov in pub/aatdb : Gopher : weeds.mgh.harvard.edu/ : Gopher : probe.nalusda.gov:7004/ : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://weeds.mgh.harvard.edu/ : WWW : http://probe.nalusda.gov:8300/plant/ : Database : AboutDB : Curator : Staffan Bergh, staffan@biochem.kth.se : Subject : ACEDB itself (meta-meta-metadata) : ACEDB_version: 3.0 : Last_update : July 1995 : WWW : http://www.biochem.kth.se/AboutDB.html : Database : ACeDB : Species : Caenorhabditis elegans : Current version: 4-8 : Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr : Curator : Richard Durbin, rd@mrc-lmb.cam.ac.u : Curator : Sylvia Martinelli, sylvia@sanger.ac.uk : Last_update : August 1995 : Availability: Unix and Macintosh versions via anonymous ftp : FTP: USA - ncbi.nlm.nih.gov in repository/acedb : FTP: England - ftp.sanger.ac.uk in pub/acedb : FTP: France - lirmm.lirmm.fr in genome/acedb : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/other/ : DataBase : AceMap : Species : Homo sapiens : Subject : Physical mapping data for human chromsome X : ACEDB_version : 4.1 : Curator : Hugues Roest Crollius, croillius@mpimg-berlin-dahlem.mpg.de : PI : Hans Lehrach : FTP : ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap : Comment: Get the README file in the directory above. : Contact : Max-Planck-Institut fur Moleulare Genetic, Ihnestrasse 73, 14195 : Berlin, Germany : Availability : beta release of the X chromosome data/models via anonymous ftp : FTP : ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap : Last_update : August 1994 : Database : AGsDB (A Genus species Database) : Species : Aspergillus nidulans : Species : Neurospora crassa : Species : Bos taurus (cow) : Species : Homo sapiens anchor loci : Species : Gossypium hirsutum (cotton) : Species : Neurospora crassa : Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast : Curator : Leland Ellis, leland@straylight.tamu.edu : Last_update : March 1994 : ACeDB_version : 3.0 : Subject: Contains extensions to the Human C21 Models to provide for multiple : species, and queries between species via Homologs (e.g., cell cycle loci with : links via Homologs between Aspergillus and budding C. cerevisiae) and fission : (S. pombe yeast); interacting loci via defined Interactions for each locus : Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have : been folded into AGsDB, and are not being developed futher as individual species : databases. : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/other/ : WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html : Database : Alfagenes : Species : Medicago sativa (alfalfa) : Curator : D. Z. Skinner, dzolek@ksu.ksu.edu : Telephone : (913) 532-7247 : ACEDB_version : 3.0 : Last_Update : July 1995 : FTP : probe.nalusda.gov in pub/alfagenes : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : Database : BeanGenes : Species : Phaseolus and Vigna : Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu : ACEDB_version : 1.0 : Last_updated : January 1995 : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : Database : ChlamyDB : Species : Chlamydomonas : Curator : Elizabeth Harris : Contact : chlamy@acpub.duke.edu : ACEDB_version : 3.0 : Data_version : 1.2 : Last_update : August 1995 : Availability : Macintosh and UNIX versions via anonymous ftp : FTP : probe.nalusda.gov in pub/chlamydb : Gopher : ftp.duke.edu/11/pub/chlamy : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : Database : CIMMYT (Wheat International Nursery Data) : Species : Triticum spp. : ACEDB_version : 4.0 : Last_update : September 1995 : Curator : Hector Sanchez, hsanchez@cimmyt.mx : FTP : probe.nalusda.gov in pub/cimmyt : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/related/ : Database : CottonDB : Species : Gossypium hirsutum (cotton) and related species : PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research : Laboratory, 2765 F&B Road, College Station, Texas 77845 : Curator : Gerard R. Lazo, lazo@tamu.edu : Curator : Sridhar Madhavan, msridhar@tamu.edu : Phone : 409-260-9311 : Fax : 409-260-9333 : Last_update : January 1995 (version 95.1) : ACEDB_version : 3.0 : FTP : probe.nalusda.gov in pub/cottondb : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : Data_submission_form : http://algodon.tamu.edu/ : Database : CSNDB : Focus : Cell Signalling Molecules and Interactions : Contact : Takako Igarashi, National Insitute of Health Sciences, Division of : Chem-Bio Informatics, Setagaya-ku, Tokyo, Japan 158, taka@nihs.go.jp : Database : EofD (Encyclopaedia of the Drosophila) : Species : Drosophilidae (primarily D. melanogaster) : Availability : Macintosh CD-ROM and SunOS executables via anonymous ftp : Developer : Suzanna Lewis, suzi@fly2.berkeley.edu : Developer : Cyrus Harmon, sly@fly2.berkeley.edu : Developer : Edward Welbourne, eddy@gen.cam.ac.uk : Collaborator : The FlyBase Consortium, flybase-help@morgan.harvard.edu : Collaborator : The Berkeley Drosophila Genome Project, : flygenome@maillink.berkeley.edu : Gopher : fly.bio.indiana.edu:70+/11/Flybase : WWW : http://fly2.berkeley.edu:3512/EofD.html : Database : EthnobotDB (orldwide plant uses) : Species : wide range of plant species : ACEDB_version : 4.0 : Last_update : June 1995 : Comment : Converted to ACEDB from the original SQL database. : Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov : Curator : James A. Duke, ngrljd@ars-grin.gov : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/related/ : Database : FoodplantDB (Native American Food Plants) : Species : Over 1,100 plant species : ACEDB_version : 4.0 : Last_update : May 1995 : Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov : Curator : James A. Duke, ngrljd@ars-grin.gov : Comment : Converted to ACEDB from ORACLE. : Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food : Plants of the North American Indians. USDA Miscellaneous Publication Number 237. : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/related/ : Database : GrainGenes : Species : Wheat, barley, oats, relatives : Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu : PI : Olin D. Anderson, oandersn@pw.usda.gov : ACEDB_version : 4_1 : Data_version : 1.5+ : Last_update : November 1995 : FTP : probe.nalusda.gov in pub/graingenes : Gopher : greengenes.cit.cornell.edu/ : Gopher : probe.nalusda.gov:7002 : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : WWW : http://wheat.pw.usda.gov/graingenes.html : Database : IGD (Integrated Genomic Database) : Species : Homo sapiens : Subject : Chromosome 21 : Availability : September 1994 by ftp, on-line server October 1994 : Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de : Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr : Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr : Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr : WWW : http://moulon.inra.fr/acedb/igd.html : Description : IGD (Integrated Genomic Database) aims to integrate multiple : public general molecular biology and human genome specific databases into single : logical database with unified interface to existing analysis tools. From data : produced by the 4th International Workshop on Chromosome 21 : (Genomics,1993,18,735-744) and from data provided by or taken from the following : databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, : and RLDB. : Database : LeishDB : Species : Leishmaia major, L. infantum, L. peruviana, L. donovani and others : PI : Jennie Blackwell : PI : Al Ivens : Last_update : September 1995 : ACEDB_version : 4.1 : Contact : Matin Aslett, ma10025@cus.cam.ac.uk : FTP : ftp://parsun1.path.cam.ac.uk : WWW : http://parsun1.path.cam.ac.uk/ : Curator : Martin Aslett : Curator : Howard Cobb : Database : LIGM-DB : Curator : Veronique Giudicelli : Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell : receptors : PI : Marie-Paule Lefranc : Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende : 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr : Database : MaizeDB : Species : Zea mays L. ssp. mays and related species : Latest_release : April 1995 : Acedb_version : 3.3 : Comment : MaizeDB is a periodically extracted ACeDB front end for the Maize : Genome Database, MaizeDB, a SYBASE database, implemented using Genera software, : developed by Stan Letovsky. : Comment : Genera provides (1) up-to-the-minute form internet access to SYBASE : databases, both for query (WWW and APT) and data entry (APT only); (2) database : design alterations by systems administrators; (3) gopher file extraction. : Comment: MaizeDB uses WWW record-to-record hard-links to 16 external databases : for (1) annotated sequences: GenBank, dbEST, GenoBase, PIR, SwissProt, Prosite, : ENZYME; (2) other species genome information: AAtDB(Arabidopsis), RiceGenes, : GrainGenes, SaachDB (yeast), CGSC(E. coli), XLocus, RiceGenes, GrainGenes (3) : germplasm: GRIN. : Data : Over 100,000 records include: 6513 mapped loci (located to chromosome or : better) including 1081 mapped genes and 1937 mapped probed sites (gene : candidates); 2448 probes; 2460 map scores; 1551 gel patterns : (Probe/Enzyme/Stock); 8777 stocks; 18,100 Variations (alleles, DNA : polymorphisms, rearrangements, etc); 596 phenotypes; 317 traits; 715 gene : products; 6158 bibliographic references; 2200 researchers with addresses. : FTP : probe.nalusda.gov in pub/maizedb : Gopher : gopher.agron.missouri.edu : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: : corncob : WWW : http://www.agron.missouri.edu/top.html : WWW : http://probe.nalusda.gov:8300/plant/ : WWW Genera information : http://gdbdoc.gdb.org/letovsky/genera/genera.html : Funding : MaizeDB USDA/ARS to E. Coe : Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn : Curator/PI : Ed Coe, ed@teosinte.agron.missouri.edu : Curator : Mary Polacco, maryp@teosinte.agron.missouri.edu : Assoc Curator : Pat Byrne, byrne@teosinte.agron.missouri.edu QTL data : Assoc Curator : Georgia Davis, gdavis@teosinte.agron.missouri.edu Map data : Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic Stock : data : Assoc Curator : Christiane Fauron, FAURON@GENE1.med.utah.edu Mitochondrion : genome : Assoc Curator : Carolyn Wetzel, cmwetzel@iastate.edu Chloroplast genome : Assoc Curator : Steve Rodermel, S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome : Design : Stan Letovsky, letovsky@gdb.org : Design : Mary Berlyn, mary@fetalpig.biology.yale.edu : Systems Manager : Denis Hancock, dhancock@teosinte.agron.missouri.edu : Contact : db_request@teosinte.agron.missouri.edu : Last_update : 11 April 1995 : Database : Mendel (plant wide gene names) : Species : wide range of plant species : Subject : standardized designations for sequenced genes : Comment : The purpose is to provide a common system of nomenclature for : substantially similar genes across the plant kingdom. Mendel is maintained by : the Commission on Plant Gene Nomenclature. : ACEDB_version : 4.0 : Last_update : July 1995 : Curator : Carl Price, price@mbcl.rutgers.edu : Curator : Ellen Reardon, reardon@mbcl.rutgers.edu : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/related/ : Database : Millet Genes : Species : Pennisetum Glaucum (Pearl Millet) : ACEDB_version : 4.1 : Availablity : Local : Curator : Matt Couchman, couchman@bbsrc.ac.uk : Curator : Katrien Devos, devos@bbsrc.ac.uk : DataBase : Mousedb : Species : Musculus Musculus : Species : Homo Sapiens : ACEDB_version : 3.0 with extensions to define and display cytogenetic data. : Description : Mouse genome data from the published literature, including mouse : genes with phenotypic effects, chromosome anomalies, imprinted regions and : man-mouse homologies with associated pathological disorders. The maps are : consensus ones. They use data, such as the HIS and anomaly data, to show : alignments between the genetic and cytogenetic maps. : Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk : PI : Mary Lyon : PI : Jo Peters : Availability : Mousedb is available publicly from the UK HGMP Resource Centre's : computing service via the INTERNET. For user id. please contact Administration, : HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. : Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 : Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD : Last_update : July 1995 : Database : MPNADB (Medicinal Plants of Native America) : Species : Over 2,100 plant species : Curator : Daniel E. Moerman, dmoerman@umich.edu : Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version : Comment : MPNADB is based on a two-volume book of the same name published in : 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was : first developed at the University of Michigan in DBase II. : ACEDB_vertion : 4.0 : Last_update : June 1995 : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/related/ : Database : MycDB : Species : Mycobacteria : Comment : MycDB is a collation of data on the mycobacteria, causative agents of : tuberculosis and leprosy. It is centered on the mapping and sequencing projects : under way in M.leprae and M.tuberculosis. : Curator : Staffan Bergh, staffan@biochem.kth.se : Curator : Stewart Cole, stcole@pasteur.fr : Last_update : November 1995 : ACEDB_version : 4.1 : Data_version : 4-9 (November 1995) : FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB : FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB : FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://www.biochem.kth.se/MycDB.html : WWW : http://probe.nalusda.gov:8300/other/ : Database : OMIA (Online Mendelian Inheritance in Animals) : Species : wide range of animal species : Subject : gene and phene (familial trait or phenotype) information : Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man : (MIM) database and was developed at the University of Sydney, Australia, in : Advanced Revelation. : Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au : Curator : Gail Juvik, gjuvik@nalusda.gov - ACEDB version : ACEDB_vertion : 4.0 : Last_update : September 1995 : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/animal/ : WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html : Database : PhytochemDB (Plant Chemicals) : Species : wide range of plant species : Subject : Consists primarily of plant chemical data, including quantity, : taxonomic occurence, and chemical activity. : Comment : Converted to ACEDB from the original SQL database. : ACEDB_version : 4.0 : Last_update : June 1995 : Data_version : July 1994 : Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov : Curator : James A. Duke, ngrljd@ars-grin.gov : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/related/ : Database : PomBase : Curator : Sean Walsh, svw@sanger.ac.uk : Curator : Marie-Adele Rajendream : PI : Bart Barrell, barrell@sanger.ac.uk : Species : Schizosaccharomyces pombe : ACEDB_version : 4.1 : Last_update : September 1995 : FTP : ftp.sanger.ac.uk in pub/PomBase : Database : PVP (Plant Variety Protection) : Species : Glycine max (soybeans) : Subject : Data about plant varieties that have been granted a Certificate of : Protection by the Plant Variety Protection Office. : Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version : ACEDB_version : 4.0 : Last_update : June 1995 : Contact: The Plant Variety Protection Office, Room. 500, National Agriculture : Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 : Telephone : 301-504-5518 : Fax : 301-504-5291 : Email : Jeff Strachan, strachan@locus.nalusda.gov : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/related/ : Database : RiceGenes : Species : Oryza sativa : Curator : Edie Paul, epaul@nightshade.cit.cornell.edu : PI : Susah McCouch : ACEDB_version : 3.0 : Last_update : July 1995 : FTP : probe.nalusda.gov in pub/ricegenes : Gopher : nightshade.cit.cornell.edu : Gopher : probe.nalusda.gov:7007 : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : Database : SacchDB : Species : Saccharomyces cerevisiae : Subject : Budding (common baker's) Yeast Genome : ACEDB_version : UNIX 2.0, MacAce 2.0b4 : Last_update : September 1995 : Data_version : 2.4.12 : Data : All Saccharomyces genes contained in the Registry of Gene Names. Results : of the completed chromosomal sequencing projects have been integrated into the : database. Physical Maps based on DNA sequencing projects, hybridization to the : Olson/Riles prime filter grids, and restriction mapping. For the completely : sequenced chromosomes the Olson prime clones have been re-mapped (on the : computer) to the DNA sequence. Saccharomyces DNA sequences contained within : GenBank are incorporated. Literature references, most including abstracts, for : the information contained within the database. Gene protein product information : obtained from the YPD database (Garrels and Latter, CSHL) and the literature. : Genetic Maps including the underlying two point tetrad data. Including all : tetrad data reported in previous additions of the Mortimer Yeast Maps. : FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB : FTP : ncbi.nlm.nih.gov in repository/SacchDB : Gopher : genome-gopher.stanford.edu : WWW : http://genome-www.stanford.edu/ : Funding : National Center for Human Genome Research, NIH : PI : David Botstein, botstein@genome.stanford.edu : Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu : Curator : Selena Dwight, dwight@genome.stanford.edu : Curator : Cathy Ball, ball@genome.stanford.edu : Curator : Rita Schmidt, bleb@genome.stanford.edu : Curator : Barbara Dunn, bdunn@genome.stanford.edu : Curator : Caroline Adler, adler@genome.stanford.edu : Programmer : Karen Davis, karen@genome.stanford.edu : Sys. Admin : Mark Schroeder, mark@genome.stanford.edu : Contact : yeast-curator@genome.stanford.edu : Data_Submission : yeast-curator@genome.stanford.edu : Database : SolGenes : Subject : Solanaceae - tomato, potato, pepper : Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu : PI : Steve Tanksley : Release : ACEDB 3.0 : Last_update : May 1995 : FTP : probe.nalusda.gov in pub/solgenes : Gopher : nightshade.cit.cornell.edu:71 : Gopher : probe.nalusda.gov:7006 : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : Database : SorghumDB : Species : Sorghum bicolor (L.) Moench : PI : Keith F. Schertz, schertz@tamvm1.tamu.edu : USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, : TX 77843-2474 : Phone : (409) 260-9252 : FAX : (409) 845-0456 : Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu : Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M : University, College Station, TX 77843-2123 : Phone : (409) 862-1523 : FAX : (409) 862-4790 : Last_update : September 1995 : ACEDB_version : 3.0 : Data_version : 2.0 : FTP : probe.nalusda.gov in pub/sorghumdb : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : Database : SoyBase : Species : Glycine max (Soybeans) and related species : PI : Randy Shoemaker : Curator : David Grant, dgrant@mendel.agron.iastate.edu : Curator : Marica Imsamde, mimsande@mendel.agron.iastate.edu : Contact : Dave Schrader, schrader@mendel.agron.iastate.edu : ACEDB-Version : 3.7 : Last_update : August 1995 : FTP : probe.nalusda.gov in pub/soybase : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : WWW : http://mendel.agron.iastate.edu:8000/main.html : Database : Syndb : Species : Homo sapiens, Mus musculus : Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 : with Mouse for syntenic comparison : ACEDB_version : acedb v3.3 plus moulon server : Last_update : October 1994 : FTP : genome.lbl.gov in pub/acedb/ : WWW : http://genome.lbl.gov/Genome/acepage.html : Curator : Donn F. Davy, DFDavy@lbl.gov : Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov : PI : Michael Palazzolo : PI : Chris Martin : PI : Jan-Fang Cheng, jcheng@genome.lbl.gov : Database : Toxo : Species : Toxoplasma gondii : PI : Jennie Blackwell : PI : Jim Ajioka : Last_update : September 1995 : ACEDB_version : 4.1 : Contact : Martin Aslett, ma10025@cus.cam.ac.uk : FTP : parsun1.path.cam.ac.uk : WWW : http://parsun1.path.cam.ac.uk/ : Curator : Martin Aslett : Curator : Howard Cobb : Database : TreeGenes : Species : Forest trees : ACEDB_version : 3.0 : Last_update : July 1995 : Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov : PI : David B. Neale, dbn@s27w007.pswfs.gov : Contact : Dendrome@s27w007.pswfs.gov : FTP : probe.nalusda.gov in /pub/treegenes : Gopher : s27w007.pswfs.gov/ : Gopher : probe.nalusda.gov:7508/ : Gopher : probe.nalusda.gov:7000/11/genome.databases/ : WWW : http://probe.nalusda.gov:8300/plant/ : WWW : http://s27w007.pswfs.gov/ : Database : Trypbase : Species : Trypanosoma brucei : PI : Sara Melville : Curator : Martin Aslett, ma10025@cus.cam.ac.uk : Curator : Howard Cobb, hc102@econ.cam.ac.uk : Contact : sm160@mole.bio.cam.ac.uk : ACEDB_version : 4.1 (Sun and Linux) : FTP : parsun1.path.cam.ac.uk : WWW : http://parsu1.path.cam.ac.uk : Database : 21Bdb : Species : Homo sapiens : Subject : STS content mapping and sequencing of Human Chromosome 21 : ACEDB_version : acedb.1-10 plus moulon server : Curator : Donn F. Davy, DFDavy@lbl.gov : Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov : PI : Michael Palazzolo : PI : Chris Martin : PI : Jan-Fang Cheng, jcheng@genome.lbl.gov : Last_update : April 1994 : FTP : ftp://genome.lbl.gov in pub/acedb/ : WWW : http://genome.lbl.gov/Genome/acepage.html : Database : 22ace : Species : Homo sapiens : Subject : Physical map of human chromosome 22, genomic sequencing and more : ACEDB_version : 4.1 : Curator : Ian Dunham, id1@sanger.ac.uk : Curator : Gareth Maslen, glm@sanger.ac.uk : PI : Ian Dunham : Last_update : August 1995 : FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ : WWW : http://www.sanger.ac.uk/hum22/ : Database : VoxPop : Species : Populus species : Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu : PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu : Last_update : September 1993 : ACEDB_version : 1.9 : FTP : poplar1.cfr.washington.edu in /pub/ : Gopher : poplar1.crf.washington.edu : Return to List of Questions : Q5: What documentation exists for ACEDB? : ++++++++++++++++++++++++++++++++++++++++ : A5: : +++ : From Sam Cartinhour: The ACEDB Documentation Server is a repository for : documentation concerned with "A C. elegans Data Base", the generic genome : database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg : (CNRS, France). The server is intended as a resource for developers, curators, : and end-users of all (not just plant) databases derived from ace. Eventually we : hope to offer all kinds of documentation, from reprints to (technical) gossip. : The ACEDB documentation server is sponsored by the Plant Genome Database Project : at the National Agricultural Library (USDA). The documentation server is listed : on the home page for the Agricultural Genome World Wide Web Server at : http://probe.nalusda.gov:8000 . : Primary documents from the developers are: : o acedb -- A C. elegans Database: I. Users' Guide. : o acedb -- A C. elegans Database: II. Installation Guide. : o acedb -- A C. elegans Database: III. Configuration Guide. : o 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 and : ftp://weeds.mgh.harvard.edu/acedb_doc . The files are in TeX (Jean Thierry-Mieg : suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. : 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 . : Japanese language guides: _Japanese ACEDB Guide Ver.1.2._ _ACEDB ver.2 for NEC : engineering workstation EWS4800 series_ are available in PostScript via : anonymous ftp at ftp.nec.co.jp as /pub/packages/acedb/acemanjp.1_2.ps.Z . There : is a Japanese language ACEDB FAQ available at : http://www.cbi.or.jp/~sano/acemanjp12/index.html : 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.hih.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. [text is : available through ftp or gopher from weeds.mgh.harvard.edu] 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. : [text is available through ftp or gopher from weeds.mgh.harvard.edu] : 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 a tool set for : integrating version 4 of ACEDB with perl and the World-Wide Web. The archive is : 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/TextConvert . : The Developers' Archive : +++++++++++++++++++++++ : Mike Cherry maintains an archive of tools that may be useful in curating ACEDB : databases. It can be reached by anonymous ftp at URL : ftp://weeds.mgh.harvard.edu/acedb_dev/ or via gopher at : gopher://genome-gopher.stanford.edu:70/11/ftp : If you have a contribution place it in : ftp://weeds.mgh.harvard.edu/acedb_dev/incoming/ and 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. : o All of the articles in biosci.software.acedb are archived by Biosci at : gopher://gopher.bio.net/1/ACEDB : o Mike Cherry makes it possible to search past articles in : biosci.software.acedb using WAIS at : gopher://genome-gopher.stanford.edu:80/77/.index/acedb-biosci and at URL : http://genome-www.stanford.edu/biosci_acedb.html . 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: : o http://moulon.inra.fr/acedb/acedb.html for C. elegans data : o http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data : o 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: : o flydb - LBL's Drosophila Acedb-style database : o 21bdb - LBL's Human Chromosome 21 Acedb-style database : o querdb - LBL's query-language extensions to Acedb : o metadata - LBL's compendium of Acedb database schema variants : o macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version : o 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 dataabases established around : specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe : etc.). Refs: : o 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in : Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). : o 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 Interated Genome : Database project in Heidelburg (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@mrc-lmb.cam.ac.uk or : mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this : list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q6 : for details] is on the mailing list. : Return to List of Questions : Q10: When and where is the Next ACEDB Workshop? : +++++++++++++++++++++++++++++++++++++++++++++++ : A10: : ++++ : The 1996 Workshop is not yet scheduled. : If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu : de Treviers, there are online collections: : o by Mike Cherry at : http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; : o by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; : o 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 latest text version of the ACEDB FAQ should be available via anonymous ftp : at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at 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. : There is an HyperText Markup Language (HTML) version of this document available : on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html and : http://s27w007.pswfs.gov/Homepage/acedbfaq.html There is a Japanese language FAQ : available at http://www.cbi.or.jp/~sano/acemanjp12/index.html : 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 : Major contributions in getting this FAQ off the ground were made by Mike Cherry, : John McCarthy, and Doug Bigwood. Other contributors include: : o Lisa Lorenzen : o David Matthews : o Edie Paul : o Donn Davy : o Eric De Mund : o Sam Cartinhour : Please cite as: : Sherman,B.K., ACEDB Genome Database Software FAQ, : ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, : http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993,1994,1995 approx. 50K : bytes. : To add or modify information in this document, please send mail to: : acedbfaq@s27w007.pswfs.gov : Bradley K. Sherman : Dendrome Project : Institute of Forest Genetics : P.O. Box 245, Berkeley, CA, 94701 : Phone: 510-559-6437 Fax: 510-559-6440 : The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome : Research Program. : Return to List of Questions : End of ACEDB FAQ --bks From owner-acedb@net.bio.net Wed Dec 06 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!swrinde!newsfeed.internetmci.com!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!macgrant.agron.iastate.edu!user From: dgrant@iastate.edu (David Grant) Newsgroups: bionet.software.acedb Subject: MacACE Date: 7 Dec 1995 15:30:12 GMT Organization: Iowa State University Lines: 20 Message-ID: NNTP-Posting-Host: macgrant.agron.iastate.edu I am trying to use MacACE 4.1b1 on a PowerMac 9500/132 with 32 megs of RAM. It mostly works fine but I can't display maps. With either the C.e. data (as distributed with MacACE) or our soybean data (which work fine in the UNIX 4.1 version), the program crashes a few seconds after the empty map window appears. Is this a known bug in this beta version or (horrors) an incompatability with my Mac. The same thing happens with or without my usual extensions. MacACE version 2.0b4 does not have this problem. Another problem occurs with the metabolic pathway displays. When I attempt to rearrange them the old line in the diagram does not go away, although a new one is drawn. This obviously quickly makes the display unusable. Does anyone have any ideas? Thanks, David Grant dgrant@iastate.edu -- David Grant dgrant@iastate.edu 515-294-1205 From owner-acedb@net.bio.net Wed Dec 13 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!Germany.EU.net!news.dfn.de!zrz.TU-Berlin.DE!fu-berlin.de!rag2.rz-berlin.mpg.DE!leser From: leser@rag100.RZ-Berlin.MPG.DE (Ulf Leser) Newsgroups: bionet.software.acedb Subject: Calling Unix from tace Date: 14 Dec 1995 13:02:27 GMT Organization: MPI "Molekulare Genetik", Berlin Lines: 22 Sender: leser@rag2.RZ-Berlin.MPG.DE (Ulf Leser) Message-ID: <4ap793$sa6@fu-berlin.de> NNTP-Posting-Host: rag2.rz-berlin.mpg.de (141.14.130.102) NNTP-Posting-User: leser X-Access: 16 25 816 Hello, I'm a real new user of acedb, but will have to work with itt a lot in future. So, at the beginning, my questions won't be very complicated. Anyway: the problem I've got is fairly easy. In the documentation of John Morris about TACE (available from the ACDEB Documentation Library) he mentions the possibility of calling UNIX-Commands from the tace-prompt or within a ace-command file by simple putting an $ in front of them, so for example $echo "Hello" This feature is also described in the help screen of me tace-version, which is 4.1. Unfortunately it doesn't work - tace always claimes that $echo (or other commands) is not a valid keyword - it is obviously not escaping the parser. Who can help me ?? It's fairly urgent... Thanks, Ulf Leser From owner-acedb@net.bio.net Thu Dec 14 22:00:00 1995 Path: biosci!BEANGENES.CWS.NDSU.NODAK.EDU!mcclean From: mcclean@BEANGENES.CWS.NDSU.NODAK.EDU (Phil McClean) Newsgroups: bionet.software.acedb Subject: Re: Importing data from dBase & ORACLE dbs Date: 15 Dec 1995 11:49:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4as8vk$2um@sun4.bham.ac.uk> NNTP-Posting-Host: net.bio.net On 15 Dec 1995, Miss E. S. Hadkins wrote: > I would like to know if there are any data transfer formats for Dbase > files, ORACLE files and spreadsheet packages like Excel into .ace files. > I am involved in a project tying together molecular and taxonomic data for > the Solanaceae family, and have access to much relevant data but would > like to avoid manual editing, as time is very limiting. > Many thanks in advance for any suggestions. > Miss Hadkins- I work on an ace database and receive many files in Excel format. I save them as text, upload them to a unix box and run macros in Emacs to convert them to .ace files. This goes pretty quickly. Because the models differ from database to database, a universal conversion program is probably not possible. Phil McClean Dept. of Plant Sciences North Dakota State University Fargo, ND 58105 mcclean@beangenes.cws.ndsu.nodak.edu From owner-acedb@net.bio.net Thu Dec 14 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!warwick!bham!usenet From: E.S.Hadkins@bham.ac.uk (Miss E. S. Hadkins) Newsgroups: bionet.software.acedb Subject: Importing data from dBase & ORACLE dbs Date: 15 Dec 1995 16:49:56 GMT Organization: University of Birmingham Lines: 6 Message-ID: <4as8vk$2um@sun4.bham.ac.uk> Reply-To: E.S.Hadkins@bham.ac.uk NNTP-Posting-Host: bcs225.bham.ac.uk X-Newsreader: WinVN 0.92.6+ I would like to know if there are any data transfer formats for Dbase files, ORACLE files and spreadsheet packages like Excel into .ace files. I am involved in a project tying together molecular and taxonomic data for the Solanaceae family, and have access to much relevant data but would like to avoid manual editing, as time is very limiting. Many thanks in advance for any suggestions. From owner-acedb@net.bio.net Sun Dec 17 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: FATAL ERROR: Duplicate tag Location.... Date: 18 Dec 1995 22:33:18 -0000 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4b4q7e$cmq@mserv1.dl.ac.uk> Original-To: eesnyder%sequana.com@earn-relay.ac.uk there is a bug in your file wspec/models.wrm look in the paragraph starting with ?Sequence actually do tace acedb> read // will read models this is the fastest way to geenrate the bug then fix the model which should not contain tag Location twice From owner-acedb@net.bio.net Sun Dec 17 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!usc!news.cerf.net!news From: "Eric E. Snyder" Newsgroups: bionet.software.acedb Subject: FATAL ERROR: Duplicate tag Location.... Date: 18 Dec 1995 21:21:27 GMT Organization: Sequana Therapeutics, Inc. Lines: 23 Message-ID: <4b4m0n$jjq@news.cerf.net> NNTP-Posting-Host: 198.207.137.13 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4m) To: mferguso@klab.agsci.colostate.edu,jason_martin@sequana.com X-URL: news:bionet.software.acedb Ace Folks, I am having a persistent problem with ACEDB. Often after adding new data to the database via .ace files, saving it and re-starting, I will find that when I try to open sequence objects, I will get the following error: FATAL ERROR: Duplicate tag Location in model Sequence ..with the obvious result of ACEDB crashing. If I make a dump file, I can always recover the data and the problem does not recur until I load more data. Presumably, there is some sort of error or inconsistency in my .ace files but it is not obvious where the problem might lie. Any suggestions on where to look or how to debug this problem would be greatly appreciated. Cheers! Eric E. Snyder, PhD Sequana Therapeutics, Inc. 11099 North Torrey Pines Road, Suite 160 La Jolla, CA 92037 (619) 452-6550 ex 279; (619) 452-6653 fax; eesnyder@sequana.com http://beagle.colorado.edu/~eesnyder/eesnyder.html From owner-acedb@net.bio.net Sun Dec 17 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!usc!news.cerf.net!news From: "Eric E. Snyder" Newsgroups: bionet.software.acedb Subject: FATAL ERROR: Duplicate tag Location.... Date: 18 Dec 1995 21:21:25 GMT Organization: Sequana Therapeutics, Inc. Lines: 23 Message-ID: <4b4m0l$j39@news.cerf.net> NNTP-Posting-Host: 198.207.137.13 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4m) To: mferguso@klab.agsci.colostate.edu,jason_martin@sequana.com X-URL: news:bionet.software.acedb Ace Folks, I am having a persistent problem with ACEDB. Often after adding new data to the database via .ace files, saving it and re-starting, I will find that when I try to open sequence objects, I will get the following error: FATAL ERROR: Duplicate tag Location in model Sequence ..with the obvious result of ACEDB crashing. If I make a dump file, I can always recover the data and the problem does not recur until I load more data. Presumably, there is some sort of error or inconsistency in my .ace files but it is not obvious where the problem might lie. Any suggestions on where to look or how to debug this problem would be greatly appreciated. Cheers! Eric E. Snyder, PhD Sequana Therapeutics, Inc. 11099 North Torrey Pines Road, Suite 160 La Jolla, CA 92037 (619) 452-6550 ex 279; (619) 452-6653 fax; eesnyder@sequana.com http://beagle.colorado.edu/~eesnyder/eesnyder.html From owner-acedb@net.bio.net Mon Dec 18 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: abignone@igecuniv.cisi.unige.it (Bignone Franco) Newsgroups: bionet.software.acedb Subject: IBM6000 Date: 18 Dec 1995 23:33:57 -0000 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4b4tp5$fsq@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk I am having problems in compilation on IBM6000, any hint on problems with this machine aside the initial variable changes ? (IBM_DEF, IBM_3_DEF) Tx Franco -- ******************************************************************************* * Franco A. Bignone, * * I.S.T., Largo Rosanna Benzi, 10, 16132, Genova, * * and, Dip. Biologia Animale e Genetica, Universita' di Firenze, * * Via Romana, 17/19, 50125, Firenze, Italy. * * e-mail: abignone@igecuniv.cisi.unige.it, fbignone@gatto.chem.utoronto.ca * * ph. home +39-10-205785(answ.); job: +39-10-3534213,+39-55-222-448 ext (204) * * fax: +39-10-353-4213 or +39-55-222565 * ******************************************************************************* From owner-acedb@net.bio.net Mon Dec 18 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Norway.EU.net!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB worm data updates 4-12 and 4-13 Date: 19 Dec 1995 06:27:07 -0000 Lines: 81 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4b5lvr$83g@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, acedb_distrib@ppsw.cam.ac.uk, celegans@dl.ac.uk This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. ACEDB data updates 4-12 and 4-13 for C. elegans =============================================== Two new updates are available. These should be used in conjunction with version 4_1 of the ACEDB program. The total database size after adding updates 4-1 to 4-13 is approximately 240 Mbytes. The additions since 4-11 are: - more genomic sequence data (there are now 918 cosmids totalling 28,081,786 bases). - a physical map update (December 1) - worm sequences from EMBL release 44 not related to the genome project - new data submitted by email to the CGC in Cambridge or direct to Sylvia has been entered - a number of errors and problems have been fixed Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb ftp.sanger.ac.uk in England, in pub/acedb lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password: your user id or email address cd repository/acedb # change to relevant directoy binary # IMPORTANT dir # display files in this directory get README get NOTES get INSTALL cd ace4 # change to ace4 directory get bin.sunos.4_1.tar.Z # get program cd ../celegans # change to worm data directory mget update* # get all update files quit -------------------------------- Get any update.4-n.tar.Z that you do not have already and read the file NOTES before proceeding further. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb"), click "Yes" to accept initialising the database if starting from scratch, then choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button. If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Comments about the data should be sent to the data curator, Sylvia Martinelli (sylvia@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- From owner-acedb@net.bio.net Wed Dec 20 22:00:00 1995 Path: biosci!MH1.LBL.GOV!mccarthy From: mccarthy@MH1.LBL.GOV (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: problem with Error_scale? Date: 20 Dec 1995 17:28:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199512210127.RAA20830@mh1.lbl.gov> Reply-To: JLMcCarthy@lbl.gov NNTP-Posting-Host: net.bio.net We're currently running **** acedb queryserver: Version 4.1 4.1, August 1995(Aug 14 1995) **** From the Magic Tags documentation, etc., I had thought that the value for Error_scale in the ?Map model would set the default Error_scale for any particular map. But when I click on the Locus column, the Error_scale box in the configuration window says 0.0 -- even though the Error_scale tag in the text representation of that map is 1 or 4 or 10. Is there something I'm doing wrong with the Error_scale tag? (e.g., should it be Error_Scale or some other variant that the code is missing? Or is the new map display code failing to pick up the Error_scale default from my input data? -John From owner-acedb@net.bio.net Wed Dec 20 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Computational biologist at NASC Date: 21 Dec 1995 10:39:14 -0000 Lines: 43 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4bbdgi$li7@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk OPPORTUNITY FOR COMPUTATIONAL BIOLOGIST AT NOTTINGHAM ARABIDOPSIS STOCK CENTRE The Nottingham Arabidopsis Stock Centre (NASC) is an international genetic resource centre for seed resources and information pertaining to the plant model system, Arabidopsis. NASC has become the European touchstone for information dissemination to the Arabidopsis research network through the establishment of its WWW server (URL=http://nasc.nott.ac.uk/). NASC also collaborates with other Arabidopsis informatics projects in the USA and is responsible for the curation of the resource information within AtDB. We are looking for a computational biologist to join the Stock Centre to develop the current bioinformatics activities. Specific duties will include the development and maintenance of the WWW server, including the establishment of a mirror site for Arabidopsis information currently distributed through the USA; preparation of ace files of Stock information for AtDB and development of the in-house database for Stock Centre administration. The ideal candidate will have a PhD in molecular biology or computer/information science. Non PhD candidates will also be considered if they have experience of computational biology or bioinformatics. The candidate should also have experience of UNIX, and programming in C or Perl. In addition, preference will be given to candidates with experience of web authoring and/or the database software ACEDB. The appointment is EU funded for 32 months (possibly extended to 36 months) and is available immediately. Starting salary will be flexible depending on experience. For further details contact Mary Anderson (arabidopsis@nottingham.ac.uk) Tel: 0115 9791216 To apply for this position please send a full cv and covering letter including the names of two referees to Mary Anderson, Nottingham Arabidopsis Stock Centre, Dept of Life Science, Nottingham University, Nottingham, NG7 2RD, UK. CLOSING DATE FOR APPLICATION IS 26th JAN 1996. From owner-acedb@net.bio.net Wed Dec 20 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!EU.net!peer-news.britain.eu.net!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.acedb Subject: who has IGD on an Aha ? Date: 21 Dec 1995 15:50:02 GMT Organization: Belgian EMBnet Node Lines: 12 Message-ID: <4bbvna$ftd@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] I am trying to install the IGD on a DEC Alpha with OSF/1 and I am experiencing many difficulties. I would like to know if there are people who have IGD installed and operational on a similar machine, in order to exchange informations. Note : we have : a DEC Alpha AXP 5000/300 OSF/1 3.2 ACEDB ted 3.5 Thanks in advance, Dr. Guy Bottu From owner-acedb@net.bio.net Mon Dec 25 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!macgrant.agron.iastate.edu!user From: dgrant@iastate.edu (David Grant) Newsgroups: bionet.software.acedb Subject: images in MacACE Date: 26 Dec 1995 16:34:47 GMT Organization: Iowa State University Lines: 12 Message-ID: NNTP-Posting-Host: macgrant.agron.iastate.edu Can some kind soul give me a quick primer on how to display images in MacACE? I know how to do it in the UNIX version and can see it happening in MacAAtDB but can't figure out how to make it work for my data. I have a folder of .gif files that work in the UNIX version of SoyBase. They open fine with JPEGView on my Mac. Replacing 'xv' with 'JPEGView' in my image.ace file does not work - all I get is an error message saying that there is "no scale". Thanks, -- David Grant dgrant@iastate.edu 515-294-1205 From owner-acedb@net.bio.net Sun Dec 31 22:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI miniFAQ, ver. 14-DEC-95 Date: 1 Jan 1996 02:00:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 199 Sender: daemon@net.bio.net Distribution: world Message-ID: <199601011000.CAA10270@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 14-DEC-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/. Contents: -------- 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. 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 in addition to the master index for the entire set. 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