From owner-acedb@net.bio.net Wed Aug 02 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!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: main window class order Date: 3 Aug 1995 14:06:45 GMT Organization: Iowa State University, Ames, Iowa USA Lines: 34 Message-ID: <3vql5l$3o1@news.iastate.edu> NNTP-Posting-Host: isum1.iastate.edu I am running ACEdb 3.7 and am having trouble getting the classes in the main window in the order I want. I was told that the order in options.wrm should be : R=row C=Column R1C1 R1C2 R1C3 R2C1 R2C2 R2C3 R3C1 . . . RnC1 RnC2 RnC3 And that appears to be true part of the time but not in all cases. For instance, it doesn't appear to matter where I put my Germplasm class because it always appears in position R1C1. Any insights into this 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 Aug 02 23:00:00 1995 Path: biosci!DOLPHIN.UPENN.EDU!stein From: stein@DOLPHIN.UPENN.EDU Newsgroups: bionet.software.acedb Subject: postdoc Date: 3 Aug 1995 16:37:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508032335.TAA23918@dolphin.upenn.edu> NNTP-Posting-Host: net.bio.net From stein Thu Aug 3 19:32:22 1995 >From stein@dolphin.upenn.edu Thu Aug 3 19:32:22 1995 Received: by dolphin.upenn.edu id TAA23911; Thu, 3 Aug 1995 19:32:22 -0400 Posted-Date: Thu, 3 Aug 1995 19:32:22 -0400 Received-Date: Thu, 3 Aug 1995 19:32:22 -0400 Subject: To: stein@dolphin.upenn.edu Date: Thu, 3 Aug 1995 19:32:22 -0400 (EDT) From: stein@alumni.upenn.edu X-Sender: "stein" X-Mailer: ELM [version 2.4 PL23-upenn2.9] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 422 Status: O SUBJECT: Seeking for postdoctoral position FIELD: Molecular Biology & Genetics of Oncogenes or Antioncogenes SKILLS: Cloning, sequencing, mutagenesis, PCR (RT-PCR), Southern & Northern blotting, immunoprecipitation, CAT, tissue culture, tumor induction, PC, publications registered in CC, etc. WHEN: available immediately, further information upon request ADDRESS: stein@dolphin.upenn.edu From owner-acedb@net.bio.net Sun Aug 06 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.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: 7 Aug 1995 17:08:05 GMT Organization: Dendrome, A genome database for forest trees Lines: 1092 Approved: news-answers-request@MIT.Edu Message-ID: <405h9l$ou0@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:679 news.answers:44417 Archive-name: acedb-faq Last-modified: 8/7/95 Version: 1.23 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.) 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/Pentium with Linux (free Unix) [note from Jeff Bryer, jbryer@darwin.mbb.sfu.ca] 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. 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 bin.linux.4_0.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 : Staffan Bergh o Contact : staffan@biochem.kth.se o Last_update : July 1995 o ACEDB_version : 3.0 o Data_version : 3-8 (June 18, 1995) o WWW : http://www.biochem.kth.se/MycDB.html o WWW : http://probe.nalusda.gov:8300/other/index.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 : Musculus 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 : 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 Rachael Selley. o Contact : rselley@har-rbu.mrc.ac.uk, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD o Last_update : July 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. 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: +++ 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. 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 Mon Aug 07 23:00:00 1995 Path: biosci!daresbury!usenet From: "M.P. Hilbers" Newsgroups: bionet.software.acedb Subject: Error when updating aatdb to 3.6 Date: 8 Aug 1995 10:48:29 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 14 Distribution: bionet Message-ID: <407fdt$3c6@mserv1.dl.ac.uk> NNTP-Posting-Host: s-crim1.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.2 IP17) X-URL: news:bionet.software.acedb Hello there, I tried to update aatdb 3.5 to 3.6, but I got an error message: !! FATAL ERROR 0: !! ERROR : diskblockread read a block not matching its address I've tried several times, downloaded the update file again from ftp.ebi.ac.uk, but things always stopped at line 26945 of the update file. I'm running xace3 on a SGI-system (Iris 5.2) Has anybody a bright idea about what went wrong ? Thanks, Martin Hilbers From owner-acedb@net.bio.net Wed Aug 09 23:00:00 1995 Path: biosci!mrc-lmb.cam.ac.uk!rd From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB 4_1 program release Date: 10 Aug 1995 10:52:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508101748.AA13025@cele.mrc-lmb.cam.ac.uk> NNTP-Posting-Host: net.bio.net 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 program version 4_1 ========================= Version 4_1 of acedb is now available. This is a full release of the latest version of acedb. A large number of bugs has been fixed from the initial version 4_0b4 release (see wdoc/bugs.4 and wdoc/bugs.4.fixed for details). As well as program bugs we believe we have fixed the installation problems for SunOS and Solaris machines (it works on the machines we can find, but these things always catch you out...). If you used the previous beta release, 4_0b4, then your wspec/ and data/ files will be completely compatible, but you must remake the database from scratch from update files or .ace files. Otherwise (1) dates will not print properly (they would never have reliably using the 4_0 system), and (2) the global search facility would not work properly (it didn't under 4_0). The official ftp sites are: 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 See the files README and NOTES in these directories for further instructions. The official acedb documentation site is at http://probe.nalusda.gov:8000/acedocs/index.html (thanks Sam Cartinhour and Doug Bigwood). Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) From owner-acedb@net.bio.net Wed Aug 09 23:00:00 1995 Path: biosci!mrc-lmb.cam.ac.uk!rd From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB C.elegans data update 4-7 Date: 10 Aug 1995 10:52:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 99 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508101748.AA13031@cele.mrc-lmb.cam.ac.uk> NNTP-Posting-Host: net.bio.net 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 update 4-7 for C. elegans ==================================== This update should be used in conjunction with updates 4-1 to 4-6, and version 4_1 of ACEDB, which is being made available at the same time (see other email). You should rebuild the database when you get code version 4_1. The total database size is now approximately 190Mbytes. The major additions since 4-6 are: - a lot more genomic sequence data (there are now 581 cosmids totalling 17,910,882 bases). - the 1995 worm meeting entries have been renamed according to page numbers, and 3 missing abstracts have been read in. - the CGC bibliography has been updated, with 106 new entries. - Tc1 insertion data from Ronald Pasterk's group has been put back; it was missing in the first version 4 release (sorry Ronald, et al.). Mapped Tc1 insertion sites are now visible on the sequence and physical map. - a new Expr_pattern class has been created to show expression data, and some has been added. Please see wbg13.5p89, and send comments/data to sylvia@sanger.ac.uk. - a number of errors and problems have been fixed. We are planning much more frequent releases in the future. Macintosh version ================= The macintosh update is not yet available, but should be released shortly. We plan to have multiple self-extracting archive files, to avoid the problem of transferring one very large file. 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 all the update.4-n.tar.Z 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 Thu Aug 10 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!newsfeed.internetmci.com!usenet.eel.ufl.edu!spool.mu.edu!torn!news.bc.net!newsserver.sfu.ca!trog!jbryer From: jbryer@trog.mbb.sfu.ca (Jeff Bryer) Newsgroups: bionet.software.acedb,bionet.celegans Subject: ANNOUNCE: ACEDB v4.1 for Linux Date: 11 Aug 95 04:16:37 GMT Organization: Simon Fraser University Lines: 71 Message-ID: NNTP-Posting-Host: @trog.mbb.sfu.ca Xref: biosci bionet.software.acedb:683 bionet.celegans:513 Following on Richard and Jean's heels for releasing ACEDB v4.1 for SUNs, SGIs, etc today, I managed to quickly port ACEDB v4.1 over to Linux the same day. The port was really quite simple. It is available for anonymous ftp from (as always): ftp://trog.mbb.sfu.ca/pub/acedb/bin.linux.4_1.tar.Z This archive contains the binaries for both xace and tace. I intend to release an ELF version shortly. I also intend to compile in all the data for C. elegans (release 4-7) and make that available on the same site for the C. elegans community. I'll try to make it available in multiple parts so you don't have to download a 60MB+ file. What follows is the readme file for the Linux port of ACEDB v4.1 Jeff Bryer jbryer@darwin.mbb.sfu.ca ------------------- README.LINUX.4_1 August 10, 1995 I've just completed a quicky port of Acedb v4.1 to Linux. This includes both xace and tace. I suppose I could do the server too if people want. Everything in the 4.0 README below applies to the v4.1 port. Either Ken or I will work on an ELF release in the near future. (First I have to upgrade one of our Linux machines to ELF. :-) 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 -- ------- Jeff Bryer | "Maybe VR.12 turns you into Fabio." jbryer@darwin.mbb.sfu.ca | -Duncan in Parallel Lives (VR.5) From owner-acedb@net.bio.net Tue Aug 15 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!newsfeed.internetmci.com!lamarck.sura.net!sprout.nalusda.gov!usenet From: JD Barnett Newsgroups: bionet.software.acedb Subject: Announce: Aceobj.pm Date: 16 Aug 1995 19:27:58 GMT Organization: National Agricultural Library Lines: 40 Message-ID: <40tgru$1kq@sprout.nalusda.gov> NNTP-Posting-Host: phage.nal.usda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4m) To: gig@gig.usda.gov X-URL: news:bionet.software.acedb?ALL Now available at: ftp://probe.nalusda.gov/pub/tools/acelib.tar.gz This distribution contains files developed for integrating acedb version 4 with perl and, in turn, the world wide web. Acedb 4, unlike previous versions, has full client-server capability. The client code has been linked into perl for direct interactive access to the aceserver from perl scripts; this is Aceclient.pm (distributed with ace 4). Acedb 4 also contains modifications for printing output in a form directly readable by perl to provide access to the complete tree structure of objects, and methods for manipulating these trees are provided in Aceobj.pm. Combining these two features is a module (AceWWW.pm) for formatting acedb objects for the World Wide Web. The actual cgi-bin scripts and accessory library routines are also included, though these contain some AGIS-specific information. The files included are: Aceobj.pm perl module for accessing acedb objects AceWWW.pm perl module for WWW formatting htmllib.pl perl library with html routines, used by AceWWW.pm dbinfo.pl template for database-specific information, for WWW hostinfo.pl template for specifying host information, for WWW markup/ example.emr examples of external markup rules, used by AceWWW.pm standard_urls examples of generic urls used for external markup by AceWWW.pm cgi-bin/ for WWW interface model view models dbrun main WWW interface pacecl.pl example perl script: interactive client cnttag.pl example perl script: count tags used in a database ------------------------------ -JD Barnett (jbarnett@nalusda.gov) From owner-acedb@net.bio.net Wed Aug 16 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: xclient Date: 17 Aug 1995 21:04:56 +0100 Lines: 3 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4107d8$mfu@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk no xclient in 4.1 is not considered as functional but i am happy that the rpc service works From owner-acedb@net.bio.net Wed Aug 16 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.moneng.mei.com!news.ecn.bgu.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!in1.uu.net!cis.ohio-state.edu!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!yuma!usenet From: "Martin L. Ferguson" Newsgroups: bionet.software.acedb Subject: xclient: compiling and running and crashing Date: 17 Aug 1995 19:53:34 GMT Organization: Colorado State University Lines: 20 Message-ID: <4106nu$26om@yuma.ACNS.ColoState.EDU> NNTP-Posting-Host: klab.agsci.colostate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4m) To: rd@sangerd.ac.uk,mieg@kaa.cnrs-mop.fr X-URL: news:bionet.software.acedb Greetings Jean, Richard, and others, Is xclient functional? I have gotten aceserver and aceclient running on our version 4.1 database. However, xclient always core dumps on me. This happens after it has made contact with the server, as I have been watching the inetd output. (I'm running the aceserver as an rpc service on a Sparc20/Solaris 2.4. Try "aceclient klab.agsci.colostate.edu -port 150002", if you want to test.) I don't know if this is relevant, but to compile xclient on this machine I had to add 3 object files to the link: seq.o seqIOSCF.o mach-io.o ###################################################################### # # Martin Ferguson Dept. of Entomology # martinf@lamar.colostate.edu Colorado State U. # 303-491-7989 Ft. Collins, CO 80523 # From owner-acedb@net.bio.net Fri Aug 18 23:00:00 1995 Path: biosci!BEANGENES.CWS.NDSU.NODAK.EDU!mcclean From: mcclean@BEANGENES.CWS.NDSU.NODAK.EDU (Phil McClean) Newsgroups: bionet.software.acedb Subject: 4.1 main menu and other Date: 18 Aug 1995 17:48:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net In my main window for ACEDB 4.1, in addition to those classes found in my options.wrm file, I have the following classes --- Gene (an additional one to the one I already have) and five for which I have no models, nor are they in my options.wrm file --- Other_Locus, Genome_Sequence, cDNA_Sequence, Repeat_Sequence, and Tc_Insertion. Any clues about why I get these in the main window? (Using the same options.wrm file in ACEDB 3.7, this problem does not occur.) I have a .ace file called bean-gene.ace which contains information regarding genes. For some reason, I can not get this file to enter the data into ACEDB 4.1 so that they appear in the Main KeySet window when I click on the Gene class name in the main window. The only genes that do appear are those that are placed there by the XREF function from another class (Locus). Interesting, though I can get to these Gene class objects by navigating through an object in another class that has an XREF link to a gene object. I checked the second Gene entry in the main window and get the same gene list as with the first. (See first paragraph.) Ideas anyone? (This is the same file I used with 3.7, and this problem did not occur.) 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 Fri Aug 18 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!swrinde!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: gene/locus etc. Date: 19 Aug 1995 17:40:51 +0100 Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <41546j$nds@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Reply to Phil McClean: You get extra classes Other_Locus, Genome_Sequence, cDNA_Sequence ... in your main display window. These are subclasses defined as being visible in wspec/subclasses.wrm, which make sense for the C. elegans data set. Either delete subclasses.wrm, or delete the things you don't want and add subclasses you do want. A subclass consists of all the items in a class that satisfy a query, called the "Filter" in subclasses.wrm, which is in .ace file format. The subclasses.wrm file is read whenever the models.wrm file is read. Richard From owner-acedb@net.bio.net Sun Aug 20 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!tank.news.pipex.net!pipex!lyra.csx.cam.ac.uk!news From: Ian Dunham Newsgroups: bionet.software.acedb,bionet.molbio.genome-program,bionet.genome.chromosomes Subject: HUMAN CHROMOSOME 22 ACEDB DATABASE Date: 21 Aug 1995 17:21:14 GMT Organization: University of Cambridge, England Lines: 171 Message-ID: <41afaa$6ai@lyra.csx.cam.ac.uk> NNTP-Posting-Host: rock.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; OSF1 V3.0 alpha) X-URL: news:bionet.software.acedb#412ha4$r8m@ixnews4.ix.netcom.com Xref: biosci bionet.software.acedb:690 bionet.molbio.genome-program:1482 bionet.genome.chromosomes:780 ================================== HUMAN CHROMOSOME 22 ACEDB DATABASE ================================== The first release of the human chromosome 22 physical mapping database (22ace) from the Sanger Centre is now available by ftp from ftp.sanger.ac.uk in directory pub/human/chr22/physical_map. The database is implemented in version 4_1 of ACEDB, the graphical database manager, developed for the nematode genome project. The database includes all the YAC and cosmid physical map data from the Sanger Centre chromosome 22 mapping group, presented in context with reagent details, relevant DNA sequences, bibliography, and so on. We are using the database to store the information generated as the Sanger Centre's part of a joint project to sequence chromosome 22 and further releases will present physical map and sequence progress, in its full genomic context. Details of how to obtain the database, and more description of its contents are contained in the README file which is included below. Many thanks go to the following for their work in helping to get this database together, The Sanger Centre chromosome 22 mapping group - John Collins, Charlotte Cole, Luc Smink, Charmain Garrett, Kathy Evans, Joanne Fay, Lisa O'Neill, Margaret Leversha, Simon Gregory. Gareth Maslen, Kate Rice, Richard Durbin, Simon Kelley and Cari Soderlund on informatics. Callum Bell, Bruce Roe, Tom Hudson and all those at the Philadelphia and Whitehead Institute genome centers for provision of data. For further information, please feel free to contact Ian Dunham at -------------------------------------------------------------------------- \ // Ian Dunham Tel: 01223 494948 \ Sanger Centre FAX: 01223 494919 // Hinxton Hall \ Hinxton // Cambridge Email: id1@sanger.ac.uk \ CB10 1RQ idunham@hgmp.mrc.ac.uk // www: http://www.sanger.ac.uk/~id1 ========================================================================== README File ----------- This is the release version of the human chromosome 22 version of ACEDB. The database uses the current release of the ACEDB code, ACEDB 4_1 which can also be obtained independently from this site in directory pub/acedb. The database contains - The YAC physical map of chromosome 22 as determined by the chromosome 22 mapping group at the Sanger Centre - Current progress on cosmid mapping and sequencing from the Sanger Centre - YAC/STS assignments from the Philadelphia Genome Center and the Whitehead Institute as described in Bell et al., Hum Mol Genet 4, 59-69 (1995) and Hudson et al., Genomics 24, 588-592 (1994) - Thanks to Callum Bell and all those at these institutes for providing these data in electronic form. See also their WWW sites as detailed in the database for more information. - Current progress on cosmid mapping and sequencing from the Sanger Centre - Information on all probes and STS markers used in the YAC map plus many others - DNA sequences from chromosome 22 including cosmid from the Sanger Centre submitted to EMBL - Representations of genetic maps of the chromosome and hybrid mapping data, including bin assignments from The Philadelphia Genome Center and the Whitehead Institute (Bell et al., Hum Mol Genet 4, 59-69 (1995) and Hudson et al., Genomics 24, 588-592 (1994) and hybrid data generated at the Sanger Centre - An extensive bibliography - Addresses of laboratories involved in chromosome 22 mapping - Representations of the CEPH mega, ICRF and ICI YAC libraries, and the flow sorted chromosome 22 cosmid library (LL22NC03) - OMIM data on diseases and loci on the chromosome To use the database get the file 22db.tar.Z by ftp. Uncompress the file in the directory of your choice - I suggest your root directory. i.e. > uncompress 22db.tar.Z then extract the tar file to form a subdirectory tree rooted on the directory 22db. i.e. > tar -xvf 22db.tar In the directory 22db/bin you will find subdirectories containing binary executables for DEC ALPHA, SunOS, Solaris and SGI. To run the database set the environment variable ACEDB to the directory 22db i.e. > setenv ACEDB 22db and run the executable you require i.e. for DEC ALPHA 22db/bin/ALPHA/ace4_1.ALPHA The database should now run. It is possible to run the same database from machines with the different operating systems and to have a script to do this. Here is an example of a script we use where the database is held in directory ~id1/22db. -----------------------------begin script---------------------- #!/bin/csh setenv ACEDB ~id1/22db echo -n "ACEDB home directory : " echo $ACEDB echo switch (`ostype`) case "OSF1": ~id1/22db/bin/ALPHA/ace4_1.ALPHA breaksw case "SunOS": ~id1/22db/bin/SunOS/ace4_1.SUN breaksw case "Irix": ~id1/22db/bin/SGI/ace4_1.SGI breaksw case "Solaris": ~id1/22db/bin/SOL/ace4_1.SOLARIS breaksw endsw ----------------------------end---------------------------------- To view the physical map of the chromosome double click on Maps and the full YAC map will be presented in scrollable form. I should stress that this is a direct copy of the laboratory database we use and as such may not contain some of the information you deem necessary. Please feel free to send me comments so that I can improve the database and correct any mistakes. If you need further information about the final release please contact me as well. Also included in the directory pub/human/chr22/physical_map/sam are the sam solution files that we used to construct the YAC map. To use these you must also pick up the latest version of the program sam, written by Cari Soderlund, from the directory pub/sam (At least version 2.5 is required). -------------------------------------------------------------------------- \ // Ian Dunham Tel: 01223 494948 \ Sanger Centre FAX: 01223 494919 // Hinxton Hall \ Hinxton // Cambridge Email: id1@sanger.ac.uk \ CB10 1RQ idunham@hgmp.mrc.ac.uk // www: http://www.sanger.ac.uk/~id1 ========================================================================== Ian Dunham 21 August 1995 From owner-acedb@net.bio.net Sun Aug 20 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: wspec/database.wrm Date: 21 Aug 1995 15:25:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508212223.AA18371@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net In moving a database from ca. ace3-0 to 4-1 there are a few gotchas in wspec to be dealt with. Phil ran into one the other day with subclasses.wrm which should not be carried over from the 4-1 distribution. The NOTES for 4-1 say "The minimal requirements for running acedb are that the database/ and wspec/ directories exist, and wspec/ contains cachesize, options, displays, models, passwd", and it seems to be working for me with all of these wspec files transferred straight over from my old database. This includes deleting tags.wrm and sys*. However one additional wspec file needs to be brought in from the 4-1 distribution: database.wrm. It looks harmless enough, but in its absence the error message is only, !! FATAL ERROR: system error 2 No such file or directory !! Disk extend cannot open the main database file , which can take a while to figure out. - Dave From owner-acedb@net.bio.net Sun Aug 20 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: ace4-1 pick_me_to_call workaround Date: 21 Aug 1995 14:38:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508212136.AA18241@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net In ace4-1, 'Pick_me_to_call xv my.gif' looks for my.gif in whatever directory the user happened to be in when he started the database, which is indeterminate. To work around this, always invoke xace via a script that first chdir's to the desired directory: #!/bin/csh setenv ACEDB /acedb/myowndb cd $ACEDB/externalFiles $ACEDB/bin/xace Thanks to Hector Sanchez for this tip! - Dave From owner-acedb@net.bio.net Mon Aug 21 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!news.sprintlink.net!in1.uu.net!cis.ohio-state.edu!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!yuma!klab4.agsci.colostate.edu!user From: martinf@lamar.colostate.edu (Martin L. Ferguson) Newsgroups: bionet.software.acedb Subject: Re: ace4-1 pick_me_to_call workaround Date: Tue, 22 Aug 1995 10:22:05 -0600 Organization: Colorado State University Lines: 41 Distribution: world Message-ID: References: <9508212136.AA18241@greengenes.cit.cornell.edu> NNTP-Posting-Host: klab4.agsci.colostate.edu Hi all, I've placed a copy of a modified action.c at: http://klab.agsci.colostate.edu/~mferguso/files.html If you recompile xace with this file, it will look for the Pick_me_to_call arguements in $ACEDB/externFiles automatically. (Hope this is OK, Richard & Jean. Should there be a $ACEDB_EXTERNAL_FILES environment variable?) Also, if you're not into recompiling, I can let you have a modified Solaris xace binary. Just email me. /s/ Martin martinf@lamar.colostate.edu In article <9508212136.AA18241@greengenes.cit.cornell.edu>, matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") wrote: > In ace4-1, 'Pick_me_to_call xv my.gif' looks for my.gif in whatever > directory the user happened to be in when he started the database, which is > indeterminate. > > To work around this, always invoke xace via a script that first chdir's to > the desired directory: > > #!/bin/csh > setenv ACEDB /acedb/myowndb > cd $ACEDB/externalFiles > $ACEDB/bin/xace > > > Thanks to Hector Sanchez for this tip! > > - Dave -- Martin Ferguson martinf@lamar.colostate.edu Dept. of Entomology 970-491-7989 CO State U. Ft. Collins, CO 80523 From owner-acedb@net.bio.net Tue Aug 22 23:00:00 1995 Path: biosci!agate!spool.mu.edu!torn!nott!bcarh189.bnr.ca!bcarh8ac.bnr.ca!corpgate!news.utdallas.edu!news.tamu.edu!news From: lazo@tamu.edu (Gerard R. Lazo) Newsgroups: bionet.software.acedb Subject: ACEDB on different machines Date: 23 Aug 1995 19:27:19 GMT Organization: USDA-ARS Southern Crops Research Laboratory Lines: 28 Message-ID: <41fven$e8k@news.tamu.edu> Reply-To: lazo@tamu.edu NNTP-Posting-Host: algodon.tamu.edu Thanks for the update on the ACE_4-1 pick_me_to_call solution; that was bugging me a bit. In trying to migrate from ACE_3-7 to ACE_4-1 I found that my models.wrm had some problems. I worked with it on one machine until it was fixed (or at least it loaded without errors). After ACE_4-1 was working, I transferred it to another machine (also a Sun SPARC 10) with the same operating system (Solaris 2.4). On this other machine the models.wrm appeared not to work, giving the message: FATAL ERROR: bsUpdate called on non B key Bat: ~(NULL KEY) What is it about the different machines that causes this? Both machine`s operating systems were loaded using the same CD, and are similarly configured. I can probably work with model.wrm on the other machine until I can clean up the problem, but it's somewhat confusing why a similarly configured machine would make this difference. I had this same problem when I was moving to ACE_3-7 from ACE_3-0. Any insight about this occurrence is appreciated. Thanks. / Gerard R. Lazo . %. (=) GLAZO@tam2000.tamu.edu USDA-ARS (.( .) / ^Off: 409-260-9533 Southern Crops Research Lab. ( ( .) .) -> (=) |^Lab: 409-260-9522 2765 F&B Road %_( ._) / ||^Fax: 409-260-9333 College Station, TX 77845 //\| (=) |||^ (( / |||||> if not at above From owner-acedb@net.bio.net Tue Aug 22 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: table.menu.wrm problem in ace4-1 Date: 23 Aug 1995 15:40:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508232238.AA23540@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Does the "Tables..." button still work in ace4-1? The wspec/table.menu.wrm attached below works fine in ace3-0 and 4_0b4, but in 4-1 when I click "Tables..." the little "Selector" window comes up just briefly and then ace exits with message "Error: Widget vertical has zero width and/or height". - Dave ~~~~~~~~~~~~~~~ // This file allows you to link specific // relational tables definition for direct access // from the standard tree-display // The format is the following: // Each paragraph starts with a class name // then each line should give a name, to appear in menus, a column, // and the name of a file down from $ACEDB // The table maker is then called from tree-display with the name // of the active object as parameter, // therefore the definition file may use %1 to refer to // that name // Example: //Gene //Map_Data : wquery/map_data.1.def Trait_Study Summary_by_Germplasm : wquery/tmenu/TS_by_GP.def Summary_by_Environment : wquery/tmenu/TS_by_Loc.def Germplasm Traits_by_Environment : wquery/tmenu/TS_all_traits.def Summary_over_Environments : wquery/tmenu/TS_GP_by_Loc.def From owner-acedb@net.bio.net Sun Aug 27 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: table.menu.wrm, cont'd Date: 28 Aug 1995 15:50:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508282247.AA02100@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > From: matthews@greengenes.cit.cornell.edu ("Dave Matthews") > Subject: table.menu.wrm problem in ace4-1 > Date: 23 Aug 1995 15:40:22 -0700 > > Does the "Tables..." button still work in ace4-1? The wspec/table.menu.wrm > attached below works fine in ace3-0 and 4_0b4, but in 4-1 when I click > "Tables..." the little "Selector" window comes up just briefly and then > ace exits with message "Error: Widget vertical has zero width and/or height". > - Dave This problem occurs on SunOS but not on Solaris or Linux. Tricky little devil. - Dave From owner-acedb@net.bio.net Mon Aug 28 23:00:00 1995 Path: biosci!MORGAN.HARVARD.EDU!flybase From: flybase@MORGAN.HARVARD.EDU (FlyBase Project Members) Newsgroups: bionet.software.acedb Subject: EofD 1 available by ftp Date: 29 Aug 1995 09:23:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 59 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508291621.AA00837@morgan.harvard.edu> NNTP-Posting-Host: net.bio.net Encyclopaedia of Drosophila Release 1 April 1995 This Spring the Berkeley Drosophila Genome Project (BDGP) and FlyBase produced the Encyclopaedia of Drosophila (EofD). The EofD is a powerful graphical interface browsing and querying tool based on the ACEDB software first developed for the C. elegans database. Multiple data sets are displayed on chromosomal maps in which text descriptions of data items are displayed on command by mouse-driven "pointing and clicking". We distributed free copies of a CD-ROM for Macintosh computers at the annual Drosophila Research Conference in Atlanta, and have made the CD-ROMs and user guides available for a nominal fee. The first EofD release is now available by ftp from the IUBio/FlyBase server. It is found in versions not only for the Mac, but also for Sun SPARCstations, DEC Alpha workstations, and SGI Iris workstations. EofD Release 1.0 requires approximately 450 MB of disk space to install in its complete form. It also needs about 32 megabytes or more of memory to run effectively. This EofD is available over the Internet from the server flybase.bio.indiana.edu using FTP in this way: ftp flybase.bio.indiana.edu user: eofd password: FlyBase binary (set binary ftp mode) cd docs get Readme.eofd (get current instructions and read ) to get instructions for the Sun SPARCstation version: cd docs (if you haven't already done so) get Readme.sun to get instructions for the Silicon Graphics version: cd docs (if you haven't already done so) get Readme.sgi to get instructions for the DEC alpha version: cd docs (if you haven't already done so) get Readme.dec to get instructions for the Macintosh version: cd docs (if you haven't already done so) get Readme.mac Inquiries concerning purchases of the Macintosh CDROM version may be made by telephone to Ms. Dawn Palmer at (617) 495-2906 or fax at (617) 495-9300 or by email to eofd-sales@morgan.harvard.edu. If you would like to receive any of the current Readme instruction files by email, simply mail your request to EofD-help@morgan.harvard.edu. From owner-acedb@net.bio.net Tue Aug 29 23:00:00 1995 Path: biosci!mrc-lmb.cam.ac.uk!rd From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB 4-8 update for C. elegans Date: 30 Aug 1995 10:22:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 142 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508301717.AA00992@cele.mrc-lmb.cam.ac.uk> NNTP-Posting-Host: net.bio.net 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 update 4-8 for C. elegans ==================================== As promised, we are now making more frequent releases. The principle is to make data available more quickly, and fix errors as they are found. Please let us know if you find errors -- they will be fixed in a subsequent release. You can add several update files at once if you want to get them less often, or if you fall behind. Because they are more frequent, updates will now be smaller, and so faster to transfer and load into acedb. Update 4-8 should be used in conjunction with version 4_1 of the ACEDB program. You can add it as an update to a 4-7 database using "Add update". The total database size is now approximately 190 Mbytes. The additions since 4-7 are: - more genomic sequence data (there are now 595 cosmids totalling 18,334,987 bases). - a physical map update (last one was April 1995). - some genetic map updates. - some more expression data, including some pictures for the first time in the worm database (see below). - a new type of map display (X-Sequence etc.), showing the status of cosmids being sequenced. Colour codes are: DARKRED(BROWN) = submitted, sequence in ACEDB, RED = finished, sequence in ACEDB, LIGHTRED = finished, sequence on ftp server, BLUE = shotgun, sequence may be on ftp server. You can get a key to this information by clicking on the green bar at the bottom of the map display, under the coloured cosmid region. The endpoints of cosmids in this map are derived from the physical map, and are not accurate in detail (in particular duplicate regions are not being sequenced, as suggested by this map!). - a number of errors and problems have been fixed. Pictures ======== This update includes some pictures, which will be stored as JPEG files in the subdirectory pictures/. In order to see these from acedb, you must have another program able to view JPEG files. We recommend xv, which can be obtained for private use from many anonymous ftp sites (e.g. wuarchive.wustl.edu). This must be installed on your computer, and in your executable path. You may have it already. To check if it is there and working, go to your acedb home directory after installing update 4-8, and type: xv pictures/b0523_5_vul.jpeg To access pictures from inside acedb, display an Expr_pattern object (e.g. Expr35), click on one of the Picture titles in bold lettering next to the tag word Picture (e.g. b0523_5_vul.jpeg). This brings up another textual record, corresponding to the Picture object. Click on the words Pick_me_to_call and WAIT. A khaki worm picture with dark blue staining (lacZ) should appear in an xview window. To remove the image, click with left mouse anywhere on the picture. this brings up the xview menu window. Click on quit. << Technical note: If you have another program than xv, or want to store the files differently, you will need to edit the file wscripts/display_script.>> We would like to thank Ian Hope and Andy Lynch of Leeds University for starting the "ball rolling" and giving us their worm pictures. We hope that lots more folk will follow suit especially people working on cDNA expression patterns. Good viewing, Sylvia Martinelli and Eric Sonnhammer. Macintosh version ================= A set of Macintosh self-extracting archive files for 4-8 is available in the macace/ subdirectory of the standard ftp sites. Follow the instructions in the README file there. Pictures are not yet available in the Macintosh version - if you follow the instructions above I am told you crash. We hope they will be working in the next release. 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 Tue Aug 29 23:00:00 1995 Path: biosci!rutgers!gatech!usenet.eel.ufl.edu!newsfeed.internetmci.com!tank.news.pipex.net!pipex!in2.uu.net!news1.digital.com!ames!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!news.cerf.net!news From: "Eric E. Snyder" Newsgroups: bionet.software.acedb Subject: GeneFinder Tables for Human Sequences Date: 30 Aug 1995 18:51:04 GMT Organization: CERFnet Lines: 14 Message-ID: <422buo$7rk@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 1.1N (X11; I; SunOS 5.4 sun4m) X-URL: news:bionet.software.acedb Does anyone know a source for human codon usage and splice site tables for Phil Green's GeneFinder program which is embedded in the sequence viewing tool in ACEDB? I have checked the web site at http://probe.nalusda.gov:8000 and wasn't able to come up with anything. Anyone have access to these tables or have any suggestions on where to look? Many thanks, 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 From owner-acedb@net.bio.net Wed Aug 30 23:00:00 1995 Path: biosci!nihs.go.jp!taka From: taka@nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: perl nersion of aceclient Date: 31 Aug 1995 04:21:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508311114.AA08968@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net Hello! I have an error of installing the perl version of aceclient. I have set the c version of aceclient and aceserver environment. It works fine. Next I recompiled perl5.001 with ./ext/Aceclient/***. I had no error at compilation. But when I try to run pacecl.pl as "pacecl.pl ", I get a following error messege: 16581:/usr/local/bin/perl: rld: Fatal Error: attemped access to unresolvable symbol in /usr/people/taka/gcc/perl5.001m/lib/auto/Aceclient/Aceclient.so: openServer ("/usr/people/taka/gcc/perl5.001m" is my perl source directory.) Please give some hints to overcome this error. Thank you in advance. Takako Igarashi National Institute of Health Sciences (Japan) taka@nihs.go.jp From owner-acedb@net.bio.net Wed Aug 30 23:00:00 1995 Path: biosci!nihs.go.jp!taka From: taka@nihs.go.jp (Takako Igarashi) Newsgroups: bionet.software.acedb Subject: perl version of aceclient (continued) Date: 31 Aug 1995 04:35:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508311128.AA08996@nihs.nihs.go.jp> NNTP-Posting-Host: net.bio.net I am sorry for forgetting to write my machine environment. I use irix5.2, acedb4.1. Takako Igarashi National Institute of Health Sciences taka@nihs.go.jp //////////////// my previous mail ///////////////////////////////////////////// Hello! I have an error of installing the perl version of aceclient. I have set the c version of aceclient and aceserver environment. It works fine. Next I recompiled perl5.001 with ./ext/Aceclient/***. I had no error at compilation. But when I try to run pacecl.pl as "pacecl.pl ", I get a following error messege: 16581:/usr/local/bin/perl: rld: Fatal Error: attemped access to unresolvable symbol in /usr/people/taka/gcc/perl5.001m/lib/auto/Aceclient/Aceclient.so: openServer ("/usr/people/taka/gcc/perl5.001m" is my perl source directory.) Please give some hints to overcome this error. Thank you in advance. Takako Igarashi National Institute of Health Sciences (Japan) taka@nihs.go.jp //////////////////////////// end ///////////////////////////////////////////////////// From owner-acedb@net.bio.net Wed Aug 30 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Pick_me_to_call in 4_1 Date: 31 Aug 1995 19:23:26 +0100 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <424umu$437@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk There has been some discussion about where Pick_me_to_call looks for files. In the 4-8 worm distribution we used Pick_me_to_call for JPEG pictures. Instead of making the second argument "xv" directly, we set it to be the name a script in wscripts/, "display_script", which explicitly specifies the directory in which to look: xv $ACEDB/pictures/$1 & This is preferable to changing directory in the script with which you invoke acedb, because it is nice to be in your own directory for writing out files. It also allows people to change the way xv is invoked, e.g. set options, or change to another image viewer, without editing the database. Richard