From owner-acedb@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!bvc.edu!yuqian From: yuqian@bvc.edu (Suicidal Freshman) Newsgroups: bionet.software,bionet.software.acedb Subject: New Dedicated Bio-tech/science/chem BBS Message-ID: <1995May2.123030.10878@bvc.edu> Date: 2 May 95 12:30:30 CDT Organization: Buena Vista College, Storm Lake, IA Lines: 27 Xref: biosci bionet.software:11961 bionet.software.acedb:580 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% A NEW BBS IS ONLINE AND NEEDS PEOPLE LIKE YOU TO HELP IT PROSPER The IDT Online Information System is now up and running and needs intelligent users such as yourselves. Anyone interested in Chemistry or Biology or any twist of the two is more than welcome. If you are a user of Oligonucleotides, there is an online order system that allows you to place your order directly into the production facility for 48 hour turnaround. THERE IS ABSOLUTELY NO CHARGE FOR USAGE. YOU DO NOT HAVE TO BE A CUSTOMER TO USE THE SYSTEM Just a sample of some of the discussion forums: Parsitology Classifieds Employment Chemical Engineering Computer Software Biochemistry Programming Molecular Medicine Genetics Organic Chemistry Oligo Design Scientific Humor BioPhysics Cell Biology Internet Topics Biomed Engineering Late Breaking News Immunology NeuroScience Suggestions The system is in place, and we are looking for good users, and a few Forum Moderators, so: Check it out: telnet 204.71.106.202 or telnet idtdna.com %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-acedb@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!nntp.crl.com!decwrl!pagesat.net!news.uoregon.edu!news.dacom.co.kr!news.kreonet.re.kr!usenet From: Baek Hie Nahm Newsgroups: bionet.software.acedb Subject: (no subject) Date: 2 May 1995 17:50:17 GMT Organization: Dept of Biological Science, Myongji University Lines: 7 Message-ID: <3o5rcp$sjq@news.kreonet.re.kr> NNTP-Posting-Host: 202.30.98.73 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.software.acedb?ALL I am looking for Mac version (Power PC) of Acedb which will be suitable for rice genome database. Would you let me know where I can get the Macace Program without data so that I can download easily, or with a little data From owner-acedb@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!nntp.crl.com!decwrl!pagesat.net!news.uoregon.edu!news.dacom.co.kr!news.kreonet.re.kr!usenet From: Baek Hie Nahm Newsgroups: bionet.software.acedb Subject: (no subject) Date: 2 May 1995 17:50:12 GMT Organization: Dept of Biological Science, Myongji University Lines: 7 Message-ID: <3o5rck$sce@news.kreonet.re.kr> NNTP-Posting-Host: 202.30.98.73 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.software.acedb?ALL I am looking for Mac version (Power PC) of Acedb which will be suitable for rice genome database. Would you let me know where I can get the Macace Program without data so that I can download easily, or with a little data From owner-acedb@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!fnnews.fnal.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Showing familiar names of Loci on GMAP's Date: 2 May 1995 18:25:30 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 16 Distribution: world Message-ID: <3o5teq$jda@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov In the same way that Paper objects are shown by their titles, rather than their key's, I'd like to show loci on GMAP's by a familiar name rather than the key. Is this possible? Thanks, --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project From owner-acedb@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!srk From: srk@handa.sanger.ac.uk (Simon Kelley) Newsgroups: bionet.software.acedb Subject: Re: Showing familiar names of Loci on GMAP's Date: 03 May 1995 08:34:37 GMT Organization: Sanger Centre, Hinxton Hall, England. Lines: 54 Distribution: world Message-ID: References: <3o5teq$jda@overload.lbl.gov> NNTP-Posting-Host: handa.sanger.ac.uk In-reply-to: bks@s27w007.pswfs.gov's message of 2 May 1995 18:25:30 GMT In article <3o5teq$jda@overload.lbl.gov> bks@s27w007.pswfs.gov (Bradley K. Sherman) writes: In the same way that Paper objects are shown by their titles, rather than their key's, I'd like to show loci on GMAP's by a familiar name rather than the key. Is this possible? Thanks, --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project It is possible to do this in both acedb3 and acedb4, the exact method differs between them. In the model for ?Map in ace3, you will find the following: Symbol Text UNIQUE Text // Class Tag: if present, for all // items in class use item following // tag in place of name for display The first Text is a class name, the second a tag. If this is set in the map, all objects of the given class are displayed not using their real names, but by the name of the object following the tag. Thus you could have ?Loci Familiar_name ?Text and in the map Symbol Loci Familiar_name Exactly the same facility exists in the ace4 GMAP, the only difference is that the name transformation is now done per-column, and the Symbol spcification has moved into the ?View object which controls all aspects of map display. Simon. ------------------------------------------------------------------------------- Simon Kelley. srk@sanger.ac.uk work: +44 223 494980 home: +44 223 832411 -- ------------------------------------------------------------------------------- Simon Kelley. srk@sanger.ac.uk work: +44 223 494980 home: +44 223 832411 From owner-acedb@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: contracted tree display Date: 3 May 1995 10:26:38 +0100 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3o7i8e$1h0@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Matt Couchman asks about the rules for the contraction: Tag_heading ----> n (where n is the no. of items) in the tree display. Currently the rule is that thing are contracted by default if there are more than 5 items in the column to the right, or more than 3 items if the top item would be displayed using a -T derived name, rather than it's default name (e.g. the Title of a paper). This rule is not under user control. It probably should be in some fashion. I am interested in collecting ideas about the most useful ways to do this, always rememberng that we would like to avoid a lot of extra complexity for both user and programmer, and that there is no implied promise that I will implement any of these ideas! Richard From owner-acedb@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!trane.uninett.no!daresbury!is.bbsrc.ac.uk!news From: couchman@bbsrc.ac.uk (Matt) Newsgroups: bionet.software.acedb Subject: Tag display mode - No. of items Date: 3 May 1995 08:24:26 GMT Organization: John Innes Centre Lines: 12 Message-ID: <3o7ejq$6nu@is.bbsrc.ac.uk> Reply-To: couchman@bbsrc.ac.uk NNTP-Posting-Host: pc0454.jic.bbsrc.ac.uk X-Newsreader: WinVN 0.92.1 Hello, Is there an easy way to force certain tags within a model to default to the: Tag_heading ----> n (where n is the no. of items) type of format? If not what are the rules that govern whether it takes this format or not? Thanks in advance, Matt. From owner-acedb@net.bio.net Wed May 03 23:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: Showing familiar names of Loci on GMAP's Date: 4 May 1995 14:59:49 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 12 Distribution: world Message-ID: <3oaq55$3ou@overload.lbl.gov> References: <3o5teq$jda@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov Thanks to Simon K. for the instructions demonstrating how to use non-key tags on GMAP displays. Note that this feature does not appear in ACEDB 3.0, but does appear in the newer releases. --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project From owner-acedb@net.bio.net Sat May 06 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Re: ACEDB font Date: 7 May 1995 13:49:41 +0100 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3oifl5$rt8@mserv1.dl.ac.uk> Original-To: ung@ash.tree.caltech.edu > How can I change the font style of the letters in the pull down > menu of ACeDB in Sparc environment? You can set the following X resource. !******************************************************** !This is the font used for the menus etc. in ACEDB, image !******************************************************** GraphPackage*font: -*-helvetica-bold-r-normal-*-14-* The font listed here is bigger and bolder than normal. We do this by adding it to our .Xdefaults file, which gets applied via: xrdb -merge $HOME/.Xdefaults during our X startup process. There are other, somewhat system-dependent, ways of doing it. Ask you local system person/guru. Richard From owner-acedb@net.bio.net Sun May 07 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!elroy.jpl.nasa.gov!lll-winken.llnl.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 8 May 1995 21:36:14 GMT Organization: Dendrome, A genome database for forest trees Lines: 1086 Approved: news-answers-request@MIT.Edu Message-ID: <3om2se$j9v@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:589 news.answers:38145 Archive-name: acedb-faq Last-modified: 5/8/95 Version: 1.21 ACEDB FAQ ********* Frequently Asked Questions about ACEDB ====================================== o Q0 : What is ACEDB? o ++++++++++++++++++++ o Q1 : What is the current version of ACEDB? o +++++++++++++++++++++++++++++++++++++++++++ o Q2 : What hardware/software do I need to run ACEDB? o ++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q3 : Where can I get ACEDB? o ++++++++++++++++++++++++++++ o Q4 : What ACEDB databases exist? o +++++++++++++++++++++++++++++++++ o Q5 : What written documentation exists for ACEDB? o ++++++++++++++++++++++++++++++++++++++++++++++++++ o Q6 : Where can I find further information about ACEDB? o +++++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q7 : How should ACEDB be cited? o ++++++++++++++++++++++++++++++++ o Q8 : Is ACEDB object-oriented? o +++++++++++++++++++++++++++++++ o Q9 : What's all this about Gopher, WAIS, FTP, WWW, URL, ... o ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q10 : How can I get on/off the ACEDB announcements mailing list? o +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q11 : When and where is the next ACEDB Workshop? o +++++++++++++++++++++++++++++++++++++++++++++++++ o Q411 : 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 (1/95) is test.source.3.6a.tar.gz. A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q10. Return to List of Questions Q2: What hardware/software do I need to run ACEDB? ++++++++++++++++++++++++++++++++++++++++++++++++++ A2: +++ The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. o Unix and X11: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series o PC 386/486 with Linux (free Unix) [note from Jeff Bryer, jbryer@darwin.mbb.sfu.ca] I just installed up Linux yesterday and today spent the many hours to compile in the C. elegans data for ACEDB v2.0 So to save other people the trouble of doing the same the entire package ACEDB for Linux 2-10 is available on trog.mbb.sfu.ca in /pub/acedb as linux.2_10.tar.Z The data was compiled in on a 486DX-33 with 16MBs of RAM running Linux 1.1.18 (Slackware 2.0.0 distribution) and a 32MB swap device (and it chugged away for a couple hours chewing up all 16MBs and half the swap space). File size is about 73MBs uncompressed, 26MBs compressed. This is based on the ACEDB v2.0 port for Linux that Ken Clark (ken@darwin.mbb.sfu.ca) did. o There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o Macintosh: o [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a 17" color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. o ACEDB for The NEC EWS4800 is available via anonymous ftp at ftp.nec.co.jp (192.135.93.2) in /pub/packages/acedb/ace2. Contact Tohru Sano Fundamental Research Laboratories NEC Corporation Tsukuba, 305, JAPAN, e-mail: sano@exp.cl.nec.co.jp, FAX: +81-298-56-6136, VOICE: +81-298-50-1507 (Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems SPARCstation II, and users can interact using Macintoshes and PC-clones by using X11 implementations for the personal computers and a LAN. --bks) X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions Q3: Where can I get ACEDB? ++++++++++++++++++++++++++ A3: +++ The standard ACEDB source and binaries are available in the following public access accounts (anonymous ftp sites) accessible via Internet: o lirmm.lirmm.fr in pub/acedb o cele.mrc-lmb.cam.ac.uk in pub/acedb o ncbi.nlm.nih.gov in repository/acedb o bioinformatics.weizmann.ac.il in pub/databases/acedb. MacAce is available from: o genome.lbl.gov in pub/macace o cele.mrc-lmb.cam.ac.uk in pub/acedb/macace Linux; ACEDB version 2.0 for Linux 2-10: o trog.mbb.sfu.ca /pub/acedb as linux.2_10.tar.Z ACEDB for The NEC EWS4800: o ftp.nec.co.jp in /pub/packages/acedb/ace2. Return to List of Questions Q4: What ACEDB databases exist? +++++++++++++++++++++++++++++++ A4: +++ In alphabetic order by Database name ------------------------------------ [Curators, please submit changes as new paragraphs] o Database : AaeDB o Species : Aedes aegypti o Last_update : December 1994 o ACEDB_version : 3.0 o WWW : http://klab.agsci.colostate.edu/index.html o PI : Dennis Knudson, dknudson@lamar.colostate.edu o Curator : Martin Ferguson, martinf@lamar.colostate.edu o Curator : Dave Severson, dave@aedes.vetsci.wisc.edu o Contact : aaedbmgr@klab.agsci.colostate.edu o Database : AAnDB-1.0 o Species : Aspergillus nidulans o PI : Leland Ellis o Last_update : February 1994 o ACEDB_version : 3.0 o Contact : leland@stralight.tamu.edu o URL: http://keck.tamu.edu/ibt.html o Comment : defunct, See AGsDB o Database : AAtDB o Species : Arabidopsis thaliana o Current version : 3-5 o Last_update : March 1995 o Curator : John Morris o Contact : curator@frodo.mgh.harvard.edu o Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x o Availability : Macintosh version in /aatdb/MacAAtDB directory o FTP : URL : ftp://weeds.mgh.harvard.edu/aatdb o Gopher : gopher://weeds.mgh.harvard.edu/ o WWW : http://weeds.mgh.harvard.edu:80/index.html o WWW : http://probe.nalusda.gov:8300/ o Database : ABtDB-1.0 o Species : Bovine, Bos taurus o ACEDB_version : 3.0 extended o PI : Leland Ellis o Last_update : February 1994 o Contact : leland@stralight.tamu.edu o URL : http://keck.tamu.edu/ibt.html o Comment : defunct, See AGsDB o Database : AboutDB o Curator : Staffan Bergh o PI : Staffan Bergh o Subject : ACEDB itself (Is this meta-meta-metadata) o ACEDB 3.0 o Contact : staffan@biochem.kth.se o URL : http://www.biochem.kth.se/AboutDB.html o Database : ACeDB o Species : Caenorhabditis elegans o Current version: 2-18 o Curator : Jean Thierry-Mieg o Curator : Richard Durbin o Contact : rd@mrc-lmb.cam.ac.uk o Contact : mieg@kaa.crbm.cnrs-mop.fr o Last_update : May 1994 o DataBase : AceMap o Species : Homo sapiens (Mus musculus under development) o Focus : Physical mapping of human chromsome X and 21 o ACEDB_version : 3.0 o Curator : Hugues Roest Crollius o PI : Hans Lehrach o Availability : beta release of the X chr. data/models by anonymous ftp to ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap. Get the README file in the directory above. o Contact : hrc@gea.lif.icnet.uk (Hugues Roest Crollius) ICRF, Lincoln's Inn Fields London, UK. o Last_update : August 94 o Database : AGsDB A Genus species Database o Species : Aspergillus nidulans o Species : Neurospora crassa o Species : cow w/ human anchor loci o Species : cotton (demo) o Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast o PI : Leland Ellis o Curator : Leland Ellis o Last_update : March 1994 o ACeDB_version : 3.0 (beta still), with extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe) yeast); interacting loci via defined Interactions for each locus o Models : as of 3.13.94 o Data : as of 3.13.94 o Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. o WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux (ducoux@moulon.inra.fr). o URL : http://keck.tamu.edu/ibt.html o Contact : leland@straylight.tamu.edu o Database : Alfagenes o Species : Medicago sativa (Alfalfa, Lucerne) o Availability : Under development o Curator : D. Z. Skinner o Contact : dzolek@ksu.ksu.edu o Telephone : (913) 532-7247 o Database : BeanGenes o Species : Phaseolus and Vigna species o PI : Phillip E. McClean o Email : mcclean@beangenes.cws.ndsu.nodak.edu o WWW : http://probe.nalusda.gov:8300 o Gopher: probe.nalusda.gov o Database : ChlamyDB o Species : Chlamydomonas o PI : Elizabeth Harris o Contact : chlamy@acpub.duke.edu o Availability : ChlamyDB 1.0, 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/chlamydirectory. A Macintosh version is avaliable in ftp://ftp.duke.edu/pub/chlamy/MacChalmy o URL : http://probe.nalusda.gov:8300 o Last_update : 25 Oct, 1994 o Database : CottonDB o Species : Gossypium hirsutum (cotton) and related species o PI : Russell J. Kohel, USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 o Curator : Gerard R. Lazo o Curator : Sridhar Madhavan o Last_update : January, 1995 (version 95.1) o ACEDB_version : 3.0 o Contact : lazo@tamu.edu (Gerard R. Lazo) o Contact : rjk0339@acs.tamu.edu (Russell J. Kohel) o URL : http://probe.nalusda.gov:8000/index.html o Data_submission_form : http://algodon.tamu.edu/ o Phone : 409-260-9311 o Fax : 409-260-9333 o Database : CSNDB o Focus : Cell Signalling Molecules and Interactions o Contact : Takako Igarashi National Insitute of Health Sciences Division of Chem-Bio Informatics Setagaya-ku, Tokyo, Japan 158 taka@nihs.go.jp o Database : EcoDB o Species : E. coli o PI : Staffan Bergh o Contact : staffan@biochem.kth.se o Availability : Proposed o Last_update : Aug. 1994 o Database : 11DB o Species : Homo sapiens o Focus : Physical mapping of chromosome 11 o Availability : under development o Curator : Benedict Arnold o PI : Peter Little o Contact : Benedict Arnold Dept. Biochemistry, Imperial College, London, SW7 2AZ b.arnold@ic.ac.uk o Database : The Encyclopaedia of the Drosophila Genome. o Acronym : (none) o Species : Drosophilidae (primarily D. melanogaster) o Availability : MacFly/FlyDB-based distribution by ftp and CD-ROM due early 1995 o Developer : Suzanna Lewis o Contact : suzi@fly2.berkeley.edu o Developer : Cyrus Harmon o Contact : sly@fly2.berkeley.edu o Developer : Edward Welbourne o Contact : eddy@gen.cam.ac.uk o Curation : Data is provided by the collaborating organisations: o Collaborator : The FlyBase Consortium, flybase@morgan.harvard.edu o Collaborator : The Berkeley Drosophila Genome Project o URL : gopher://fly.bio.indiana.edu:70+/11/Flybase o Database : Flydb o Species : Drosophila melanogaster o Curator : Suzanna Lewis o Contact : suzi@fly2.berkeley.edu o Database : GrainGenes o Species : Wheat, barley, oats, relatives o Availability : Anonymous ftp from probe.nalusda.gov:pub/grains o Availability : Gopher greengenes.cit.cornell.edu port 70 o Availability : Gopher probe.nalusda.gov port 7002 o Curator : David E. Matthews o PI : Olin D. Anderson o Contact : matthews@greengenes.cit.cornell.edu o Contact : oandersn@wheat.usda.gov o URL : gopher://greengenes.cit.cornell.edu/1/ o Data_version : 1.3 o Released : 12 Jan 1994 o Based_on : acedb.1-10 o Availability : See following WWW URL o URL : http://probe.nalusda.gov:8300 o Last_update : Feb. 1994 o Database : human.c17 o Species : Homo sapiens o Availability : the database is under development o Contact : lsprilus@weizmann.weizmann.ac.il o Focus : mapping & sequencing of Human Chromosome 17 o Based_on: acedb.3-0 o Last_update : Jan. 1994 o Database : IGD - the Integrated Genomic Database o Species : Homo sapiens (later mouse and other mammalian species) o Availability : September 1994 by ftp, on-line server October 1994 o Contact : Otto Ritter [ o.ritter@dkfz-heidelberg.de ] o Curator : tba o Description : IGD - the Integrated Genomic Database - aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. o Database : LIGM-DB o Curator : Veronique Giudicelli o Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors o PI : Marie-Paule Lefranc o Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr o Database : Maize o Species : Zea mays L. ssp. mays and related o Focus : Maize genome o Latest_release : April 1995 o Acedb_version : 3.3 o FTP : probe.nalusda.gov, pub/maize directory o Comment : Maize is a periodically extracted ACeDB front end for the Maize Genome Database, MaizeDB, a SYBASE database, implemented using Genera software, developed by Stan Letovsky. o Comment : Genera provides (1) up-to-the-minute form internet access to SYBASE databases, both for query (WWW and APT) and data entry (APT only); (2) database design alterations by systems administrators; (3) gopher file extraction. o Comment: MaizeDB uses WWW record-to-record hard-links to 16 external databases for (1)annotated sequences: GenBank, dbEST, GenoBase, PIR, SwissProt, Prosite, ENZYME; (2)other species genome information: AAtDB(Arabidopsis), RiceGenes, GrainGenes, SaachDB (yeast), CGSC(E. coli), XLocus, RiceGenes, GrainGenes (3) germplasm: GRIN. o Data : Over 100,000 records include: 6513 mapped loci (located to chromosome or better) including 1081 mapped genes and 1937 mapped probed sites (gene candidates); 2448 probes; 2460 map scores; 1551 gel patterns (Probe/Enzyme/Stock); 8777 stocks; 18,100 Variations (alleles, DNA polymorphisms, rearrangements, etc); 596 phenotypes; 317 traits; 715 gene products; 6158 bibliographic references; 2200 researchers with addresses. o Gopher : host = gopher.agron.missouri.edu, port = 70 . o Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: corncob o HTTP : http://www.agron.missouri.edu/top.html o HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant Genome Database - Moulon WWW gateway to several ACeDB databases o HTTP : Genera information http://gdbdoc.gdb.org/letovsky/genera/genera.html o Funding : MaizeDB USDA/ARS to E. Coe o Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn o Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu o Curator : Mary Polacco maryp@teosinte.agron.missouri.edu o Assoc Curator : Pat Byrne byrne@teosinte.agron.missouri.edu QTL data o Assoc Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu Map data o Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic Stock data o Assoc Curator : Christiane Fauron FAURON@GENE1.med.utah.edu Mitochondrion genome o Assoc Curator : Carolyn Wetzel cmwetzel@iastate.edu Chloroplast genome o Assoc Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome o Design : Stan Letovsky letovsky@gdb.org o Design : Mary Berlyn mary@fetalpig.biology.yale.edu o Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu o Contact : db_request@teosinte.agron.missouri.edu o Last_update : 11 April 1995 o Database : MycDB o Species : Mycobacteria o Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. o PI : Staffan Bergh o Curator : Thierry Garnier o Curator : Staffan Bergh o Contact : staffan@biochem.kth.se o Last_update : Feb. 1995 (version 3-6) o ACEDB_version : 3.0 o WWW : http://www.biochem.kth.se/MycDB.html o ftp : www.biochem.kth.se (130.237.52.64) in pub/MycDB o ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB o ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb o Database : PomBase o Curator : Sean Walsh o Curator : Marie-Adele Rajendream o PI : Bart Barrell o Species : Schizosaccharomyces pombe o Contact : svw@sanger.ac.uk o Contact : barrell@sanger.ac.uk o Comment : Not yet available for distribution o DataBase : Mousedb o Species : Mus Musculus o Species : Homo Sapiens o ACEDB_version : 3.0 with extensions to define and display cytogenetic data. o Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. o Curator : Michelle Kirby o Curator : Rachael Selley o PI : Mary Lyon o PI : Jo Peters o Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 For other information contact Michelle Kirby. o Contact : kirbym@har-rbu.mrc.ac.uk (or mkirby@hgmp.mrc.ac.uk) rselley@har-rbu.mrc.ac.uk MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD o Last_update : February 1995 o Database : RiceGenes o Species : Rice (O. sativa) o Availability : Anonymous ftp from probe.nalusda.gov:pub/rice o Availability : Gopher nightshade.cit.cornell.edu port 70 o Availability : Gopher probe.nalusda.gov port 7007 o Curator : Edie Paul o PI : Susah McCouch o Contact : epaul@nightshade.cit.cornell.edu o ACEDB_version : 3.0 o Last_update : May 1994 o Database : SacchDB o Species : Saccharomyces cerevisiae o Focus : Budding (common baker's) Yeast Genome o ACEDB_version : UNIX 2.0, MacAce 2.0b4 o FTP : genome-ftp.stanford.edu in /pub/SacchDB o FTP : ncbi.nlm.nih.gov in /repository/SacchDB o Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. o Gopher : host = genome-gopher.stanford.edu, port = 70 o HTTP : http://genome-www.stanford.edu/ o Funding : National Center for Human Genome Research, NIH o PI : David Botstein, botstein@genome.stanford.edu o Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu o Curator : Selena Dwight, dwight@genome.stanford.edu o Curator : Cathy Ball, ball@genome.stanford.edu o Curator : Rita Schmidt, bleb@genome.stanford.edu o Curator : Barbara Dunn, bdbunnenome.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 1994 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 : Lisa Lorenzen o PI : Randy Shoemaker o Contact : lorenzen@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 : 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 written documentation exists for ACEDB? ++++++++++++++++++++++++++++++++++++++++++++++++ A5: +++ From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000 . Primary documents from the developers are: o acedb -- A C. elegans Database: I. Users' Guide. o acedb -- A C. elegans Database: II. Installation Guide. o acedb -- A C. elegans Database: III. Configuration Guide. o Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z and ftp://weeds.mgh.harvard.edu/acedb_doc The files are in tex (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. Japanese language guides: _Japanese ACEDB Guide Ver.1.2._ _ACEDB ver.2 for NEC engineering workstation EWS4800 series_ are available in PostScript via anonymous ftp at ftp.nec.co.jp as /pub/packages/acedb/acemanjp.1_2.ps.Z . 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 Angisturte.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: Where can I find further information about 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). 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 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: What's all this about Gopher, WAIS, FTP, WWW, URL, ... ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A9: +++ These terms all refer to Internet protocols. An excellent introduction to the Internet is: _The Whole Internet User's Guide & Catalog_, by Ed Krol, O'Reilly & Associates, 1992. Or ask your system administrator to provide you with a gopher client or mosaic client and begin navigating on your own. URL is a Universal Resource Locator on the World-Wide Web (WWW). There are many free Internet browsers available that allow you to use an Internet connection and a URL to access services. Mosaic may be the most popular and it is available for Mac, PC or Unix via anonymous ftp from ftp.ncsa.uiuc.edu. Return to List of Questions Q10: How can I get on/off the ACEDB announcements mailing list? +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A10: ++++ 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 Q11: When and where is the Next ACEDB Workshop? +++++++++++++++++++++++++++++++++++++++++++++++ A11: ++++ The 1995 ACEDB Conference and Workshop will be held May 14-27, 1995, at the Isis Oasis, a small retreat center in Geyserville, about 80 miles north of SanFrancisco in Sonoma County, California. We will have exclusive use of the entire retreat center, including the theater (for workstations and primary sessions), dining room, lodge, and other residential facilities. For more information send email to ace95@genome.lbl.gov or vist URL http://genome.lbl.gov/ace95.html on the WWW. 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 Q411:Who prepared this document & where is the current version? +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A411: +++++ (Note to international readers: 411 is the phone number for information in the USA.) 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 Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov Major contributions in getting this FAQ off the ground were made by Mike Cherry, John McCarthy, and Doug Bigwoody. Other contributors include: o Lisa Lorenzen o David Matthews o Edie Paul o Donn Davy o Eric De Mund o Sam Cartinhour Please cite as: Sherman,B.K., ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993,1994,1995 approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome Research Program. Return to List of Questions End of ACEDB FAQ --bks From owner-acedb@net.bio.net Tue May 09 23:00:00 1995 Newsgroups: bionet.software.acedb,bionet.genome.arabidopsis,bionet.plants,bionet.general,bionet.celegans Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!uwvax!newssinet!news.u-tokyo.ac.jp!wnoc-tyo-news!nec-tyo!necspl!nmitnews!newssv1.tmg.nec!dsp.cl.nec!necscc!tgn.cl.nec!sano@exp.cl.nec.co.jp From: Tohru Sano Subject: announcing A WWW Site of ACEDB document written in Japanese Sender: daemon@tgn.cl.nec.co.jp (0000-Admin(0000)) Message-ID: <199505101650.BAA05047@kirara.exp.cl.nec.co.jp> Date: Wed, 10 May 1995 16:50:43 GMT X-Mailer: WeMail[1.11] ID:1A0148 Organization: NEC Corp., Tsukuba JP Lines: 12 Xref: biosci bionet.software.acedb:590 bionet.genome.arabidopsis:3264 bionet.plants:6721 bionet.general:15136 bionet.celegans:386 ACEDB document written in Japanese are available via WWW. Thank you for many accesses to the postscript file of our ACEDB document written in Japanese (Ver. 1.2) on ftp.nec.co.jp. Now, html version of the document is available via WWW; URL=http://www.cbi.or.jp/~sano/acemanjp12/index.html. Tohru Sano NEC Corporation From owner-acedb@net.bio.net Thu May 11 23:00:00 1995 Path: biosci!informatik.uni-stuttgart.de!Baumann From: Baumann@informatik.uni-stuttgart.de (Joachim Baumann) Newsgroups: bionet.software.acedb Subject: Announcement: TextConvert 1.2 Date: 12 May 1995 02:28:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 68 Sender: daemon@net.bio.net Distribution: world Message-ID: <199505120927.LAA02449@habakuk.informatik.uni-stuttgart.de> NNTP-Posting-Host: net.bio.net Hi all, just a month since the announcement of the last version of TextConvert. There has to be something awfully wrong, if someone needs only 30 days to produce a new version. Just like Microsoft (oops, no pun intended...). But wait, this isn't a bugfix. I enhanced the functionality of TextConvert. Now it is possible to define subroutines in your description file and even to include other description files. This makes the creation of libraries possible and easy. And I added a ASCII version and a HTML version of the documentation to the archive. Now follows the announcement: Announcing TextConvert ---------------------- TextConvert is a tool to ease the conversion of data in flat file libraries to ACEDB format. It takes as input a description file in a format that resembles the format of AWK-scripts, reads a data stream and produces another data stream according to patterns and attached code, so called actions, in a given description file. The patterns can be formed according to Perl's regular expressions, and the actions are formulated as Perl source code enriched with additional commands to ease the conversion of text-based data. The additional commands support the ACEDB format. It is even possible to add one's own subroutines to the description file and to include other description files, thus effectively maintaining libraries of common functionality (subroutines and/or Action/Pattern pairs). In fact, the program is written in Perl, and builds a program from the description file. This program is then evaluated. The additional commands support input, output, an object stack and decoding of 2-Bit coded data. Included are 25 pages of documentation including a tutorial, and in case this doesn't help, the author is reachable via EMail :-) The documentation is available in Framemaker-, Postscript-, HTML- and plain text format. The address is: joachim.baumann@informatik.uni-stuttgart.de Program and documentation can be ftp'ed from ftp.informatik.uni-stuttgart.de in the directory /pub/DART/TextConvert under the names textconvert-1.2.tar.gz (This is the whole archive) TextConvert.1.2.ascii.gz (This is the plain text documentation) TextConvert.1.2.html (This is the HTML version of the docs) TextConvert.1.2.html.gz (The gzipped HTML documentation) Cheers, Joachim ------------------------------------------------------------------------------- Snail: Joachim Baumann, | Universitaet Stuttgart, IPVR, | Phone: (+49 | 0 ) 711/7816-218 Breitwiesenstr. 20-22, | Fax: (+49 | 0 ) 711/7816-424 70565 Stuttgart, Germany | EMail: joachim.baumann@informatik.uni-stuttgart.de(.sol_3.milky-way.universe) PGP: finger baumann@orgel.informatik.uni-stuttgart.de From owner-acedb@net.bio.net Thu May 18 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!lamarck.sura.net!sprout.nalusda.gov!usenet From: Gail Juvik Newsgroups: bionet.software.acedb Subject: New AGIS WWW Server Date: 18 May 1995 14:15:25 GMT Organization: USDA-ARS-NAL Lines: 59 Message-ID: <3pfkpt$c39@sprout.nalusda.gov> NNTP-Posting-Host: lars.nalusda.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) X-URL: news:bionet.software.acedb The Agricultural Genome Information Servers (WWW and gopher) have been completely overhauled. What's New? - Basically everything. All server software has been updated and moved to a newer, faster machine. Data resources have been updated and new information has been added. Documentation has been greatly enhanced. The organization of the servers has been changed to make it easier to find the information you are looking for. Data formatting is also much improved. A brief summary of the information you will find on the servers: Databases include information on: Arabidopsis, common bean and soybean, Chlamydomonas, cotton, small grains (wheat, barley, etc.), maize, rice, tomato, potato, pepper, sorghum, forest trees, C. elegans, Mycobacteria, and human 21 and X. Also included is Mendel, the database from the Commission on Plant Gene Nomenclature. Many links to WWW data resources (e.g. sequence and germplasm databases) have been added to these databases. Searching can be done by WAIS, agrep (fuzzy searching), and ACeDB queries. --- A full complement of ACeDB documentation. --- Electronic newsletter, journals, and other publications including: Plant Genome I,II, & III meeting abstracts, Weeds World, the Rice Genetics Newsletter, Report of the Tomato Genetic Cooperative, the National Animal Genome Resources Program Newsletter, and the announcement for the new peer-reviewed electronic journal, The Journal of Quantiative Trait Loci. --- A Tools section which contains tools not found elsewhere. ------------------------------------------------------------------- Please feel free to come and poke around. If you haven't visited in awhile you might want to check back to see what's new. The What's New page will always include any updates/changes to the servers. To reach these servers: World Wide Web: http://probe.nalusda.gov/ [*preferred*] [NOTE: If you do not have a WWW browser, but have telnet capability, then you can use our lynx, text-based browser. Telnet to probe.nalusda.gov and use the login "lynx" (no quotes) and just hit return at the Password prompt. You MUST use vt100 terminal emulation in order to use lynx. Also, lynx has been modified so that you can only browse our WWW server along with a few related servers.] Gopher: probe.nalusda.gov Anonymous Ftp: probe.nalusda.gov Comments can be sent to feedback@probe.nalusda.gov Requests for help can be sent to help@probe.nalusda.gov Genome Informatics Group USDA, National Agricultural Library 10301 Baltimore Blvd. Beltsville, MD 20705 From owner-acedb@net.bio.net Thu May 18 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!lamarck.sura.net!sprout.nalusda.gov!usenet From: Steve Beckstrom-Sternberg Newsgroups: bionet.software.acedb Subject: Announcing: Plant Genome Database CD-ROM Date: 18 May 1995 15:02:41 GMT Organization: Genome Informatics Group - USDA - ARS - NAL Lines: 30 Message-ID: <3pfnih$cel@sprout.nalusda.gov> NNTP-Posting-Host: rapd.nalusda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3 sun4c) X-URL: news:bionet.software.acedb Announcing the availability of the Plant Genome Database CD-ROM, a compilation of plant genome databases, which have been dumped as text from their ACEDB versions and marked up with hypertext links. The data are browsable from the Sun UNIX X-Windows, PC Windows, and Mac Mosaic hypertext browsers. In addition, the genome data have been indexed to allow full-text Boolean searching for Mac, Sun, Windows, and DOS. Where images exist, they have been linked to their respective databases. Databases include information on: Arabidopsis, soybean, Chlamydomonas, small grains (wheat, barley, etc.), maize, rice, tomato, potato, pepper, and forest trees. Also included, are various related documents: newsletters for Arabidopsis (Weeds World), forest trees (Dendrome), rice (The Rice Genetics Newsletter), and tomato (Report of the Tomato Genetic Cooperative); plant genome thesauri for cytogenetics, morphology, and references; a controlled genetic vocabulary; and a listing of the Agricultural Genome curators. The CD-ROM can be obtained by sending e-mail to the Plant Genome Data and Information Center: pgenome@nalusda.gov Comments can be sent to feedback@probe.nalusda.gov Requests for help can be sent to help@probe.nalusda.gov Genome Informatics Group USDA, National Agricultural Library 10301 Baltimore Blvd. Beltsville, MD 20705 From owner-acedb@net.bio.net Thu May 18 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!fnnews.fnal.gov!overload.lbl.gov!news From: John McCarthy Newsgroups: bionet.software.acedb Subject: ACEDB 1995 Workshop On-Line Date: 19 May 1995 20:06:34 GMT Organization: Lawrence Berkeley Laboratory, Berkeley CA Lines: 30 Message-ID: <3pitob$o9b@overload.lbl.gov> NNTP-Posting-Host: gossyp.lbl.gov The 1995 ACEDB Conference just concluded day before yesterday, and the 1995 ACEDB Workshop will continue through the end of next week in Geyserville, California. Some 70 people attended the conference, and 45 are staying on for the workshop. We invite people interested in ACEDB to join us via the Internet. We will be posting summaries from working groups, papers, etc. via the ACE95 WWW page: http://genome.lbl.gov/ace95.html Documents under this page will be evolving during the next week, so keep checking back. We also invite you to send comments, suggestions, and questions -- as well as pointers to other URL's we should consider including here and as part of other ACEDB WWW documents. You can either send those to this newsgroup or if you don't want to broadcase it to the whole newsgroup, just send email to ace95@genome.lbl.gov. There are a lot of exciting new developments in ACEDB, and we'd like to get your feedback. We look forward to hearing from you. -John McCarthy (ace95 organizer) From owner-acedb@net.bio.net Mon May 22 23:00:00 1995 Path: biosci!MORGAN.HARVARD.EDU!flybase From: flybase@MORGAN.HARVARD.EDU (FlyBase Project Members) Newsgroups: bionet.software.acedb Subject: Encyclopaedia of Drosophila CD-ROM Date: 23 May 1995 08:37:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 121 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505231541.AA13266@morgan.harvard.edu> NNTP-Posting-Host: net.bio.net The Encyclopaedia of Drosophila CD-ROM Macintosh Compatible only Release 1.0 The Berkeley Drosophila Genome Project (BDGP) and FlyBase announce Release 1.0 of the Macintosh CD-ROM version of the Encyclopaedia of Drosophila (EofD). This is the same version of the EofD CD-ROM that was distributed to registrants at the April 1995 Drosophila Research Conference in Atlanta. The EofD is a graphical interface based on the ACeDB software first developed for the C. elegans database and now in use as a powerful browsing and querying tool for many genome databases. 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". Release 1.0 combines data from the BDGP and from FlyBase in an integrated view. In Release 1.0, all BDGP data (except DNA sequences) and much (but not all) FlyBase data are contained. In contrast, the FlyBase World Wide Web home page (URL = http://morgan.harvard.edu/) contains more FlyBase data but only a subset of BDGP data. Our long term goal is that both the EofD and the FlyBase home page will provide different views of the same comprehensive data set. However, we are probably about a year away from achieving this goal. Before purchasing the EofD, you should make sure you have access to a Macintosh computer with the following attributes: The EofD CD-ROM can only be run on higher end Macintosh computers, those equipped with 68040 or PowerPC processors and a CD-ROM drive. The application runs in native mode on the Power Macintosh and we recommend the Power Macintosh for optimal performance. The EofD requires System 7.1 or higher. System 7.5 is required to use the EofD Guide help facilities. In addition, QuickTime is required to play movies supplied on the CD-ROM. The EofD requires a minimum of 16 Megabytes (MB) of RAM. We recommend turning on Virtual Memory and setting it to at least 32 MB. ------------------------------------------------------------------------ The costs of the EofD, including shipping and handling, are, per CD-ROM and user manual: $10 for U.S. purchases and shipment to a U.S. address $15 for international purchases and shipment Order forms must be accompanied by checks or money orders in US dollars made out to "EofD". Only prepaid orders will be accepted. *** Please do *not* send in your order by email! *** Inquiries concerning EofD purchases may be made by telephone to Ms. Palmer at (617) 495-2906 or fax at (617) 495-9300 or by email to eofd-sales@morgan.harvard.edu. Questions concerning the structure or operation of the EofD should be e-mailed to eofd@fly2.berkeley.edu. ------------------------------------------------------------------------- ------------------------------------------------------------------------- PRINT OUT AND MAIL THE FOLLOWING FORM TO EofD c/o Dawn Palmer AT THE ADDRESS BELOW. ORDERS MUST BE PREPAID. THE ORDER MUST BE ACCOMPANIED BY PAYMENT IN FULL IN A CHECK IN U.S. CURRENCY. ANY OTHER FORM OF PAYMENT WILL BE RETURNED AS INCOMPLETE. ------------------------------------------------------------------------- ------------------------------------------------------------------------- *************************** EofD Release 1.0 ORDER FORM *************************** Name __________________________________________________ Address _______________________________________________ _______________________________________________ _______________________________________________ _______________________________________________ Telephone ________________________________________ Fax ______________________________________________ Email ____________________________________________ ---------------------------------------------------------------- ALL ORDERS MUST BE ACCOMPANIED BY FULL PAYMENT IN U.S. CURRENCY DRAWN ON A U.S. BANK MAKE CHECKS PAYABLE TO "EofD" Orders accompanied by insufficient funds will be returned. No purchase orders, credit card or standing orders can be accepted. _______ copies of EofD at $10 per copy for shipment within the USA $__________ _______ copies of EofD at $15 per copy for international shipment $__________ Orders must be mailed to: EofD c/o Dawn Palmer The Biological Laboratories Harvard University 16 Divinity Avenue Cambridge, MA 02138 USA *** Please do *not* send in your order by email! *** From owner-acedb@net.bio.net Thu May 25 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.belwue.de!news.belwue.de!News.Uni-Marburg.DE!pc2011.Humangenetik.Humanmedizin.Uni-Marburg.DE!otto From: otto@pc2011.humangenetik.humanmedizin.uni-marburg.de (Michael Otto) Newsgroups: bionet.software.acedb Subject: CONTIG9/CONTIGC Date: Fri, 26 May 1995 09:19:40 GMT Organization: Humangenetik Marburg Lines: 5 Message-ID: NNTP-Posting-Host: pc2011.humangenetik.humanmedizin.uni-marburg.de Hi Netters, anyone who can tell me where to get the program CONTIG9 or CONTIGC thanks in advance From owner-acedb@net.bio.net Thu May 25 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!sgiblab!rpal.rockwell.com!news.Stanford.EDU!stout.Stanford.EDU!cherry From: cherry@stout.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: "The Scientist" is looking for the best freeware and shareware Date: 26 May 1995 05:29:51 GMT Organization: Stanford University Genetics Department Lines: 16 Message-ID: <3q3p0f$v11@nntp.Stanford.EDU> References: NNTP-Posting-Host: stout.stanford.edu In article Robert Finn (finn@netcom.com) wrote: > For an article in "The Scientist" I am looking for suggestions for the best > freeware and shareware programs of special interest to life scientists. I'm > looking for everything from statistics packages to molecular modeling to > sequence matching, etc. Please post here or send me e-mail describing > your favorite freeware and shareware, where to obtain it, and why it's so > great. I'm also looking for suggestions for the best sites on the Internet > to obtain science-related software. Sent your messages on the best freeware to: finn@netcom.com I would argue that ACEDB is THE best freeware (better than any pay-out-the-nose-ware) for biology. Mike From owner-acedb@net.bio.net Thu May 25 23:00:00 1995 Path: biosci!rutgers!gatech!news.sprintlink.net!cs.utexas.edu!news.tamu.edu!algodon!lazo From: lazo@sun.com (Gerard R. Lazo) Newsgroups: bionet.software.acedb Subject: Re: CONTIG9/CONTIGC Date: 26 May 1995 22:16:09 GMT Organization: Sun Microsystems, Inc. Lines: 4 Distribution: world Message-ID: <3q5jv9$ku2@news.tamu.edu> References: Reply-To: lazo@sun.com NNTP-Posting-Host: algodon.tamu.edu I recall last seeing Contig9 at genome.wi.mit.edu along with mapmaker and primer. From owner-acedb@net.bio.net Fri May 26 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!gatech!news.sprintlink.net!pipex!sunic!sunic.sunet.se!trane.uninett.no!daresbury!not-for-mail From: rdurbin@watson.wustl.edu (Richard Durbin) Newsgroups: bionet.software.acedb Subject: contigc/cpontig9 Date: 27 May 1995 06:39:20 +0100 Lines: 7 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3q6du8$11n@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk contigc is available from ftp://sanger.ac.uk/pub/contigc. It was developed at the Sanger Centre, froJohn Sulston's VAX VMS CONTIG9 software, and is actively maintained. CONTIG9 is no longer maintained or distributed to my knowledge, certainly not by anyone closely connected to John Sulston. Richard Durbin From owner-acedb@net.bio.net Fri May 26 23:00:00 1995 Path: biosci!WATSON.WUSTL.EDU!rdurbin From: rdurbin@WATSON.WUSTL.EDU (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB 4_0b4 code Date: 27 May 1995 16:01:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505272300.AA23814@watson.gscnis> NNTP-Posting-Host: net.bio.net We have made available a version 4_0 beta4 code release on the NCBI repository in directory acedb/ace4. This is the final code from the ACE95 workshop, and contains a number of enhancements over previous versions, coming from many participants. In particular there have been major advances with the server/client version, which now supports dumping perl objects. 4_0 is binary incompatible with versions 3_x, although in most other respects it it an incremental advance, not a major rewrite. We are using this code to support the current C. elegans public data release, but advise that it is not used for active data management before further testing has taken place. We expect a 4_1 code release in the fairly near future. Richard Durbin and Jean Thierry-Mieg From owner-acedb@net.bio.net Sat May 27 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mieg@watson.wustl.edu (Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: ACE4, bugs and description Date: 29 May 1995 00:15:46 +0100 Lines: 129 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3qb072$91@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, mieg@watson.wustl.edu #############BUGS############### Leon Avery already found 2 bugs in tace 1) you must ace comment out several lines in options.wrm as follows /* use these for synmap // _VMap -V -D SYN -M STSMAP // _VAssembly -V -D SYN -M DOGMAP // _VClone -V -D SYN -M CloneMAP */ 2) list option in tace is bugged Easy to fix but very annoying, I suppose the code was never tested after modification at ace95 3) solaris linking is a problem best is to recompile on your own solaris machine ******************************************************* ############ DESCRIPTION ############################ Ace 4.0 is a very hasty distribution motivated by the worm meeting taking place this week, the code nevertheless contains many interesting advances, which can be described as follows: A number of people have contributed different more or less independant pieces Kernel Level: Overall, the system is faster and uses less memory: The lists in the main window are 'instantaneous' The cache manager balanced was modified, the dictionary system now has 2 levels These modifications were motivated by teh IGD project and developped in Montpellier (D&J Th-M) with fixes from Cambridge (rd & srk) Acedb now recognise the platform it runs on, it automatically byte swaps if needed, but you should initialise it on the platform (DEC-SUN-IBM ...) which you intend to use most. This system was written by Simon Kelley Table Maker: The table maker (JTM) now works correctly inside complex objects this was fixed in 3.5, but not in 2.0 Query Builder A new version of the query buider interface has been contributed by Suzana Lewis, replacing an older version also from LBL. Server/Client: Indisagreement with Richard, who wanted to transmit compiled byte streams, we constructed in Montpellier over the last year, with the help of the Heidelberg group, a client server exchanging ace streams thru rpc. This amounts to writing a multiphreaded tace who can answer and give write access to several clients in parallel. During the ace95 workshop the system was enhanced to allow configurable ports and perl exports. The purpose of this perl interface is the enhancement of the ace server run by Bigwood at the national agriculture library. This Web server augments the acedb data with url to other database before returning the answers. A server client architecture is complex to handle and not useful in small labs. Configurability of the models: The models have been completely rewritten with the tag2 system introduced in ace.3.0 This allows the curators to name their classes at will, without losing the displays, i.e. one may call a gene a locus without penalty. This modification affects the genetic map and the grid display, so you may have to modify your personal data. It does not affect the vMap (introduced in 3.0 which was alreay tag2) nor the horizontal physical map which was kept as is. Configurability of the genetic map display: Simon Kelley has thorougly rewritten the control of the genetic map display. New features include: an easier control of what is displayed, the possibility to configure the color code, and a simple way to save and reuse your choices. Comments welcome. Sequence Map display: Richard has introduced several new functionalities in the display of homologies and their scores. Also a possibility to read and write peptide sequences. Blixem: This sequence algnment tool by Erik Sonnhammer is enhanced since 2.0, it gives an example of a contributed tool, with its own user interface, somehow different from the rest of acedb, despite the fact that it uses the same toolbox Molecular Pathways This code, originally written by Stan Letowsky, was adapted and linked into ace4.0 by Richard. You may need some new data to test it. Mosaic Help A number of people, including Sam Cartinhour, John Barnett and Jaime Prilusky have modified the acedb help system so that, if possible, the help will be displayed in a mosaic window, allowing direct access to the documentation servers. ############## WORM DATA ############################### The worm dataset distributed on the ncbi server (update.4*) was collated in Cambridge by Richard and co. ************************************* ############## ACEMBLY ################################# The sequence assembly and edition package Acembly, written to support shotgun sequencing and study of dna variations, by Ulrich Sauvage, Danielle and Jean T-M will be distributed independantly in the near future. This programs relies on the acedb database and toolbox but its complex graphic interface is nearly enterely new. We consider it to be an example of the modularity of acedb. In acembly, all the new work went into the conception of the display, with the acedb system considered as a reliable black-box. *************************************** ############## Using ace 4.0 ############################## Again this is a test release, Send comments, try it on public datafiles, port your data to the new format when needed, but I do not yet garantee that the database kernel is as reliable as 3.7 and will not accidentally loose the data. ############################################################ Jean T-M From owner-acedb@net.bio.net Sun May 28 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!demon!doc.news.pipex.net!pipex!sunic!sunic.sunet.se!trane.uninett.no!due.uninett.no!alf.uib.no!pc-40.isf.uib.no!hogne.sandvik From: hogne.sandvik@isf.uib.no (Hogne Sandvik) Newsgroups: bionet.software.acedb Subject: Reducing study sizes - sequential design Date: 29 May 1995 16:23:51 GMT Organization: University of Bergen Lines: 31 Message-ID: NNTP-Posting-Host: pc-40.isf.uib.no In ordinary, classical experimentation, observations are examined when the experiment itself is finished. In sequential experiments, the observations are examined in a systematic manner as the experiment proceeds, in order to terminate the experiment at the earliest possible time. Sequential experimentation is attractive from many points of view. In medicine, ethical and economical arguments weigh heavily in favour. An average saving in study size of about 1/3, compared to a fixed-size study, is possible. Many experiments said to be classical are in fact of the sequential type, because researchers allow themselves informal analyses of the results before the experiment is finished. Would it not be nicer to include these 'looks' into the formal design? Egil H. Lehmann, GP and statistician, has developed a computer program (MEDSEQ) that enables clinicians with only a limited background of statistics to design sequential experiments. It is freeware. More information is provided here: http://www.uib.no/isf/medseq.htm >////<< l """ l (0) (0) --OOO--(_)--OOOo-- Hogne.Sandvik@isf.uib.no http://www.uib.no/isf/people/hogne.htm From owner-acedb@net.bio.net Sun May 28 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!demon!doc.news.pipex.net!pipex!sunic!sunic.sunet.se!trane.uninett.no!due.uninett.no!alf.uib.no!pc-40.isf.uib.no!hogne.sandvik From: hogne.sandvik@isf.uib.no (Hogne Sandvik) Newsgroups: bionet.software.acedb Subject: Reducing study sizes - sequential design Date: 29 May 1995 16:23:32 GMT Organization: University of Bergen Lines: 7 Message-ID: NNTP-Posting-Host: pc-40.isf.uib.no >////<< l """ l (0) (0) --OOO--(_)--OOOo-- Hogne.Sandvik@isf.uib.no http://www.uib.no/isf/people/hogne.htm From owner-acedb@net.bio.net Mon May 29 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: mieg@watson.wustl.edu (Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: WARNING, ace 4 is bugged Date: 30 May 1995 04:38:40 +0100 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3qe400$b22@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk I hope you noticed that the ace4.0 code at ncbi is not a distribution, but a test crippled with bugs. I will not be available to debug for one more month, and will probably make a real distribution only at the end of the summer. please mail your complaints to durbin. In my opinion , this test is not meant for real users, i.e. neither for nematode biologists nor for curators of other databases. It only serves as a progress report for the computer people who attended the ace95 conference last week. Jean Thierry- Mieg From owner-acedb@net.bio.net Mon May 29 23:00:00 1995 Path: biosci!GENOME.STANFORD.EDU!cherry From: cherry@GENOME.STANFORD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: bug with mono display Date: 29 May 1995 19:49:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <199505300250.TAA11441@fafner.Stanford.EDU> NNTP-Posting-Host: net.bio.net Here is a minor bug in the new ACEDB 4.0 beta 4 software. If you are on a monochrome display you'll get a Segmentation fault unless you set the ACEDB_COLOR enviroment variable. For those who wish to look at the code here is the gdb message and the appropriate region of the source. Program received signal SIGSEGV, Segmentation fault. 0x17e9a0 in setXcolors (gc=0x7451c8, fcol=20, bcol=20) at graphxlib.c:799 799 XSetStipple (display, gc, *stipple[fcol]) ; (gdb) l 794 { 795 if (isMono) 796 { 797 XSetBackground (DG, BlackPixelOfScreen(XtScreen(root_widget))); 798 XSetForeground (DG, WhitePixelOfScreen(XtScreen(root_widget))); 799 XSetStipple (display, gc, *stipple[fcol]) ; 800 XSetFillStyle( display, gc, FillOpaqueStippled); 801 } 802 else 803 { Mike P.S. As talked about on the last day of the ACEDB workshop it was of interest that bugs and source enhancements be sent to the ACEDB list, and of course to Jean and Richard. From owner-acedb@net.bio.net Mon May 29 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!sunic.sunet.se!news.kth.se!sibirien.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: WARNING, ace 4 is bugged Date: 30 May 1995 08:27:03 +0200 Organization: Biochemistry, KTH, Stockholm Lines: 19 Sender: staffan@biochem.kth.se Distribution: bionet Message-ID: <3qedrn$dsd@sibirien.physchem.kth.se> References: <3qe400$b22@mserv1.dl.ac.uk> NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article <3qe400$b22@mserv1.dl.ac.uk> mieg@watson.wustl.edu (Jean Thierry-Mieg) writes: > >I hope you noticed that the ace4.0 code at ncbi is not a >distribution, but a test crippled with bugs. Here's a pretty serious one that you might look out for - the KeySet display loses the last column of keys in a window, when there are more keys than fit in one window. Flipping through objects with the arrow keys in the KeySet window will skip past the missing keys. Only if you resize the window to be big enough to fit all the keys in the keyset will you be shown all of them. [SunOS 4.1.4, distributed binary] /staffan PS Also sent this to Richard DS PPS To a novice programmer like me this has the mark of a one-off error in some array ... DDS From owner-acedb@net.bio.net Wed May 31 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 1 Jun 1995 02:00:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 347 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506010900.CAA07538@net.bio.net> Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions on how to subscribe/unsubscribe will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. 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If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. 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This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-acedb@net.bio.net Wed May 31 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: Genetic maps (gifs) in _C. elegans_ acedb Date: 1 Jun 1995 14:02:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506012102.AA26518@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > Could someone tell me how to interpret the genetic map > gifs found in the _C. elegans_ acedb? In particular, I'd like to > know what the vertical line in the center of the gif with loci > next to it covers. Does it signify the high-lighted deletion > range to the left or some other range? > A place to look for this information would also do fine. Hi Chris, I'm currently working on some documentation for the ACEDB genetic map display. I'm afraid I can't tell which vertical line you're referring to here, but if you'll look at the explanation I've written up so far maybe you can either find your answer or find what name I call it by. It's currently (temporarily) located at http://genome.lbl.gov/ace95/public/matthews/GMAP.html. regards, - Dave From owner-acedb@net.bio.net Wed May 31 23:00:00 1995 Newsgroups: bionet.celegans,bionet.software.acedb Path: biosci!rutgers!uwm.edu!uwvax!uchinews!quads!ccb1 From: ccb1@quads.uchicago.edu (Chris B.) Subject: Genetic maps (gifs) in _C. elegans_ acedb X-Nntp-Posting-Host: midway.uchicago.edu Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Reply-To: ccb1@midway.uchicago.edu Organization: University of Chicago -- Academic Information Technologies Date: Thu, 1 Jun 1995 20:21:26 GMT Lines: 11 Xref: biosci bionet.celegans:410 bionet.software.acedb:611 Could someone tell me how to interpret the genetic map gifs found in the _C. elegans_ acedb? In particular, I'd like to know what the vertical line in the center of the gif with loci next to it covers. Does it signify the high-lighted deletion range to the left or some other range? A place to look for this information would also do fine. Thanks all, Chris Bauer