From owner-acedb@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 5 Jul 1995 18:20:55 GMT Organization: Dendrome, A genome database for forest trees Lines: 1083 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <3tel67$ikq@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 database system ACEDB. ACEDB is used to collect information regarding the molecular biology of the genome. Xref: biosci bionet.software.acedb:652 news.answers:41974 Archive-name: acedb-faq Last-modified: 7/5/95 Version: 1.22 ACEDB FAQ 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.) Most production sites are using 3.0 (or 2.0) binaries. The most recent beta source code distribution (3/95) is test.source.3.7.tar.gz. 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 with Linux (free Unix) [note from Jeff Bryer, jbryer@darwin.mbb.sfu.ca] I just installed up Linux yesterday and today spent the many hours to compile in the C. elegans data for ACEDB v2.0 So to save other people the trouble of doing the same the entire package ACEDB for Linux 2-10 is available on trog.mbb.sfu.ca in /pub/acedb as linux.2_10.tar.Z The data was compiled in on a 486DX-33 with 16MBs of RAM running Linux 1.1.18 (Slackware 2.0.0 distribution) and a 32MB swap device (and it chugged away for a couple hours chewing up all 16MBs and half the swap space). File size is about 73MBs uncompressed, 26MBs compressed. This is based on the ACEDB v2.0 port for Linux that Ken Clark (ken@darwin.mbb.sfu.ca) did. 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 2.0 for Linux 2-10: o trog.mbb.sfu.ca /pub/acedb as linux.2_10.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] o Database : AaeDB o Species : Aedes aegypti o Last_update : December 1994 o ACEDB_version : 3.0 o WWW : http://klab.agsci.colostate.edu/index.html o PI : Dennis Knudson, dknudson@lamar.colostate.edu o Curator : Martin Ferguson, martinf@lamar.colostate.edu o Curator : Dave Severson, dave@aedes.vetsci.wisc.edu o Contact : aaedbmgr@klab.agsci.colostate.edu o Database : AAnDB-1.0 o Species : Aspergillus nidulans o PI : Leland Ellis o Last_update : February 1994 o ACEDB_version : 3.0 o Contact : leland@stralight.tamu.edu o URL: http://keck.tamu.edu/ibt.html o Comment : defunct, See AGsDB o Database : AAtDB o Species : Arabidopsis thaliana o Current version : 3-5 o Last_update : March 1995 o Curator : John Morris o Contact : curator@frodo.mgh.harvard.edu o Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x o Availability : Macintosh version in /aatdb/MacAAtDB directory o FTP : URL : ftp://weeds.mgh.harvard.edu/aatdb o Gopher : gopher://weeds.mgh.harvard.edu/ o WWW : http://weeds.mgh.harvard.edu:80/index.html o WWW : http://probe.nalusda.gov:8300/ o Database : ABtDB-1.0 o Species : Bovine, Bos taurus o ACEDB_version : 3.0 extended o PI : Leland Ellis o Last_update : February 1994 o Contact : leland@stralight.tamu.edu o URL : http://keck.tamu.edu/ibt.html o Comment : defunct, See AGsDB o Database : AboutDB o Curator : Staffan Bergh o PI : Staffan Bergh o Subject : ACEDB itself (Is this meta-meta-metadata) o ACEDB 3.0 o Contact : staffan@biochem.kth.se o URL : http://www.biochem.kth.se/AboutDB.html o Database : ACeDB o Species : Caenorhabditis elegans o Current version: 2-18 o Curator : Jean Thierry-Mieg o Curator : Richard Durbin o Contact : rd@mrc-lmb.cam.ac.uk o Contact : mieg@kaa.crbm.cnrs-mop.fr o Last_update : May 1994 o DataBase : AceMap o Species : Homo sapiens (Mus musculus under development) o Focus : Physical mapping of human chromsome X and 21 o ACEDB_version : 3.0 o Curator : Hugues Roest Crollius o PI : Hans Lehrach o Availability : beta release of the X chr. data/models by anonymous ftp to ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap. Get the README file in the directory above. o Contact : hrc@gea.lif.icnet.uk (Hugues Roest Crollius) ICRF, Lincoln's Inn Fields London, UK. o Last_update : August 94 o Database : AGsDB A Genus species Database o Species : Aspergillus nidulans o Species : Neurospora crassa o Species : cow w/ human anchor loci o Species : cotton (demo) o Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast o PI : Leland Ellis o Curator : Leland Ellis o Last_update : March 1994 o ACeDB_version : 3.0 (beta still), with 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 o Models : as of 3.13.94 o Data : as of 3.13.94 o 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. o WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux (ducoux@moulon.inra.fr). o URL : http://keck.tamu.edu/ibt.html o Contact : leland@straylight.tamu.edu o Database : Alfagenes o Species : Medicago sativa (Alfalfa, Lucerne) o Availability : Under development o Curator : D. Z. Skinner o Contact : dzolek@ksu.ksu.edu o Telephone : (913) 532-7247 o Database : BeanGenes o Species : Phaseolus and Vigna species o PI : Phillip E. McClean o Email : mcclean@beangenes.cws.ndsu.nodak.edu o WWW : http://probe.nalusda.gov:8300 o Gopher: probe.nalusda.gov o Database : ChlamyDB o Species : Chlamydomonas o PI : Elizabeth Harris o Contact : chlamy@acpub.duke.edu o Availability : ChlamyDB 1.1, using ACEDB 3.0, is now on WWW and gopher (probe.nalusda.gov). Complete version using ACECB 3.0 now available by ftp from probe.nalusda.gov in the pub/chlamy directory. A Macintosh version is avaliable in ftp://ftp.duke.edu/pub/chlamy/MacChlamy o URL : http://probe.nalusda.gov:8300 o Last_update : 14 April 1995 o Database : CottonDB o Species : Gossypium hirsutum (cotton) and related species o PI : Russell J. Kohel, USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 o Curator : Gerard R. Lazo o Curator : Sridhar Madhavan o Last_update : January, 1995 (version 95.1) o ACEDB_version : 3.0 o Contact : lazo@tamu.edu (Gerard R. Lazo) o Contact : rjk0339@acs.tamu.edu (Russell J. Kohel) o URL : http://probe.nalusda.gov:8000/index.html o Data_submission_form : http://algodon.tamu.edu/ o Phone : 409-260-9311 o Fax : 409-260-9333 o Database : CSNDB o Focus : Cell Signalling Molecules and Interactions o Contact : Takako Igarashi National Insitute of Health Sciences Division of Chem-Bio Informatics Setagaya-ku, Tokyo, Japan 158 taka@nihs.go.jp o Database : EcoDB o Species : E. coli o PI : Staffan Bergh o Contact : staffan@biochem.kth.se o Availability : Proposed o Last_update : Aug. 1994 o Database : 11DB o Species : Homo sapiens o Focus : Physical mapping of chromosome 11 o Availability : under development o Curator : Benedict Arnold o PI : Peter Little o Contact : Benedict Arnold Dept. Biochemistry, Imperial College, London, SW7 2AZ b.arnold@ic.ac.uk o Database : The Encyclopaedia of the Drosophila Genome. o Acronym : (none) o Species : Drosophilidae (primarily D. melanogaster) o Availability : MacFly/FlyDB-based distribution by ftp and CD-ROM due early 1995 o Developer : Suzanna Lewis o Contact : suzi@fly2.berkeley.edu o Developer : Cyrus Harmon o Contact : sly@fly2.berkeley.edu o Developer : Edward Welbourne o Contact : eddy@gen.cam.ac.uk o Curation : Data is provided by the collaborating organisations: o Collaborator : The FlyBase Consortium, flybase@morgan.harvard.edu o Collaborator : The Berkeley Drosophila Genome Project o URL : gopher://fly.bio.indiana.edu:70+/11/Flybase o Database : Flydb o Species : Drosophila melanogaster o Curator : Suzanna Lewis o Contact : suzi@fly2.berkeley.edu o Database : GrainGenes o Species : Wheat, barley, oats, relatives o Availability : Anonymous ftp from probe.nalusda.gov:pub/grains o Availability : Gopher greengenes.cit.cornell.edu port 70 o Availability : Gopher probe.nalusda.gov port 7002 o Curator : David E. Matthews o PI : Olin D. Anderson o Contact : matthews@greengenes.cit.cornell.edu o Contact : oandersn@wheat.usda.gov o URL : gopher://greengenes.cit.cornell.edu/1/ o Data_version : 1.3 o Released : 12 Jan 1994 o Based_on : acedb.1-10 o Availability : See following WWW URL o URL : http://probe.nalusda.gov:8300 o Last_update : Feb. 1994 o Database : human.c17 o Species : Homo sapiens o Availability : the database is under development o Contact : lsprilus@weizmann.weizmann.ac.il o Focus : mapping & sequencing of Human Chromosome 17 o Based_on: acedb.3-0 o Last_update : Jan. 1994 o Database : IGD - the Integrated Genomic Database o Species : Homo sapiens (later mouse and other mammalian species) o Availability : September 1994 by ftp, on-line server October 1994 o Contact : Otto Ritter [ o.ritter@dkfz-heidelberg.de ] o Curator : tba o Description : IGD - the 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. o Database : LIGM-DB o Curator : Veronique Giudicelli o Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors o PI : Marie-Paule Lefranc o Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr o Database : Maize o Species : Zea mays L. ssp. mays and related o Focus : Maize genome o Latest_release : April 1995 o Acedb_version : 3.3 o FTP : probe.nalusda.gov, pub/maize directory o Comment : Maize is a periodically extracted ACeDB front end for the Maize Genome Database, MaizeDB, a SYBASE database, implemented using Genera software, developed by Stan Letovsky. o 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. o 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. o 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. o Gopher : host = gopher.agron.missouri.edu, port = 70 . o Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: corncob o HTTP : http://www.agron.missouri.edu/top.html o HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant Genome Database - Moulon WWW gateway to several ACeDB databases o HTTP : Genera information http://gdbdoc.gdb.org/letovsky/genera/genera.html o Funding : MaizeDB USDA/ARS to E. Coe o Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn o Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu o Curator : Mary Polacco maryp@teosinte.agron.missouri.edu o Assoc Curator : Pat Byrne byrne@teosinte.agron.missouri.edu QTL data o Assoc Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu Map data o Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic Stock data o Assoc Curator : Christiane Fauron FAURON@GENE1.med.utah.edu Mitochondrion genome o Assoc Curator : Carolyn Wetzel cmwetzel@iastate.edu Chloroplast genome o Assoc Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome o Design : Stan Letovsky letovsky@gdb.org o Design : Mary Berlyn mary@fetalpig.biology.yale.edu o Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu o Contact : db_request@teosinte.agron.missouri.edu o Last_update : 11 April 1995 o Database : MycDB o Species : Mycobacteria o 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. o PI : Staffan Bergh o Curator : Thierry Garnier o Curator : Staffan Bergh o Contact : staffan@biochem.kth.se o Last_update : Feb. 1995 (version 3-6) o ACEDB_version : 3.0 o WWW : http://www.biochem.kth.se/MycDB.html o ftp : www.biochem.kth.se (130.237.52.64) in pub/MycDB o ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB o ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb o Database : PomBase o Curator : Sean Walsh o Curator : Marie-Adele Rajendream o PI : Bart Barrell o Species : Schizosaccharomyces pombe o Contact : svw@sanger.ac.uk o Contact : barrell@sanger.ac.uk o Comment : Not yet available for distribution o DataBase : Mousedb o Species : Mus Musculus o Species : Homo Sapiens o ACEDB_version : 3.0 with extensions to define and display cytogenetic data. o 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. o Curator : Michelle Kirby o Curator : Rachael Selley o PI : Mary Lyon o PI : Jo Peters o 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 For other information contact Michelle Kirby. o Contact : kirbym@har-rbu.mrc.ac.uk (or mkirby@hgmp.mrc.ac.uk) rselley@har-rbu.mrc.ac.uk MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD o Last_update : February 1995 o Database : RiceGenes o Species : Rice (O. sativa) o Availability : Anonymous ftp from probe.nalusda.gov:pub/rice o Availability : Gopher nightshade.cit.cornell.edu port 70 o Availability : Gopher probe.nalusda.gov port 7007 o Curator : Edie Paul o PI : Susah McCouch o Contact : epaul@nightshade.cit.cornell.edu o ACEDB_version : 3.0 o Last_update : May 1994 o Database : SacchDB o Species : Saccharomyces cerevisiae o Focus : Budding (common baker's) Yeast Genome o ACEDB_version : UNIX 2.0, MacAce 2.0b4 o FTP : genome-ftp.stanford.edu in /pub/SacchDB o FTP : ncbi.nlm.nih.gov in /repository/SacchDB o 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. o Gopher : host = genome-gopher.stanford.edu, port = 70 o HTTP : http://genome-www.stanford.edu/ o Funding : National Center for Human Genome Research, NIH o PI : David Botstein, botstein@genome.stanford.edu o Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu o Curator : Selena Dwight, dwight@genome.stanford.edu o Curator : Cathy Ball, ball@genome.stanford.edu o Curator : Rita Schmidt, bleb@genome.stanford.edu o Curator : Barbara Dunn, bdunn@genome.stanford.edu o Curator : Caroline Adler, adler@genome.stanford.edu o Programmer : Karen Davis, karen@genome.stanford.edu o Sys. Admin : Mark Schroeder, mark@genome.stanford.edu o Contact : yeast-curator@genome.stanford.edu o Data_Submission : yeast-curator@genome.stanford.edu o Last_update : 2 February 1995 o Database : SolGenes o Coverage: Solanaceae - tomato, potato, pepper o Availability : Anonymous ftp from probe.nalusda.gov:pub/solgenes o Availability : Gopher nightshade.cit.cornell.edu port 71 o Availability : Gopher probe.nalusda.gov port 7006 o Curator : Clare Nelson o PI : Steve Tanksley o Contact : cnelson@nightshade.cit.cornell.edu o Release : ACEDB 3.0 o Last_update : May 1995 o Database : SorghumDB o Species : Sorghum bicolor (L.) Moench o PI : Keith F. Schertz USDA-ARS Dept. of Soil & Crop Sciences Texas A&M University College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 E_mail : schertz@tamvm1.tamu.edu o Curator : Najeeb U. Siddiqui Southern Crop Improvement Facility Crop Biotechnology Center Texas A&M University College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 E_mail : nus6389@tamsun.tamu.edu o Last_update : July 1994 o ACEDB_version : 3.0 o Availability : Under Development o Database : SoyBase o Species : Soybeans o Curator : Marica Imsamde o PI : Randy Shoemaker o Contact : mimsande@mendel.agron.iastate.edu o Phone : 515-294-1297 o Contact : schrader@mendel.agron.iastate.edu o Phone : 515-294-0421 o Fax : 515-294-2299 o Last_update : Sept. 1993 o Gopher : probe.nalusda.gov port 7005 o Database : Sybace o Species : Homo sapiens o Creator : Detlef Wolf o Comment : Custom software --ACEDB front-end to SYBASE data o Contact : D.Wolf@dfkz-heidelberg.de o See_also : IGD o Database : Syndb o Species : Homo sapiens, Mus musculus o Focus : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison o Availability : by request, via ftp, world-wide-web o Based_on : acedb v3.3 plus moulon server o URL: ftp://genome.lbl.gov/pub/acedb/syndb.tar.Z o URL: http://genome.lbl.gov/Genome/acepage.html o Curator : Donn F. Davy o Contact : DFDavy@lbl.gov o Contact : aggarwal@genome.lbl.gov o Focus : STS content mapping & directed sequencing of Human Chromosomes 21 and 5, with Mouse data for syntenic comparison o PI : Michael Palazzolo o PI : Chris Martin o PI : Jan-Fang Cheng o Last_update : Oct. 1994 o Database : TreeGenes o Species : Forest trees o ACEDB_version : 3.0 o Curator : Bradley K. Sherman o PI : David B. Neale o Contact : Dendrome@s27w007.pswfs.gov o Contact : bks@s27w007.pswfs.gov o Contact : dbn@s27w007.pswfs.gov o Last_update : March 1994 o Gopher: s27w007.pswfs.gov o WWW: http://probe.nalusda.gov:8300/plant/index.html . o WWW: http://s27w007.pswfs.gov/ o FTP: probe.nalusda.gov in /pub/trees o Database : Trypbase o Species : Trypanosoma brucei o ACEDB_version : 3.0 o PI : Sara Malville o Contact : sm160@mole.cam.ac.uk o Comment : Under development, feedback welcome. o ACEDB_version : 3.0 and 4.0 o Database : 21Bdb o Species : Homo sapiens o Focus : STS content mapping & sequencing of Human Chromosome 21 o Availability : by request, via ftp, world-wide-web o Based_on : acedb.1-10 plus moulon server o URL: ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z o URL: http://genome.lbl.gov/Genome/acepage.html o Curator : Donn F. Davy o Contact : DFDavy@lbl.gov o Contact : aggarwal@genome.lbl.gov o Focus : STS content mapping & sequencing of Human Chromosome 21 o PI : Michael Palazzolo o PI : Chris Martin o PI : Jan-Fang Cheng o Last_update : Apr. 1994 o Database : 22ace o Species : Homo sapiens o Curator : Ian Dunham o Focus : Physical mapping of chromosome 22 o PI : Ian Dunham o Contact : Ian Dunham Sanger Centre Hinxton Hall, Cambs. UK. id1@sanger.ac.uk o Database : VoxPop o Species : Populus spp. o Availability : contact curator o Curator : Carl G. Riches o PI : Reinhard F. Stettler o Contact : cgr@poplar1.cfr.washington.edu o Contact : STETTLER@coyote.cfr.washington.edu o Gopher : poplar1.crf.washington.edu o Last_update : Sept. 1993 o Database : Xace o Species : Homo sapiens o Curator : Gareth Maslen o Focus : Physical mapping of chromosome X o PI : David Bentley o Contact : Gareth Maslen Sanger Centre Hinxton Hall, Cambs. UK. glm@sanger.ac.uk o Database : ? o Species : Homo sapiens o Focus : Physical mapping of human chromosome 6. o Curator : Ioannis Ragoussis o Availability : Unknown o Contact : Guy's hospital o Database : ? o PI : Scott Chasalow o Species : Potato o Contact : Scottish Crop Institute, Dundee o Last_update : Sept. 1993 o Database : ? o PI : George Murphy o PI : David Flanders o Species : Arabidopsis thaliana o Contact : John Innes Center, Norwich, England o Last_update : Sept. 1993 o Database : ? o Species : Homo Sapiens o Focus : Physical and linkage mapping of chromosome 8 o Availability : o Curator : Stephen Wood o PI : Stephen Wood o Contact : Stephen Wood Dept. Medical Genetics University of B. C. Vancouver, B. C. Canada swood@unixg.ubc.cq 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. 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: +++ 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). 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 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. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/index.html 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 Bigwoody. 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 Tue Jul 04 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!emory!cssun.mathcs.emory.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: version 3.7 errors Date: 5 Jul 1995 20:36:58 GMT Organization: University of Georgia, Athens Lines: 50 Message-ID: <3tet5a$asf@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi all: Many times I have compiled version 3.7 on our Sparcstation, running Solaris 2.4, using gcc 2.6.3 without unusual compilation errors. Each time, when I try to start it for the first time, I get the following series of warnings: .................................................................... Type of Locus does not check in B object "Gene" Type of Locus does not check in B object "Other_Locus" Type of Clone does not check in B object "Expression" Type of Sequence does not check in B object "Genome_Sequence" Type of Sequence does not check in B object "cDNA_Sequence" Type of Sequence does not check in B object "Repeat_Sequence" Type of Allele does not check in B object "Tc_Insertion" Missing or unrecognised Class #Class# after FIND Less than 3 visible classes. Add-Update file or Read-Models from main menu. Save, Quit, and restart Acedb. Notice that as of release 1-9, Classes are declared visible in options.wrm. Can't find the meta class 79 = Species Can't find the meta class 78 = Library Further similar warnings suppressed Can't find the Class object for Class:Clone Can't find the Class object for Class:Allele Can't find the Class object for Class:Locus Can't find the Class object for Class:Sequence You are missing the model for UserSession. To bring your database up to date please Read Models. You will not be able to save until you do this. FATAL ERROR: Missing model of class: Model .................................................................... I noticed that the "Type of" errors trace through the subclasses.wrm file. These errors occur although I am using only the .wrm files that shipped with the distribution. Since I never get a Main Window, of course, I can't read models or do anything. Does any of this look familiar to anyone? Thanks. -- Paul Brunk, ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!cssun.mathcs.emory.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: KeySet in Main Display Date: 5 Jul 1995 20:22:52 GMT Organization: University of Georgia, Athens Lines: 14 Message-ID: <3tesas$9l0@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi folks, We're running the 3.6 version of ACEDB for our peanut database, and I'd like to get "KeySet" and "Keyword" out of the main display window. I tried listing them as hidden ("-H") in options.wrm, but they're still there. Does anyone know how to get rid of them? Thanks. -- Paul Brunk, ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Wed Jul 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!EU.net!uknet!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Re: KeySet in Main Display Date: 6 Jul 1995 10:45:56 +0100 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3tgbck$q7b@mserv1.dl.ac.uk> Original-To: pbrunk@dogwood.botany.uga.edu From Paul Brunk: > We're running the 3.6 version of ACEDB for our peanut database, and > I'd like to get "KeySet" and "Keyword" out of the main display window. > I tried listing them as hidden ("-H") in options.wrm, but they're > still there. Does anyone know how to get rid of them? Unfortunately, the version 3 and current version 4 codes set these visible in the inbuilt equivalent of options.wrm for system classes. So you can't change it without changing whooks/sysclass.c and recompiling. We came across the same problem ourselves, and plan to allow options.wrm to override the internal default. Richard From owner-acedb@net.bio.net Fri Jul 07 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.bc.net!newsserver.sfu.ca!trog!jbryer From: jbryer@trog.mbb.sfu.ca (Jeff Bryer) Newsgroups: bionet.celegans,bionet.software.acedb Subject: ANNOUNCE: ACEDB v4 Linux binary now available Date: 8 Jul 95 04:22:11 GMT Organization: Simon Fraser University Lines: 62 Message-ID: NNTP-Posting-Host: @trog.mbb.sfu.ca Xref: biosci bionet.celegans:458 bionet.software.acedb:656 I have just made available via ftp the Linux binary for version 4 of ACEDB. Thanks immensely to Ken Clark for doing the actual port. You can pick up the binary from trog.mbb.sfu.ca in /pub/acedb as bin.linux.4_0.tar.Z. This is based on the source code for the beta version 4 available from ncbi.nlm.nih.gov. We intend to make available a release version of the Linux binary once ACEDB ver 4 final has been released. As usual, for the C. elegans community I have compiled in the current set of updates (4-6) and will be making available an archive containing the Linux ACEDB 4 binary and the C. elegans dataset (so you don't have to wait a few hours compiling in the data yourself). The filename is linux.4_6.tar.Z and is in the same location as the linux binary. Uncompressed this archive is about 170MBs in size. I don't actually have access to the machine that has this archive on it right now but I will place it on trog Monday the 10th at the latest. If you need the archive in smaller chunks (for ftp'ing) please let me know. What follows is the readme file for the Linux ACEDB version 4 binary. Jeff Bryer jbryer@darwin.mbb.sfu.ca ----- README.LINUX.4_0 July 7, 1995 A port of Acedb 4.0 test 4_0b4a for Linux can be found on ftp://trog.mbb.sfu.ca/pub/acedb/bin.linux.4_0.tar.Z It will apear on ncbi.nlm.nih.gov when the official Acedb 4.0 is released. Linux is a free Unix-like OS available for the Intel [345]86 platform. You can find out more about Linux in the comp.os.linux.* groups on usenet. Acedb runs very well on Linux, but you will need a fairly loaded system. I reccomend at _least_ 16MB of RAM and a 486/33. You will also want a large disk that can accomodate the database's growth. More RAM is much better than a faster processor. A 486/66 with 32MB RAM will blow the doors off a Pentium/100 with 8M. You should have 32MB of swap for updates. You should be running Linux 1.0 or better and the a.out shared libraries (I am using libc 4.5.26). Other versions should work, but are untested. Note that this release will NOT work if you are running with only Linux ELF libraries. I will release an ELF port when the official Acedb 4.0 is released. The port to Linux was very simple. If you are familiar with Makefiles and C, do not be afraid to compile it yourself. Ken Clark ken@darwin.mbb.sfu.ca From owner-acedb@net.bio.net Tue Jul 11 23:00:00 1995 Path: biosci!rutgers!gatech!news.uoregon.edu!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!dave_s From: dave_s@iastate.edu (David A Schrader) Newsgroups: bionet.software.acedb Subject: error running v3.7 Date: 12 Jul 1995 17:31:27 GMT Organization: Iowa State University, Ames, Iowa USA Lines: 19 Message-ID: <3u10tf$qg5@news.iastate.edu> NNTP-Posting-Host: isum1.iastate.edu I am running ace version 3.7 and get an "intersting" error. It occurs when I am attempting to do a save from the main menu after having rearranged things in metabolic pathways. The message printed when ace exits is : Metab.c:1226 FAILED ASSERTION `bsAddKey(pw,_Diagram,diagkey)' Any insights into the cause of this ( and any solutions ) would be greatly appreciated. Dave S. -- =============================================================================== | Dave Schrader | But remember, as you stare into the abyss,| |schrader@mendel.agron.iastate.edu| so the abyss also stares into you. | | (515) 294-0421 | -Nietzsche | =============================================================================== From owner-acedb@net.bio.net Wed Jul 12 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Re: 3.7 pathway problem Date: 13 Jul 1995 14:18:44 +0100 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3u36fk$g6@mserv1.dl.ac.uk> Original-To: schrader@mendel.agron.iastate.edu OK. Thanks. I know what the problem is. It requires a code change, which I will make here in out master copy of the code. Presumably you want to use this. Can you recompile your code? If so, then before the line: assert(bsAddKey(pw,_Diagram,diagkey)); add if(!bsFindKey (diag,_Diagram,diagkey)) so you get if(!bsFindKey (diag,_Diagram,diagkey)) assert(bsAddKey(pw,_Diagram,diagkey)); If you don't want to recompile, there is a slightly painful work-around. You can delete the Diagram entry from the pathway object by hand, using the interactive Update mode from the text display window. You would have to do this before saving the diagram each time. Richard From owner-acedb@net.bio.net Wed Jul 12 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: stop nuclear tests Date: 13 Jul 1995 18:49:07 +0100 Lines: 99 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3u3maj$f1p@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, labo@kaa.crbm.cnrs-mop.fr #### ##### #### ##### # # # # # # #### # # # # # # # # # ##### # # # # # # #### # #### # # # # # #### # ###### ## ##### ## # # # # # # # # # # # # # # # # # # ##### # # # # # # # # # # # # ###### ##### # ## # # # # # # # # # # # # #### #### ###### ###### # # # # ##### ###### #### ##### #### # # # # # # # # ##### #### # #### # # # # # # # # # # # # # # # ###### #### # #### # 1 SHIMIZU Seishi Physics,University of Tokyo,Japan 2 Yuichi Nishihara Physics,University of Tokyo,Japan 3 Hirohisa TANIGUCHI Physics,University of Tokyo,Japan 4 Takashi Tomoeda Physics,University of Tokyo,Japan 5 Tomoki KOBAYASHI Physics,University of Tokyo,Japan 6 Munehito ARAI Physics,University of Tokyo,Japan 7 Akira Okazaki Physics,University of Tokyo,Japan 8 Atsushi Matsumura Physics, Tohoku University, Japan 9 Kouta Yamamoto Chemistry,Tohoku University,Japan 10 Yasushi UJIOKA Degremont S.A., France 11 Toru Hara Universite de Paris Sud, France 12 Rene Bakker CEA - Sacley, France 13 David Garzella Universite de Paris Sud, France 14 Henk Blok Vrije Universiteit/NIKHEF, Amsterdam 15 Igor Passchier NIKHEF, Amsterdam 16 Ard van Sighem NIKHEF, Amsterdam 17 Johan Noordhoek KOL Leiden 18 C.M.C.M. van Woerkens Kamerlingh Onnes Laboratory, Leiden 19 Annemarie Borst, Vrije Universiteit Amsterdam 20 Gijs Nelemans Universiteit Utrecht 21 Susanne Buiter Universiteit Utrecht 22 Yvo Kok Paleomagnetic Lab., Utrecht 23 Thom Pick Paleomagnetic Lab., Utrecht University 24 Dagmar Olbertz Universiteit Utrecht 25 Eleonore Stutzmann Institut de Physique du Globe de Paris, France 26 Nicole Girardin Institut de Physique du Globe de Paris, France 27 Francois Girardin Ecole Nat. Sup. des Telecommunications,France 28 Axel Manthey Comnets RWTHJ Aachen, Germany 29 Frank Brockners LfBS RWTH Aachen, Germany 30 Marcus Dormanns LfBS RWTH Aachen, Germany 31 Roger Butenuth Uni (GH) Paderborn, Germany 32 Markus Mock University of Washington, Seattle, USA 33 Wei-Der Shu Department of Sociology, Syracuse University, USA 34 Hung-Liang Lai Physics, Michigan State University, USA 35 Wu-Ki Tung Dept. of Physics/Astronomy, Michigan State Univ. USA 36 Markus Hofmann Institut f. Theoretische Physik, Uni Frankfurt, Germany 37 Juergen Schaffner Niels Bohr Institute, Copenhagen, Denmark 38 Michael Mang Gesellschaft fuer Schwerionenforschung,Darmstadt,Germany 39 Christian Doerr 40 Stephan Mohr Psychologisches Instit Tuebingen, Germany 41 Ulf Reips Psychologisches Instit Tuebingen, Germany 42 Jamie Cope MRC-LMB, Hills Rd., Cambridge CB1 2ET 43 Cameron Smith Department of Chemistry, University of Cambridge, UK 44 Alison Hill Department of Chemistry, Brown University, USA 45 Helen Hailes Department of Chemistry, University College London 46 Simon Kelley Sanger Centre, Hinxton, Cambridge. 47 Danielle Thierry-Mieg CNRS, CRBM , Montpellier, France 48 Jean Thierry-Mieg CNRS, Physique Theorique, Montpellier, France ************ Dear Sirs, This is a chain letter to urge the French government to stop nuclear tests. If you agree with us, please add your name to the list above, and send copies to your friends. We will add up the lists that come back to us, and send it to the French government. If you happen to be the hundredth, two hundredth, three hundredth, and so on, on the list, please send a copy of the mail back to the addresses below, so that we can keep track of this project. If you have any comment please send mails to us. And also, if you are multi-lingual and have friends who may not understand English, please translate this message and add it to the end of the mail. Thank you very much. ******* addresses of the organizers shimizu@femto.phys.s.u-tokyo.ac.jp keshi@uticeaix1.icepp.s.u-tokyo.ac.jp <- please use this adress ******* From owner-acedb@net.bio.net Sun Jul 16 23:00:00 1995 Path: biosci!rutgers!goliath.montclair.edu!newsserver.jvnc.net!newsserver2.jvnc.net!howland.reston.ans.net!usc!nic-nac.CSU.net!csulb.edu!paris.ics.uci.edu!ucivax!gateway From: salro@nd.edu (Ellen Eng) Subject: ===>> FREE 1 yr. Magazine Sub sent worldwide- 300+ Popular USA Titles (fwd) X-Sender: salro@amanda.dorsai.org Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII MIME-Version: 1.0 Newsgroups: bionet.software.acedb Lines: 1228 Date: 17 Jul 95 18:20:53 GMT ---------- Forwarded message ---------- Date: Mon, 17 Jul 1995 12:40:19 -0400 (edt) From: Ellen Eng To: cl.fluechtlinge@paris.ics.uci.edu, cl.freie_liebe.schwule@paris.ics.uci.edu, cl.gruppen.bund@paris.ics.uci.edu, de.org.in@paris.ics.uci.edu, de.org.sub@paris.ics.uci.edu, de.org.sub.d@paris.ics.uci.edu, de.rec.fahrrad@paris.ics.uci.edu, de.rec.games@paris.ics.uci.edu Subject: ===>> FREE 1 yr. Magazine Sub sent worldwide- 300+ Popular USA Titles Hi, my name is Ellen Eng and I recently started using a magazine subscription club in the USA that has a FREE 1 yr. magazine subscription deal with your first paid order- and I have been very pleased with them. They have over 1,500 different USA titles that they can ship to any country on a subscription basis. They saved me a lot of money on my Economist subscription: over $40 off the best subscription price on I had seen anywhere else and they got me a great deal on USA Today newspaper, which arrives the same day as the cover date. (I still don't know how they manage to do that!) They will send you some FREE info. via E-mail (the short version (around 40K) of their catalogue, or if you request it the DELUXE LONG VERSION (around 400K-big and juicey) !)...if you fill out the form below. Please do not email me as I am just a happy customer and a *busy* student. I don't have time to even complete my thesis in time, let alone run my part-time software business! Email them directly at: jta@panix.com *------------cut here-----------------------------------------------* REQUEST FOR MORE INFO: please copy this section *only* and email to: jta@panix.com (sorry, but they cannot acknowledge incomplete forms sent back) Name: Internet email address: Smail home address: City-State-Zip: Country: Work Tel. #: Work Fax #: Home Tel. #: Home Fax #: Name of USA mags you currently get: Name of USA mags you would like price quotes on when we call you: Do you want the short (~40K) or long version (~400K) of our catalogue emailed to you?: How did you hear about us (name of person who referred you or the area of the internet that you saw us mentioned in): Ellen Eng 071795 *------------cut here-----------------------------------------------* They guarantee to beat all their competitors' prices. Sometimes they are less than half of the next best deal I have been able to find and other times, just a little cheaper - but I have never found a lower rate yet. 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INCOME OPPORTUNITIES INCOME PLUS INCREDIBLE HULK (COMIC) INDIVIDUAL INVESTOR IINDUSTRIAL MARKET PLACE INSIDE EDGE INSIDE IRELAND INSIDE KARATE INSIDE KUNG FU INSIDE SPORTS INSIGHT INSTITUTIONAL INVESTOR INSTRUCTOR INTERIOR DECORATOR'S HANDBOOK INTERIOR DESIGN INTERIORS INTERNATIONAL LIVING INTERNATIONAL NURSING INDEX INTERNET WORLD INTERVIEW INTIMATE FASHION NEWS INVESTOR'S DAILY IRON MAN (COMIC) ISLANDS ISRAEL SCENE JACK & JILL JERSEY WOMAN JERUSALEM POST INTERNATIONAL WEEKLY EDITION JERUSALEM REPORT JET JEWISH EXPONENT JEWISH HOMEMAKER JEWISH POST & OPINION JEWISH PRESS JUSTICE LEAGUE AMERICA (COMIC) JUSTICE LEAGUE EUROPE ( COMIC) KARATE / KUNG FU ILLUSTATED KEYBOARD KID CITY KIDSPORTS KIPLINGER'S PERSONAL FINANCE KIT CAR KITPLANES KNIFE WORLD KNITTING DIGEST KNITTING WORLD L'ACTUALITE LA LUZ LA VIE LADIES HOME JOURNAL LADY'S CIRCLE LADYBUG LAKELAND BOATING LAN MAGAZINE (LOCAL AREA NETWORK) LAPIDARY JOURNAL LEADERSHIP LEARNING '94 LEFTHANDER LEGAL GUIDE FOR THE FAMILY LEGION OF SUPER-HEROES (COMIC) LET'S LIVE LIBRARY OF NATURAL WONDERS LIFE LIGHTING DIMENSIONS LINK-UP LINN'S STAMP NEWS LITTLE MERMAID LLUMO VOGUE LONGEVITY LOONEY TUNES (COMIC) LOOSE CHANGE LOS ANGELES LOTTERY PLAYERS MAGAZINE MAC HOME JOURNAL MACLEANS MACUSER MACWORLD MADEMOISELLE MARKETERS FORUM MARRIAGE PARTNERSHIP MARVEL AGE (COMIC) MARVEL COMICS PRESENTS MARVEL TALES SPIDERMAN (COMIC) MCCALL'S MCCALL'S NEEDLEWORK & CRAFTS MECANICA POPULAR MECHANICA POPULAR MEDIA & METHODS MEDICAL & HEALTH ENCYCLOPEDIA MEDICAL HOTLINE MEDICAL UPDATE MEGA PLAY MEMPHIS MAGAZINE MEN'S CONFIDENTIAL MEN'S FITNESS MEN'S HEALTH MEN'S JOURNAL METROPOLIS METROPOLITAN HOME MICKEY MOUSE MICRO COMPUTER JOURNAL MICROSOFT SYSTEMS JOURNAL MID-ATLANTIC COUNTRY MIDSTREAM MIDWEST LIVING MILITARY HISTORY MILWAUKEE MINISTRIES TODAY MINNESOTA MONTHLY MIRABELLA MOBILE OFFICE MODEL AIRPLANE NEWS MODEL NEWS MODEL SHOPPER MODELS & TALENT/CASTING NEWS MODERN BRIDE MODERN GUN MODERN HORSE BREEDING MODERN SALON MOMENT MONEY MONEYPAPER MOODY MAGAZINE MOODY MONTHLY MOPAR MUSCLE MORIBUS (COMIC) MOTHER EARTH NEWS MOTHER JONES MOTHERING MOTOR BOATING & SAILING MOTOR TREND MOTORCROSS ACTION MOTORCYCLE CONSUMER NEWS MOTORCYCLIST MOTORHOME MOUNTAIN BIKE MOVIE MARKETPLACE MOVIELINE MUNDO 21 MUSCLE & FITNESS MUSCLECAR REVIEW MUSICIAN MUSTANG MONTHLY MUSTANGS & FORDS MUSTANGS MONTHLY NAILS NAMOR (COMIC) NATION NATION'S BUSINESS NATION'S RESTAURANT NEWS NATIONAL AUCTION REPORT NATIONAL ENQUIRER NATIONAL FISHERMAN NATIONAL LAW JOURNAL NATIONAL OTC STOCK JOURNAL NATIONAL PARK MAGAZINE NATIONAL REVIEW NATIONAL TRIAL LAWYER NATURAL HEALTH NATURAL HISTORY NAVY TIMES NBA INSIDE STUFF *THE NET* (about the Internet) NEEDLE & CRAFT NEVADA MAGAZINE NEW AGE JOURNAL NEW BUSINESS OPPORTUNITIES NEW CHOICES NEW ENGLAND JOURNAL OF MEDICINE NEW FARM NEW JERSEY MONTHLY NEW JERSEY OUTDOORS NEW MEXICO NEW REPUBLIC NEW TITANS (COMIC) NEW WARRIORS (COMIC) NEW WOMAN NEW YORK MAGAZINE NEW YORK REVIEW OF BOOKS NEW YORKER NEWSWEEK NICE & EASY FAMILY 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Once you get in, you'll love them. I do. For more info, just fill out the form near the top of this message and email it to their email address shown there. Thanks, Ellen Eng From owner-acedb@net.bio.net Sun Jul 16 23:00:00 1995 Path: biosci!KLAB.AGSCI.COLOSTATE.EDU!mferguso From: mferguso@KLAB.AGSCI.COLOSTATE.EDU (Martin Ferguson) Newsgroups: bionet.software.acedb Subject: Announcement: genbank to ace conversion program. Date: 17 Jul 1995 15:17:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <9507172215.AA00282@klab> NNTP-Posting-Host: net.bio.net Greetings all, I don't know how much people want something like this, but... I've written a Genbank to .ace conversion script in perl. It handles the latest version of Genbank flat format files and outputs into ACEDB version 4 type ?Sequence and ?Paper models. (The models we use have been slightly changed from the distribution - a copy is enclosed.) Most of the Genbank features are handled, and the user can set an option to generically handle the features for which I did not write specific code. The feature handling routines are in a separate file, so it's easy to extend them. The tar file is available at: http://klab.agsci.colostate.edu/~mferguso/files.html Enjoy. Also, please send me your comments (or requests, even). /s/ Martin Ferguson mferguso@klab.agsci.colostate.edu P.S. If anyone knows of some perl libraries to handle asn.1 data, please let me know. From owner-acedb@net.bio.net Mon Jul 17 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!grape.epix.net!sc2c526a.ra.osd.mil!nova.sti.nasa.gov!lerc.nasa.gov!purdue!yuma!klab3.agsci.colostate.edu!user From: martinf@lamar.colostate.edu (Martin Ferguson) Newsgroups: bionet.software.acedb Subject: Re: Announcement: genbank to ace conversion program. Date: Tue, 18 Jul 1995 10:31:26 -0600 Organization: CO State University Lines: 6 Distribution: world Message-ID: References: <9507172215.AA00282@klab> NNTP-Posting-Host: klab3.agsci.colostate.edu Hello again, Regarding the genbank to ace conversion script, I should mention that Perl version 5.001 or later is required. /s/ Martin From owner-acedb@net.bio.net Tue Jul 18 23:00:00 1995 Newsgroups: bionet.software.acedb Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.rhrz.uni-bonn.de!news.uni-stuttgart.de!news.belwue.de!news.informatik.uni-stuttgart.de!baumann From: baumann@hermes.informatik.uni-stuttgart.de (Joachim Baumann) Subject: Re: Announcement: genbank to ace conversion program. In-Reply-To: mferguso@KLAB.AGSCI.COLOSTATE.EDU's message of 17 Jul 1995 15:17:43 -0700 X-Nntp-Posting-Host: habakuk Message-ID: Sender: news@informatik.uni-stuttgart.de Organization: IPVR, University of Stuttgart, Germany References: <9507172215.AA00282@klab> Date: Wed, 19 Jul 1995 08:15:43 GMT Lines: 17 Hello, we've written such a beast also, but for the binary representation (ASN.1) as well as for text files. It is written in C, uses the NCBI toolkit (see http://www.ncbi.nlm.nih.gov/), and is able to decode Entrez Data with the help of an additional program. It can be found at ftp.informatik.uni-stuttgart.de:/pub/DART/ASN2ACE/asn2ace-1.0.tar.gz Greetings, Joachim ------------------------------------------------------------------------------- Snail: Joachim Baumann, | Universitaet Stuttgart, IPVR, | Phone: (+49 | 0 ) 711/7816-218 Breitwiesenstr. 20-22, | Fax: (+49 | 0 ) 711/7816-424 70565 Stuttgart, Germany | EMail: joachim.baumann@informatik.uni-stuttgart.de(.sol_3.milky-way.universe) PGP: finger baumann@orgel.informatik.uni-stuttgart.de From owner-acedb@net.bio.net Wed Jul 19 23:00:00 1995 Path: biosci!rutgers!gatech!emf.emf.net!overload.lbl.gov!news From: John McCarthy Newsgroups: bionet.software.acedb Subject: ACEDB 1995 Conference and Workshop Documents Date: 20 Jul 1995 17:40:08 GMT Organization: Lawrence Berkeley Laboratory, Berkeley CA Lines: 16 Message-ID: <3um4do$9a6@overload.lbl.gov> NNTP-Posting-Host: slavsing.lbl.gov The final report and other documents from the recently concluded ACEDB 1995 Conference and Workshop are now available via the WWW server at the National Agricultural Library. For the final summary report, see http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html For the complete set of documents, see http://probe.nalusda.gov:8000/acedocs/ace95/index.html Further contributions are welcome! John McCarthy, Chair ACEDB 1995 Conference and Workshop From owner-acedb@net.bio.net Wed Jul 26 23:00:00 1995 Path: biosci!agate!uclink.berkeley.edu!tomyeh From: tomyeh@uclink.berkeley.edu (Tom Yu-San Yeh) Newsgroups: bionet.software.acedb Subject: Re: Help with Computer Date: 27 Jul 1995 08:13:36 GMT Organization: University of California, Berkeley Lines: 15 Distribution: bionet Message-ID: <3v7hrg$e2l@agate.berkeley.edu> NNTP-Posting-Host: uclink.berkeley.edu Hello Everyone, I am recently having problems with my home-ip program. I am currently using Winsock version 2.0B. It worked fine for a while until recently after logging on to the school computer with Winsock, I am not able to run netscape or qvtnet. The windows do appear but netscape will remain in trying to "look up host" or "waiting for reply" and QVTNET is not able to open up a terminal and log in. I don't know what is wrong with the system but if anyone out there wanted to help and think they might know what the problem is, please email me at tomyeh@uclink.berkeley.edu Thanks in advance. ---Tom P.S. I also recently installed Delrina Winfax Pro. Could that be the problem? From owner-acedb@net.bio.net Wed Jul 26 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!newsfeed.internetmci.com!news.uoregon.edu!tank.news.pipex.net!pipex!news.sprintlink.net!news.interserv.net!usenet From: Dave Newsgroups: bionet.software.acedb Subject: FREE SOFTWARE CATALOG! 800-569-7900 Date: 27 Jul 1995 18:27:55 GMT Organization: InterServ News Service Lines: 14 Message-ID: <3v8lrb$dg5@data.interserv.net> NNTP-Posting-Host: dd04-026.compuserve.com X-Newsreader: SPRY News 3.03 (SPRY, Inc.) FREE SOFTWARE CATALOG! 800-569-7900 Call toll free for your 65 page, full color catalog! This catalog is filled with hundreds of hot new titles for low prices. Also, tell them you got the message from Dave! 1-800-569-7900 From owner-acedb@net.bio.net Wed Jul 26 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!gatech!news.uoregon.edu!tank.news.pipex.net!pipex!swrinde!emory!cssun.mathcs.emory.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: WWW-ACEDB interface Date: 27 Jul 1995 20:24:06 GMT Organization: University of Georgia, Athens Lines: 20 Message-ID: <3v8sl6$lls@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi all: I'm using the WWW-ACEDB interface from moulon.inra.fr (version 3.6 of ACeDB and version 3.6 of the interface, and we're using the interface compiled into the NCSA httpd, rather than the cgi script one) and I have a strange problem: In our model for "Colleague", there's a Text field called "Email". This field simply doesn't show up in the WWW interface to our acedb, although it's there in the X interface. I took a brief look at the WWW-ACEDB interface source code (grepped for "Email") without results, though haven't looked more closely. Maybe there's something about the "@" sign in there somewhere. Any ideas? Thanks. -- Paul Brunk, ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Wed Jul 26 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!tank.news.pipex.net!pipex!swrinde!emory!cssun.mathcs.emory.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: Re: WWW-ACEDB interface Date: 27 Jul 1995 20:29:52 GMT Organization: University of Georgia, Athens Lines: 11 Message-ID: <3v8t00$mcd@hobbes.cc.uga.edu> References: <3v8sl6$lls@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi all: Turns out that I had to restart the httpd in order to make it read changes to the database. This was a complete kill-and-restart, not just a "kill -1". -- Paul Brunk, ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Thu Jul 27 23:00:00 1995 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: couchman@BBSRC.AC.UK (Matt) Newsgroups: bionet.software.acedb Subject: Agarose Gel Window Date: 28 Jul 1995 15:01:59 GMT Organization: John Innes Centre Lines: 17 Message-ID: <3vau57$k9n@is.bbsrc.ac.uk> NNTP-Posting-Host: pc0454.jic.bbsrc.ac.uk X-Newsreader: WinVN 0.92.1 Hello, I'm having a few problems running the "Agarose Gel" and "DNA Analysis" windows in conjunction with the sequence displays. Everything is OK when analysing the c. elegans data. I'm just wondering how to obtain a similar set up, viewing a new set of sequences. At the moment I can get good results by specifying mini sequences to search for but I get nothing when I specify a restriction enzyme. That is the enzymes are recognised (there is no warning box) but produce no results in the sequence window. The executable and specification of ?Motif are the same as those used for the c. elegans data so I would guess i've missed a step somewhere along the way. Any help much appreciated (doubly so considering how badly I've explained myself!), Matt. From owner-acedb@net.bio.net Thu Jul 27 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!news.sprintlink.net!grape.epix.net!grape.epix.net!zarathu From: Eric J Uberseder Newsgroups: bionet.software.acedb Subject: Shareware News Date: Fri, 28 Jul 1995 12:17:36 -0400 Organization: epix.net Lines: 16 Message-ID: NNTP-Posting-Host: grape.epix.net Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For Macintosh Computer Users: Do you remember a time a few years ago when MacUser Magazine made its reputation by providing mac users with abundant low cost shareware software solutions? That time is long past in all the magazines. If it was available to you, would you be interested in paying a nominal fee for a monthly shareware review digest. You could expect at least 15 reviews a month, by a reviewer with a machine like yours and who is not so connected to the programmer, that he can't pan the item. If you are interested, please reply at: zarathu@epix.net From owner-acedb@net.bio.net Sat Jul 29 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!nntp-trd.UNINETT.no!nac.no!news.kth.se!usenet From: Staffan Bergh Newsgroups: bionet.software.acedb Subject: AboutDB is back! Date: 30 Jul 1995 17:05:02 GMT Organization: Biochemistry, Royal Institute of Technology Lines: 18 Message-ID: <3vge3v$m7t@news.kth.se> NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.4 sun4m) X-URL: news:bionet.software.acedb Finally! AboutDB has metamorphosed somewhat, by losing the Communication and Bug classes, and gaining direct links into the documentation on Magic tags worked out during the Ace95 workshop. What is still lacking are updating the old documentation links and tool links. That's coming, I promise! AboutDB still uses Ace3.0 and the Ace3.0 Moulon server. As soon as Ace4 is released and the perl client is available, I plan to switch over to that combination. In recognition of that fact, this is version 0.9 of AboutDB - it will be version 1.0 when the switch happens. As usual, I welcome comments and corrections. /staffan From owner-acedb@net.bio.net Sun Jul 30 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!nntp-trd.UNINETT.no!nac.no!news.kth.se!sibirien.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: AboutDB is back! Date: 31 Jul 1995 08:33:14 +0200 Organization: Biochemistry, KTH, Stockholm Lines: 16 Message-ID: <3vhtfa$gku@sibirien.physchem.kth.se> References: <3vge3v$m7t@news.kth.se> NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Ooops, forgot to give the address ... http://www.biochem.kth.se/AboutDB.html /staffan Staffan Bergh Biochemistry, KTH, S-100 44 Stockholm, Sweden email: staffan@biochem.kth.se + Don't let that horse eat that violin phone: int+46 8 790 9230 + cried Chagall's mother fax: int+46 8 24 54 52 + but he kept right on painting + -- Lawrence Ferlinghetti Webmaster and MycDB maintainer From owner-acedb@net.bio.net Mon Jul 31 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 1 Aug 1995 02:00:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 347 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508010900.CAA13320@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions on how to subscribe/unsubscribe will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. Any text placed on the Subject: line of your message will be ignored, so be sure to put the "help" command in the body of the message. If you need personal assistance, a BIOSCI staff member can be contacted at either of the following addresses. Please contact the address designated for your location. Support Address Location --------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim **** SEARCHING BIOSCI ARCHIVES **** The easiest way to search the BIOSCI archives is to use Mosaic or another World Wide Web browser and connect to the BIOSCI WWW home page at URL http://www.bio.net/. Select the hypertext link to the BIOSCI archives. This gives you read access to all newsgroup messages and the ability to search the indexes described below. You can also use gopher software and connect over the Internet to net.bio.net, the U.S. BIOSCI computer. We maintain three indexes which are searchable from the main gopher menu on net.bio.net: (1) an index of all BIOSCI postings; (2) an index of individual journal article references from the Table of Contents postings on the BIO-JOURNALS newsgroup; and (3) an index of BIOSCI users including regular mail and e-mail addresses, phone/FAX numbers, research interests, and newsgroup participation. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). Finally, the BIOSCI archive files are accessible by anonymous FTP to net.bio.net [134.172.2.69] in the directory pub/BIOSCI. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and fix problems that you might encounter in using the newsgroups. The FAQ and other BIOSCI documentation is available through our WWW home page at URL http://www.bio.net/. It is also available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS, waismail, gopher, and WWW access (the URL is http://www.bio.net). If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 14. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > > 6. Information in English/ > > 5. Scientific and other topics/ > > 1. Finnish EMBnet BioBox/ > > 9. FAQ Files/ > > 5. Bionauts Address Database (questionaire) > IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 15-05-93 for 15 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 15-05-93, not 15-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: