From owner-acedb@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: saving Longtexts Date: 2 Oct 1995 12:51:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510021516.AA25548@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Can LongTexts be saved to a file from xace4_1? This works from tace, but the Save button in the xace LongText window doesn't do it. - Dave From owner-acedb@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: from Jean re: saving Longtexts Date: 3 Oct 1995 17:05:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510040003.AA28533@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net I asked: > Can LongTexts be saved to a file from xace4_1? Jean had several good suggestions: > to dump > select all longtetxs > from the little triangl next to Class in the main window > > all longtetx then go in the main keyset > then you ace dump them > > you can always print a window in ascii mode into a file > > ofcourse if youput a name in the yellow box before > selecting the triangle, you reduce the number of text > > you can also chose an author > follow papers > follow abstract from keyset menu > then ace dump From owner-acedb@net.bio.net Thu Oct 05 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!tank.news.pipex.net!pipex!news.sprintlink.net!simtel!zombie.ncsc.mil!cs.umd.edu!info.usuhs.mil!hivgenome.hjf.org!user From: msalminen@hiv.hjf.org (Mika Salminen) Newsgroups: bionet.software.acedb Subject: ACEDB database for viruses Date: Fri, 06 Oct 1995 14:33:17 -0500 Organization: Henry M. Jackson Foundation Lines: 14 Message-ID: NNTP-Posting-Host: 131.158.31.163 We are thinking of porting a large collection of genbank formatted viral sequences into an ACEDB based database. We are concerned with trying to retain as much of the information of the fields in the genbank entries as possible, and specifically wonder if someone outhere has tools developed for this purpose already (filters I mean). We would especially appreciate advice ofrom someone who might have done this with another virus, since that would propably be really helpful for the deign of the database model. Thanks in avance for your replies, Mika Salminen From owner-acedb@net.bio.net Thu Oct 05 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: security of the ace server Date: 6 Oct 1995 15:33:56 +0100 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <453eok$r7m@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr I don t know about the perl client but the security is on the server side and requires the client to have write/read access on your disk so that your disk is nsf mounted unless the database is declared open explicitelly in wspec/server.wrm so, as far as i see it, only authorised clients local to your machine running locally will ever be able to talk to the server the wspec/server.wrm file should belong to acedb user and be 600 so nobody can tamper with it the server cannot subshell unless setenv ACEDB_SUBSHELL the server itself (my code) will not edit server.wrm so i beleive that the server, even ran a s a daemon is secure From owner-acedb@net.bio.net Thu Oct 05 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!fnnews.fnal.gov!unixhub!news.Stanford.EDU!stout.Stanford.EDU!cherry From: cherry@stout.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: ACEDB database for viruses Date: 6 Oct 1995 21:25:18 GMT Organization: Stanford University Genetics Department Lines: 71 Message-ID: <4546ru$sn1@nntp.Stanford.EDU> References: NNTP-Posting-Host: stout.stanford.edu In article , Mika Salminen wrote: >We are thinking of porting a large collection of genbank formatted viral >sequences into an ACEDB based database. We are concerned with trying to >retain as much of the information of the fields in the genbank entries as >possible, and specifically wonder if someone outhere has tools developed >for this purpose already (filters I mean). > >We would especially appreciate advice ofrom someone who might have done >this with another virus, since that would propably be really helpful for >the deign of the database model. > > >Thanks in avance for your replies, > >Mika Salminen I think you will find that any feature used in GenBank/EMBL is available in ACEDB. There are a variety of converters available. Below is a short list as a starting point. -Mike All of these converters might be specific to a particular database project. That is they will take what they want from GenBank and discard the rest. ----- My converter ----- Anonymous ftp from weeds.mgh.harvard.edu look in the /acedb_dev/utilities/gb2ace.sgd.c There are a few others in that directory too. ----- A recently announced Perl script ----- I don't know how much people want something like this, but... I've written a Genbank to .ace conversion script in perl. It handles the latest version of Genbank flat format files and outputs into ACEDB version 4 type ?Sequence and ?Paper models. (The models we use have been slightly changed from the distribution - a copy is enclosed.) Most of the Genbank features are handled, and the user can set an option to generically handle the features for which I did not write specific code. The feature handling routines are in a separate file, so it's easy to extend them. The tar file is available at: http://klab.agsci.colostate.edu/~mferguso/files.html Enjoy. Also, please send me your comments (or requests, even). /s/ Martin Ferguson mferguso@klab.agsci.colostate.edu P.S. If anyone knows of some perl libraries to handle asn.1 data, please let me know. ----- GenBank ASN.1 to ACE ----- Hello, we've written such a beast also, but for the binary representation (ASN.1) as well as for text files. It is written in C, uses the NCBI toolkit (see http://www.ncbi.nlm.nih.gov/), and is able to decode Entrez Data with the help of an additional program. It can be found at ftp.informatik.uni-stuttgart.de:/pub/DART/ASN2ACE/asn2ace-1.0.tar.gz From owner-acedb@net.bio.net Tue Oct 10 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: table maker Date: 11 Oct 1995 18:44:58 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <45gvqq$eaa@mserv1.dl.ac.uk> Original-To: matthews@greengenes.cit.cornell.edu i fixed the text condition however you can use it already by going in obj itself and putting the condiont there 1: Image, condition Pick = "xv" 2: Pick, type Text whereas 1: Image, 2: Pick, type Text, conditon "xv" does not work in 4.1, will agin in 4.2 From owner-acedb@net.bio.net Wed Oct 11 23:00:00 1995 Path: biosci!dkfz-heidelberg.de!D.Wolf From: D.Wolf@dkfz-heidelberg.de (Detlef Wolf) Newsgroups: bionet.software.acedb Subject: fixed acediffs version Date: 12 Oct 1995 10:08:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510121706.AA28395@mbp-sun5.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net To: acediffs users thanks to Richard, a bug in acediffs, a fast version of acediff operating on sorted .ace data, was discoverd and fixed. the new code is in: ftp://genome.dkfz-heidelberg.de/igd/people/D.Wolf/acediffs.dist.951012.tar.gz please discard the pervious version, if you have one. the bug did not occur often, but is serious (it mixed adjacent objects). many greetings, Detlef ----------------------------------------------------------------------------- Detlef Wolf, European Data Resource for Human Genome Research eMail: D.Wolf@dkfz-heidelberg.de phone: +49 6221 42 -2331 fax: -2333 sMail: DKFZ (German Cancer Research Centre), Abt. Molekulare Biophysik (0810) Im Neuenheimer Feld 280, 69120 Heidelberg, Germany finger: dok256@genome.dkfz-heidelberg.de WWW: http://genome.dkfz-heidelberg.de/igd/developers/D.Wolf From owner-acedb@net.bio.net Wed Oct 11 23:00:00 1995 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!elvis.delphi.com!uunet!in2.uu.net!csn!nntp-xfer-2.csn.net!yuma!usenet From: "Martin L. Ferguson" Newsgroups: bionet.software.acedb Subject: Medline and Genbank conversion updates. Date: 12 Oct 1995 15:22:21 GMT Organization: Colorado State University Lines: 22 Message-ID: <45jbrd$2lc4@yuma.ACNS.ColoState.EDU> NNTP-Posting-Host: klab.agsci.colostate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4m) X-URL: news:bionet.software.acedb Hello ACEDB users, To the 30, or so, of you who have downloaded my perl programs for converting Genbank and Medline data into .ace format: I have recently placed updates of these on our system. They can be retrieved from: http://klab.agsci.colostate.edu/~mferguso/files.html Some bugs have been fixed and a few features added. Also, if you download, you will be voluntarily asked to supply your email address. If you give it to me, I will mail you notifications of future updates/bug fixes. Cheers, /s/ Martin -- ###################################################################### # # Martin Ferguson Dept. of Entomology # martinf@lamar.colostate.edu Colorado State U. # 970-491-7989 Ft. Collins, CO 80523 # From owner-acedb@net.bio.net Sun Oct 15 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: parameters in tables in 4.1 Date: 16 Oct 1995 13:00:15 +0100 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <45thgf$r3@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr I just noticed that in 4.1 parameters in spread sheets: // Spread sheet definition for the ACeDB software // Date: 1995-10-13_09:04:16 // %n (%%n in the graphic) are parameter to be given on the command line in tace // \%n (%n in the graphic) are substituted by the value of column n at run time // Line starting with // are ignored, starting with # are comments do not work, becasu of some indirect effect i fixed it, so parameters worked in 3.7, will in 4.2, don't in 4.1 the reason is that the parameter \%1 in the external file that you load is not stripped to %1 in the table that you see on the screen, if on the screen, you type %1 (for the value in column 1) the system works. very sorry From owner-acedb@net.bio.net Sun Oct 15 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!EU.net!uknet!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: accessing constructed types in table maker Date: 13 Oct 1995 10:05:31 +0100 Lines: 65 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <45la4r$ch1@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr Somebody asked how to do that since it looks like a general question, here is the way col 1: Locus col 2: From 1, Map-?Map col 3: right_of 2 Position-float col 4: right of 3 Error-float the secret is to touch the From button, which then turns into: Right_of, then you get in the atg button the proper model The exact .def file is: // Spread sheet definition for the ACeDB software // Date: 1995-10-13_09:04:16 // %n (%%n in the graphic) are parameter to be given on the command line in tace // \%n (%n in the graphic) are substituted by the value of column n at run time // Line starting with // are ignored, starting with # are comments Colonne 1 Width 12 Mandatory Visible Class Class Locus From 0 Condition ace* Colonne 2 Width 12 Optional Visible Class Class Map From 1 Tag Map Colonne 3 Width 12 Optional Visible Float Right_of 2 Tag HERE # Position Colonne 4 Width 12 Optional Visible Float Right_of 3 Tag HERE # Error // End of these definitions From owner-acedb@net.bio.net Mon Oct 16 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!zombie.ncsc.mil!cs.umd.edu!haven.umd.edu!purdue!lerc.nasa.gov!magnus.acs.ohio-state.edu!slip2-16.acs.ohio-state.edu!jesse.5 From: jesse.5@postbox.ohio-state.edu (Jonathan Jesse) Newsgroups: bionet.software,bionet.software.acedb,bionet.software.gcg Subject: Using GRASP molecular modeling program. Date: Tue, 17 Oct 1995 17:06:56 GMT Organization: The Ohio State University Lines: 10 Message-ID: NNTP-Posting-Host: slip2-16.acs.ohio-state.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] Xref: biosci bionet.software:13636 bionet.software.acedb:751 bionet.software.gcg:1418 If anyone out there is familair with "GRASP", what I am trying to do is set up a macro that will configure the image in a specific way. Basically, I have many different residues that need to be colored various colors, and it is a tedious process typing all of them in at the command line. If anyone knows how to write a macro that can do things like this, I would appreciate the help. Jon jesse.5@osu.edu From owner-acedb@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!CS.Arizona.EDU!math.arizona.edu!noao!news.eas.asu.edu!cs.utexas.edu!news.sprintlink.net!newsfeed.internetmci.com!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 25 Oct 1995 17:04:15 GMT Organization: Dendrome, A genome database for forest trees Lines: 1134 Approved: news-answers-request@MIT.Edu Message-ID: <46lqmf$g4g@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:752 news.answers:49749 Archive-name: acedb-faq Last-modified: 10/25/95 Version: 1.25 ACEDB FAQ ********* Curated by: Bradley K. Sherman Frequently Asked Questions about ACEDB ++++++++++++++++++++++++++++++++++++++ o Q0 : What is ACEDB? o -------------------- o Q1 : What is the current version of ACEDB? o ------------------------------------------- o Q2 : What hardware/software do I need to run ACEDB? o ---------------------------------------------------- o Q3 : Where can I get ACEDB? o ---------------------------- o Q4 : What ACEDB databases exist? o --------------------------------- o Q5 : What documentation exists for ACEDB? o ------------------------------------------ o Q6 : What other resources are available for ACEDB? o --------------------------------------------------- o Q7 : How should ACEDB be cited? o -------------------------------- o Q8 : Is ACEDB object-oriented? o ------------------------------- o Q9 : How doe one get on/off the ACEDB announcements mailing list? o ------------------------------------------------------------------ o Q10 : When and where is the next ACEDB Workshop? o ------------------------------------------------- o Q11 : Who prepared this document & where is the current version? o ----------------------------------------------------------------- Questions marked with '+' are new, those with '!' have substantially changed answers. Q0: What is ACEDB? ++++++++++++++++++ A0: +++ ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [Q4 gives contact information]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions Q1: What is the current version of ACEDB? +++++++++++++++++++++++++++++++++++++++++ A1: +++ (This answer refers to the software not the C. elegans data.) Current version is 4_1 (as of 10 August 1995). A test (beta) version of ACEDB 4.0b4 (5/95) is available. A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q9. Return to List of Questions Q2: What hardware/software do I need to run ACEDB? ++++++++++++++++++++++++++++++++++++++++++++++++++ A2: +++ The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. o Unix and X11: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series o PC 386/486/Pentium with Linux (free Unix) Jeff Bryer, jbryer@darwin.mbb.sfu.ca and Ken Clark provide a linux version of 4.1 and a complete C. elegans data set at trog.mbb.sfu.ca in /pub/acedb as bin.linux.4_1.tar.Z. o There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o Macintosh: o [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a 17" color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. o ACEDB for The NEC EWS4800 is available via anonymous ftp at ftp.nec.co.jp (192.135.93.2) in /pub/packages/acedb/ace2. Contact Tohru Sano Fundamental Research Laboratories NEC Corporation Tsukuba, 305, JAPAN, e-mail: sano@exp.cl.nec.co.jp, FAX: +81-298-56-6136, VOICE: +81-298-50-1507 (Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems SPARCstation II, and users can interact using Macintoshes and PC-clones by using X11 implementations for the personal computers and a LAN. --bks) X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions Q3: Where can I get ACEDB? ++++++++++++++++++++++++++ A3: +++ The standard ACEDB source and binaries are available in the following public access accounts (anonymous ftp sites) accessible via Internet: o lirmm.lirmm.fr in pub/acedb o cele.mrc-lmb.cam.ac.uk in pub/acedb o ncbi.nlm.nih.gov in repository/acedb o bioinformatics.weizmann.ac.il in pub/databases/acedb. MacAce is available from: o genome.lbl.gov in pub/macace o cele.mrc-lmb.cam.ac.uk in pub/acedb/macace Linux; ACEDB version 4.1 (and earlier versions) for Linux 2-10: o trog.mbb.sfu.ca /pub/acedb as bin.linux.4_1.tar.Z. ACEDB for The NEC EWS4800: o ftp.nec.co.jp in /pub/packages/acedb/ace2. Return to List of Questions Q4: What ACEDB databases exist? +++++++++++++++++++++++++++++++ A4: +++ In alphabetic order by Database name ------------------------------------ [Curators, please submit changes as new paragraphs] Database : AaeDB Species : Aedes aegypti (Mosquito) Last_update : December 1994 ACEDB_version : 3.0 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Database : AAtDB Species : Arabidopsis thaliana Current version : 3-5 Last_update : August 1995 Curator : John Morris Contact : curator@frodo.mgh.harvard.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : Macintosh version - weeds.mgh.harvard.edu in aatdb/MacAAtDB FTP : UNIX version - weeds.mgh.harvard.edu in aatdb/aatdb.3x FTP : probe.nalusda.gov in pub/aatdb Gopher : weeds.mgh.harvard.edu/ Gopher : probe.nalusda.gov:7004/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://weeds.mgh.harvard.edu/ WWW : http://probe.nalusda.gov:8300/plant/ Database : AboutDB Curator : Staffan Bergh, staffan@biochem.kth.se Subject : ACEDB itself (meta-meta-metadata) ACEDB_version: 3.0 Last_update : July 1995 WWW : http://www.biochem.kth.se/AboutDB.html Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@mrc-lmb.cam.ac.u Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Last_update : August 1995 Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ DataBase : AceMap Species : Homo sapiens Subject : Physical mapping YAC data for human chromsome X ACEDB_version : 3.0 Curator : Hugues Roest Crollius, hrc@gea.lif.icnet.uk Curator : Mark Ross, humanX@gea.lif.icnet.uk Curator : Richard Mott, rmott@gea.lif.icnet.uk Availability : beta release of the X chromosome data/models via anonymous ftp FTP : ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap Comment: Get the README file in the directory above. Contact : Genome Analysis Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, London WC2A 3PX, UK Last_update : August 1994 Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu Last_update : March 1994 ACeDB_version : 3.0 Subject: Contains extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe yeast); interacting loci via defined Interactions for each locus Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 Last_Update : July 1995 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 1.0 Last_updated : January 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Last_update : August 1995 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Last_update : September 1995 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 Last_update : January 1995 (version 95.1) ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ Database : CSNDB Focus : Cell Signalling Molecules and Interactions Contact : Takako Igarashi, National Insitute of Health Sciences, Division of Chem-Bio Informatics, Setagaya-ku, Tokyo, Japan 158, taka@nihs.go.jp Database : EofD (Encyclopaedia of the Drosophila) Species : Drosophilidae (primarily D. melanogaster) Availability : Macintosh CD-ROM and SunOS executables via anonymous ftp Developer : Suzanna Lewis, suzi@fly2.berkeley.edu Developer : Cyrus Harmon, sly@fly2.berkeley.edu Developer : Edward Welbourne, eddy@gen.cam.ac.uk Collaborator : The FlyBase Consortium, flybase-help@morgan.harvard.edu Collaborator : The Berkeley Drosophila Genome Project, flygenome@maillink.berkeley.edu Gopher : fly.bio.indiana.edu:70+/11/Flybase WWW : http://fly2.berkeley.edu:3512/EofD.html Database : EthnobotDB (orldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Last_update : June 1995 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Last_update : May 1995 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : GrainGenes Species : Wheat, barley, oats, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_1 Data_version : 1.4+ Last_update : September 1995 FTP : probe.nalusda.gov in pub/graingenes Gopher : greengenes.cit.cornell.edu/ Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://wheat.pw.usda.gov/graingenes.html Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr WWW : http://moulon.inra.fr/acedb/igd.html Description : IGD (Integrated Genomic Database) aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : LeishDB Species : Leishmaia major, L. infantum, L. peruviana, L. donovani and others PI : Jennie Blackwell PI : Al Ivens Last_update : September 1995 ACEDB_version : 4.1 Contact : Matin Aslett, ma10025@cus.cam.ac.uk FTP : ftp://parsun1.path.cam.ac.uk WWW : http://parsun1.path.cam.ac.uk/ Curator : Martin Aslett Curator : Howard Cobb Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie-Paule Lefranc Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr Database : MaizeDB Species : Zea mays L. ssp. mays and related species Latest_release : April 1995 Acedb_version : 3.3 Comment : MaizeDB is a periodically extracted ACeDB front end for the Maize Genome Database, MaizeDB, a SYBASE database, implemented using Genera software, developed by Stan Letovsky. Comment : Genera provides (1) up-to-the-minute form internet access to SYBASE databases, both for query (WWW and APT) and data entry (APT only); (2) database design alterations by systems administrators; (3) gopher file extraction. Comment: MaizeDB uses WWW record-to-record hard-links to 16 external databases for (1) annotated sequences: GenBank, dbEST, GenoBase, PIR, SwissProt, Prosite, ENZYME; (2) other species genome information: AAtDB(Arabidopsis), RiceGenes, GrainGenes, SaachDB (yeast), CGSC(E. coli), XLocus, RiceGenes, GrainGenes (3) germplasm: GRIN. Data : Over 100,000 records include: 6513 mapped loci (located to chromosome or better) including 1081 mapped genes and 1937 mapped probed sites (gene candidates); 2448 probes; 2460 map scores; 1551 gel patterns (Probe/Enzyme/Stock); 8777 stocks; 18,100 Variations (alleles, DNA polymorphisms, rearrangements, etc); 596 phenotypes; 317 traits; 715 gene products; 6158 bibliographic references; 2200 researchers with addresses. FTP : probe.nalusda.gov in pub/maizedb Gopher : gopher.agron.missouri.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: corncob WWW : http://www.agron.missouri.edu/top.html WWW : http://probe.nalusda.gov:8300/plant/ WWW Genera information : http://gdbdoc.gdb.org/letovsky/genera/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe, ed@teosinte.agron.missouri.edu Curator : Mary Polacco, maryp@teosinte.agron.missouri.edu Assoc Curator : Pat Byrne, byrne@teosinte.agron.missouri.edu QTL data Assoc Curator : Georgia Davis, gdavis@teosinte.agron.missouri.edu Map data Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic Stock data Assoc Curator : Christiane Fauron, FAURON@GENE1.med.utah.edu Mitochondrion genome Assoc Curator : Carolyn Wetzel, cmwetzel@iastate.edu Chloroplast genome Assoc Curator : Steve Rodermel, S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome Design : Stan Letovsky, letovsky@gdb.org Design : Mary Berlyn, mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock, dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 11 April 1995 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Last_update : July 1995 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : Millet Genes Species : Pennisetum Glaucum (Pearl Millet) ACEDB_version : 4.1 Availablity : Local Curator : Matt Couchman, couchman@bbsrc.ac.uk Curator : Katrien Devos, devos@bbsrc.ac.uk DataBase : Mousedb Species : Musculus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD Last_update : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_vertion : 4.0 Last_update : June 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. Curator : Staffan Bergh, staffan@biochem.kth.se Last_update : July 1995 ACEDB_version : 3.0 Data_version : 3-8 (June 18, 1995) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au Curator : Gail Juvik, gjuvik@nalusda.gov - ACEDB version ACEDB_vertion : 4.0 Last_update : September 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Last_update : June 1995 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 Last_update : September 1995 FTP : ftp.sanger.ac.uk in pub/PomBase Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Last_update : June 1995 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susah McCouch ACEDB_version : 3.0 Last_update : July 1995 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 2.0, MacAce 2.0b4 Last_update : September 1995 Data_version : 2.4.12 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB Gopher : genome-gopher.stanford.edu WWW : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Rita Schmidt, bleb@genome.stanford.edu Curator : Barbara Dunn, bdunn@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Programmer : Karen Davis, karen@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu PI : Steve Tanksley Release : ACEDB 3.0 Last_update : May 1995 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 Last_update : September 1995 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker Curator : David Grant, dgrant@mendel.agron.iastate.edu Curator : Marica Imsamde, mimsande@mendel.agron.iastate.edu Contact : Dave Schrader, schrader@mendel.agron.iastate.edu ACEDB-Version : 3.7 Last_update : August 1995 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://mendel.agron.iastate.edu:8000/main.html Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server Last_update : October 1994 FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Database : Toxo Species : Toxoplasma gondii PI : Jennie Blackwell PI : Jim Ajioka Last_update : September 1995 ACEDB_version : 4.1 Contact : Martin Aslett, ma10025@cus.cam.ac.uk FTP : parsun1.path.cam.ac.uk WWW : http://parsun1.path.cam.ac.uk/ Curator : Martin Aslett Curator : Howard Cobb Database : TreeGenes Species : Forest trees ACEDB_version : 3.0 Last_update : July 1995 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ Database : Trypbase Species : Trypanosoma brucei PI : Sara Malville Contact : sm160@mole.bio.cam.ac.uk Comment : Under development, feedback welcome. ACEDB_version : 4.0 Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Last_update : April 1994 FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Database : 22ace Species : Homo sapiens Subject : Physical map of human chromosome 22, genomic sequencing and more ACEDB_version : 4.1 Curator : Ian Dunham, id1@sanger.ac.uk Curator : Gareth Maslen, glm@sanger.ac.uk PI : Ian Dunham Last_update : August 1995 FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu Last_update : September 1993 ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions Q5: What documentation exists for ACEDB? ++++++++++++++++++++++++++++++++++++++++ A5: +++ From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000 . Primary documents from the developers are: o acedb -- A C. elegans Database: I. Users' Guide. o acedb -- A C. elegans Database: II. Installation Guide. o acedb -- A C. elegans Database: III. Configuration Guide. o Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z and ftp://weeds.mgh.harvard.edu/acedb_doc . The files are in TeX (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/index.html A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html . Japanese language guides: _Japanese ACEDB Guide Ver.1.2._ _ACEDB ver.2 for NEC engineering workstation EWS4800 series_ are available in PostScript via anonymous ftp at ftp.nec.co.jp as /pub/packages/acedb/acemanjp.1_2.ps.Z . There is a Japanese language ACEDB FAQ available at http://www.cbi.or.jp/~sano/acemanjp12/index.html SampleDB, by Dave Matthews, is an ACEDB database constructed to demonstrate features of ACEDB, especially map and sequence displays. Anonymous ftp to probe.nalusda.gov:pub/acedocs/sampledb You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angistute.ps and angistute.hqx available by anonymous ftp at ncbi.hih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). URL : http://genome-www.stanford.edu/docs/aatdb_man.html . A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. [text is available through ftp or gopher from weeds.mgh.harvard.edu] URL : http://probe.nalusda.gov:8000/acedocs/overview.html . Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Return to List of Questions Q6: What other resources are available for ACEDB? +++++++++++++++++++++++++++++++++++++++++++++++++ A6: +++ Perl and WWW tools ++++++++++++++++++ > The AGIS server at the National Agricultural Library provides a tool set for integrating version 4 of ACEDB with perl and the World-Wide Web. The archive is ftp://probe.nalusda.gov/pub/tools/acelib.tar.gz For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/TextConvert . The Developers' Archive +++++++++++++++++++++++ Mike Cherry maintains an archive of tools that may be useful in curating ACEDB databases. It can be reached by anonymous ftp at URL ftp://weeds.mgh.harvard.edu/acedb_dev/ or via gopher at gopher://genome-gopher.stanford.edu:70/11/ftp If you have a contribution place it in ftp://weeds.mgh.harvard.edu/acedb_dev/incoming/ and send a message to Mike (cherry@genome.stanford.edu). The Biosci conference bionet.software.acedb +++++++++++++++++++++++++++++++++++++++++++ There is a USENET/Biosci conference titled bionet.software.acedb created expressly for discussion of ACEDB. The best way to interact with the Biosci conferences is via a newsreader like rn, trn, tin or a WWW browser. Consult your system administrator for more information. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. o All of the articles in biosci.software.acedb are archived by Biosci at gopher://gopher.bio.net/1/ACEDB o Mike Cherry makes it possible to search past articles in biosci.software.acedb using WAIS at gopher://genome-gopher.stanford.edu:80/77/.index/acedb-biosci and at URL http://genome-www.stanford.edu/biosci_acedb.html . If your WWW browser is configured properly you may be able to read the newsgroup at news:biosci.software.acedb . And more ++++++++ The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: o http://moulon.inra.fr/acedb/acedb.html for C. elegans data o http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data o http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html A how-to manual on the Moulon server is available at http://keck.tamu.edu/cgi/staff/ace-mosaic-howto.html The Genome Computing Group, Lawrence Berkeley Laboratory, has an anonymous ftp service at machine genome.lbl.gov which contains: o flydb - LBL's Drosophila Acedb-style database o 21bdb - LBL's Human Chromosome 21 Acedb-style database o querdb - LBL's query-language extensions to Acedb o metadata - LBL's compendium of Acedb database schema variants o macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version o There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to dataabases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: o 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). o 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier Jean Thierry-Mieg et al), and the Interated Genome Database project in Heidelburg (Otto Ritter, Detlef Wolf et al). Return to List of Questions Q7: How should ACEDB be cited? ++++++++++++++++++++++++++++++ A7: +++ From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions Q8: Is ACEDB object-oriented? +++++++++++++++++++++++++++++ A8: +++ From the ACEDB User's Guide: A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions Q9: How can I get on/off the ACEDB announcements mailing list? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A9: +++ To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q6 for details] is on the mailing list. Return to List of Questions Q10: When and where is the Next ACEDB Workshop? +++++++++++++++++++++++++++++++++++++++++++++++ A10: ++++ The 1996 Workshop is not yet scheduled. If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, there are online collections: o by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; o by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; o and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions Q11:Who prepared this document & where is the current version? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ A11: ++++ This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu as pub/usenet/news.answers/acedb-faq . If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html and http://s27w007.pswfs.gov/Homepage/acedbfaq.html There is a Japanese language FAQ available at http://www.cbi.or.jp/~sano/acemanjp12/index.html Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov Major contributions in getting this FAQ off the ground were made by Mike Cherry, John McCarthy, and Doug 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 Oct 24 22:00:00 1995 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: four Tablemaker questions/comments Date: 25 Oct 1995 14:06:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 58 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510252104.AA22344@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net 1. Is there any way to recover all the values of a tag that is defined as REPEAT in the model? E.g. all the ?Text's from ?Presence Present ?Text REPEAT // e.g. 14.5 6.6 4.4 Absent ?Text REPEAT Neither From nor Right_of in the table definition seems to work. All I get is the first value of each REPEAT series. 2. It is possible to sort on multiple columns using the "Switch" button. If column 3, for example, is switched into the first position, the whole table is sorted on the column 3 values, thus: Position(3) Map(2) Locus(1) 0 Hordeum-NABGMP2-1H aHor2 0 Hordeum-NABGMP2-2H MWG844 0 Hordeum-NABGMP2-4H WG622 0.7 Hordeum-NABGMP2-7H dRpg1 0.8 Hordeum-NABGMP2-7H Plc 1.5 Hordeum-NABGMP2-6H PSR167 2.1 Hordeum-NABGMP2-7H ABG077 2.3 Hordeum-NABGMP2-2H ABG058 ... Then by switching column 2 into the first position, the values of column 3 remain sorted within each value of column 2: Map(2) Position(3) Locus(1) Hordeum-NABGMP2-1H 0 aHor2 Hordeum-NABGMP2-1H 11.1 Act8A Hordeum-NABGMP2-1H 81.1 MWG943 Hordeum-NABGMP2-1H 93.3 His4A Hordeum-NABGMP2-1H 105.4 Dor3 Hordeum-NABGMP2-1H 119.6 AtpB Hordeum-NABGMP2-1H 137.9 ABC261 Hordeum-NABGMP2-1H 147 ABG710B Hordeum-NABGMP2-1H 159.3 MWG912 Hordeum-NABGMP2-2H 0 MWG844 Hordeum-NABGMP2-2H 2.3 ABG058 Hordeum-NABGMP2-2H 5.4 WG516 Hordeum-NABGMP2-2H 19.9 MWG682 ... This "Switch" interface for specifying the column to sort on has been made more intuitive in ace4_1. There is now a field "Sort column" at the top of the table definition window. However the new interface doesn't work for sorting on multiple columns: setting the Sort column to 3, then to 2 leaves column 3 scrambled again. (The "Switch" routine still works.) 3. In ace3-0 it was possible to ascii dump a table with the columns aligned with Space characters, as in the examples above. This was a really nice feature. I guess I should have said so while we had it, rather than waiting to complain now that it seems to have disappeared. 4. There are a lot of really nice features in the Tablemaker. From owner-acedb@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Germany.EU.net!news.dfn.de!news.ruhr-uni-bochum.de!news.rhrz.uni-bonn.de!hy From: schmidt@nuklear.meb.unibonn.de (Herbert Schmidt) Newsgroups: bionet.software.acedb Subject: test Date: 25 Oct 1995 16:19:05 GMT Organization: Nuklear Medizin Lines: 4 Message-ID: <46lo1p$n7p@news.rhrz.uni-bonn.de> NNTP-Posting-Host: hy.meb.uni-bonn.de Keywords: nothing To: group X-Newsreader: News Xpress Version 1.0 Beta #3 only a test -+-+-+-+-+-+- ----hy----hy----hy----hy---- From owner-acedb@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: about table maker Date: 25 Oct 1995 22:59:50 -0000 Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <46mfh6$582@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr I was told today that tace does not dump tables in exact alphabetic order they are only listed correctly by chunks it is easy to fix and will be available in next code i think you can still ascii dump aligned tables by asking for tab otherwise i ll fix that the "Switch" interface was passed into the command system by Suzy, merci, but seems incomplete, i ll try top fix that too. the condition on Text, which does not work in 4.1, will also be restored sorry for all these bugs From owner-acedb@net.bio.net Thu Oct 26 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!usc!sdd.hp.com!col.hp.com!csn!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!yuma!klab4.agsci.colostate.edu!user From: martinf@lamar.colostate.edu (Martin L. Ferguson) Newsgroups: bionet.software.acedb Subject: Help: unable to leave 'Int' fields blank in .ace files Date: Thu, 26 Oct 1995 16:54:37 -0600 Organization: Colorado State University Lines: 26 Message-ID: NNTP-Posting-Host: klab4.agsci.colostate.edu Greetings ACEDB users, I am unable to leave 'Int' fields blank in a .ace file being read into v4.1. My model looks like this: ?SomeClass MyTag UNIQUE Int UNIQUE Int Text In version 3, I could read an .ace file that looked like this: SomeClass : "name" MyTag "" "" "I only want to store text" But in version 4, I get the following error: internal system error : parse error near line 27 in name : not an integer after MyTag Is there a way to leave an Int field blank? Thanks. -- Martin Ferguson martinf@lamar.colostate.edu Dept. of Entomology 970-491-7989 CO State U. Ft. Collins, CO 80523 From owner-acedb@net.bio.net Thu Oct 26 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Norway.EU.net!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: null int Date: 27 Oct 1995 17:15:55 -0000 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <46r44b$f8d@mserv1.dl.ac.uk> Original-To: net@admcnrs.cnrs-mop.fr Sorry, it was a bug of 3.1, you cannot have an empty field in a line use 0 0 or something like that or change the model note that if you were to say: SomeClass : "name" MyTag "" "" "I only want to store text" and later SomeClass : "name" MyTag 1 2 then "I only want to store text" would be lost anyway so the model is ackward From owner-acedb@net.bio.net Sat Oct 28 22:00:00 1995 Path: biosci!mrc-lmb.cam.ac.uk!rd From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Acedb data updates 4-9, 4-10, 4-11 for C.elegans Date: 29 Oct 1995 11:00:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 97 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510291854.AA03587@cele.mrc-lmb.cam.ac.uk> NNTP-Posting-Host: net.bio.net This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. ACEDB data updates 4-9, 4-10 and 4-11 for C. elegans ==================================================== It is nearly two months since update 4-8. We are making three new updates available at once to keep them a reasonable size. These should be used in conjunction with version 4_1 of the ACEDB program. The total database size after adding updates 4-1 to 4-11 is approximately 240 Mbytes. The additions since 4-8 are: - more genomic sequence data (there are now 707 cosmids totalling 21,762,318 bases). - over 12000 more cDNA EST sequences from Yuji Kohara, more than doubling the number available. Thank you Yuji and colleagues. - Worm Breeders Gazette issue 14.1, plus some old missing abstracts - coordinate data for an embryonic lineage from Harald Hutter (most cells up to 270mins, some up to 430 mins). We plan to link images to this data directly in a future version of acedb. In the mean time, we propose making TIFF images available packed up into timepoint-based ftp archives (700 images at 28 timepoints; more details in a future email). - the new CGC subscribers list - various other new data, including more genetic and expression data. - a physical map update (October 13). - a number of errors and problems have been fixed -- in particular a whole set of Df/Dup data were behaving incorrectly. Macintosh version ================= There will be a macace.4-11 shortly. There will be a further broadcast email message announcing this. Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb ftp.sanger.ac.uk in England, in pub/acedb lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password: your user id or email address cd repository/acedb # change to relevant directoy binary # IMPORTANT dir # display files in this directory get README get NOTES get INSTALL cd ace4 # change to ace4 directory get bin.sunos.4_1.tar.Z # get program cd ../celegans # change to worm data directory mget update* # get all update files quit -------------------------------- Get any update.4-n.tar.Z that you do not have already and read the file NOTES before proceeding further. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb"), click "Yes" to accept initialising the database if starting from scratch, then choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button. If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Comments about the data should be sent to the data curator, Sylvia Martinelli (sylvia@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- From owner-acedb@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!lamarck.sura.net!sprout.nalusda.gov!usenet From: JD Barnett Newsgroups: bionet.software.acedb Subject: wwwace now available Date: 30 Oct 1995 16:09:03 GMT Organization: National Agricultural Library Lines: 20 Message-ID: <472tav$6f@sprout.nalusda.gov> NNTP-Posting-Host: phage.gig.usda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4m) To: genome@locus.nalusda.gov X-URL: news:bionet.software.acedb wwwace provides a world wide web interface to ACeDB's graphical displays. This package includes modifications to the ACeDB source code to build wwwace, and the CGI scripts in perl to be run from the web. It is designed for ACeDB version 4, to be run along with the text-based WWW interface to ACeDB developed at NAL. The interface acts like xace with only the left button available. Only single clicks can be passed back from a clickable image in an HTML document. Thus, any right button actions (e.g., pop-up menus) or any drag operations are not supported. (The only exception is the modification to the gmap display to allow scrolling.) In wwwace as in xace, two clicks are required to follow a link to another object on the display. wwwace can be downloaded at: ftp://probe.nalusda.gov/pub/tools/wwwace.tar.gz See http://probe.nalusda.gov:8000/acedocs/wwwace.html for more details, and send questions or comments to gig@gig.usda.gov -JD Barnett From owner-acedb@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!lyra.csx.cam.ac.uk!news From: pd@mole.bio.cam.ac.uk (Phil Davey) Newsgroups: bionet.software.acedb Subject: Changing from SIGMA to ACEDB? Date: 30 Oct 1995 17:50:14 GMT Organization: University of Cambridge, England Lines: 9 Message-ID: <47338m$kup@lyra.csx.cam.ac.uk> Reply-To: pd@mole.bio.cam.ac.uk NNTP-Posting-Host: nab.path.cam.ac.uk I have a database in SIGMA format, and I was wondering if anyone knows how to change this format into one that either ACEDB or SAM can use. Thanks very much for any help, Phil [E-mail pd@mole.bio.cam.ac.uk] From owner-acedb@net.bio.net Mon Oct 30 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!news.sesqui.net!oitnews.harvard.edu!purdue!yuma!klab4.agsci.colostate.edu!user From: martinf@lamar.colostate.edu (Martin L. Ferguson) Newsgroups: bionet.software.acedb Subject: Need help with query syntax. Date: Mon, 30 Oct 1995 15:51:34 -0600 Organization: Colorado State University Lines: 13 Message-ID: NNTP-Posting-Host: klab4.agsci.colostate.edu Hi all, Is there a query which can be used with tace or aceserver/client which will produce a listing of thoses classes which have greater than X number of objects? Thanks, -- Martin Ferguson martinf@lamar.colostate.edu Dept. of Entomology 970-491-7989 CO State U. Ft. Collins, CO 80523 From owner-acedb@net.bio.net Tue Oct 31 22:00:00 1995 Path: biosci!biosci!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.announce,bionet.microbiology,bionet.software.acedb,sci.med Subject: MycDB 4-9 Followup-To: bionet.microbiology Date: 1 Nov 1995 13:23:19 -0800 Organization: Biochemistry, KTH, Stockholm Lines: 112 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <478dal$gal@sibirien.physchem.kth.se> NNTP-Posting-Host: net.bio.net Keywords: MycDB, mycobacteria, ACEDB Xref: biosci bionet.announce:2590 bionet.microbiology:3796 bionet.software.acedb:765 sci.med:99031 MycDB 4-9 Stockholm & Paris November 1, 1995 The ninth release of the Mycobacterium database, MycDB, is now available. MycDB is funded by the WHO and the Fondation Raoul Follereau and is maintained jointly by the Unite de Genetique Moleculaire Bacterienne at the Institut Pasteur in Paris, France and the Department of Biochemistry at The Royal Institute of Technology in Stockholm, Sweden. MycDB is available free of charge via Internet network transfer. A complete description of the procedure to retrieve and install the software and database is available through the Internet. MycDB is also available through the WorldWideWeb servers at the Royal Institute of Technology (URL: http://www.biochem.kth.se/MycDB.html) and (through the good offices of the Genome Informatics Group at the National Agricultural Library) on the Agricultural Genome Information Server, AGIS, in Beltsville, Maryland, USA (WorldWideWeb - URL: http://probe.nalusda.gov:8300/other/index.html or gopher - URL: gopher://probe.nalusda.gov:7000/11/genome.databases/mycdb/). Be aware that it may take some time for the update to reach NAL. MycDB uses the excellent database software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg (CNRS, France). The ACEDB software allows the user to browse information by simply pointing and clicking with the workstation mouse. A variety of powerful query methods are also available. However, our experience is that most users choose the mouse interface to find the information they are interested in. As far as possible all information is connected to other information in the database. The database software presents the information in separate windows that allow many parts of the database to be viewed at one time. There are also many paths to any piece of information, allowing the user to easily navigate the connections between the various types of information. New in release 4-9: * We are now using version 4.1 of of the database manager, ACEDB. Versions exist for Unix/X11 and Macintosh. A complete package with the Macintosh application and a preloaded database is available. Update files for version 3.0 of the database manager are also available (this support will be discontinued in the near future). Ace 4.1 has the following new features: o Less diskspace needed for the database (size is roughly halved - MycDB 4-9 takes about 25MB of diskspace, compared to 40MB for MycDB 3-9). o Faster display of large KeySets, due to presorting of keys. o Blixem, the alignment display, is now fully integrated in AceDB. MycDB 4-9 contains blastn alignments for all sequences in MycDB against MycDB itself. With the correct external script, it will also fetch sequences not present in the database from an external source. A script for doing this is included, in the wscripts directory. At present, MycDb only contains blastp data for a few sequences. o The Map display is now customizable to a great degree, both regarding the look and what objects to display. o A new, WorldWideWeb-based, help system. This also requires an external script. The old help system is still there, as a backup. * New and edited sequences from EMBL/GenBank/DDBJ, current as of Oct 30, 1995. The number of Sequence objects is now 3234, of which 2891 are nucleotide sequences, and 343 Protein sequences. 591 of the nucleotide sequences contain DNA (the others are subsequences in some form or Peptide sequences). The total amount of sequence is now 2,238,856 nt, an increase of more than 43%. Most of this is due to the inclusion of a number of new cosmid sequences from M. leprae. Blastn searches have been performed on all the sequences in the database, against the complete database itself. This data is included. The data can be visualized with the Blixem tool. * The number of literature citations have increased with 263. Included are citations from MedLine, current up to Oct 4, 1995. The references for sequences have been cleaned up to remove redundancies. * The Locus class now includes some information on the function of the products. In the future this information will move to a new Protein class (for those products that are proteins). * The webserver has a new sequence search facility, where you can make a blast search on all the sequences in MycDB or on strain-specific subsets for M.leprae, M.tuberculosis complex or M.smegmatis. The fasta files used for these searches are also available from the ftp site. For information on earlier releases, see the file MycDB.3-8.Release.txt. If you have any questions, problems or comments please contact us, via e-mail, fax, mail or telephone. If you are impatient and are already familiar with internet/ftp, all relevant information can be found at * the WWW server at the Department of Biochemistry, KTH: http://www.biochem.kth.se/MycDB.html * the ftp server at the Department of Biochemistry, KTH: ftp.biochem.kth.se (130.237.52.64) in pub/MycDB * the ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in pub/MycDB * or the mirror site at the Weizmann Institute in Israel (thanks Jaime!): bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb The file MycDB.Retrieval.txt describes in more detail the database system requirements, network retrieval procedures for obtaining the database and methods of obtaining future updates. For more information contact Staffan Bergh or Stewart Cole. Staffan Bergh Biochemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden Email: staffan@biochem.kth.se Fax: (46 8) 24 54 52 Voice: (46 8) 790 9230 Stewart Cole Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris Cedex 15, France Email: stcole@pasteur.fr Fax: (33 1) 45.68.85.93 Voice: (33 1) 45.68.84.46 From owner-acedb@net.bio.net Tue Oct 31 22:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: IMPORTANT: BIOSCI miniFAQ Date: 1 Nov 1995 02:03:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511011000.CAA15134@net.bio.net> This is a new "miniFAQ" designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. Contents: -------- 1) What to do about "spams," i.e., junk mail, ads, etc. 2) Examples of subscribing and unsubscribing to the mailing lists. 3) How to access BIOSCI/bionet newsgroup archives. 4) The BIOSCI user address and research interest directory. 1) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups) and mailing lists. The same postings are distributed on both media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the newsgroups from about 95% of the spams that are being sent to date. This means that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings. Unfortunately there are easy ways for determined spammers to override the moderation mechanism. We are working on new systems to provide access to our newsgroups over the WWW. These should be available soon, probably November 1995, and will allow you to use your Web browser to look at the news postings. While this will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. 2) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 3) How to access BIOSCI/bionet newsgroup archives. -------------------------------------------------- Back postings of all BIOSCI/bionet newsgroups can be found on the World Wide Web at URL http://www.bio.net/. There are several searchable newsgroup indices at this site. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net