Usenet 1994 October/usenetsourcesnewsgroupsinfomagicoctober1994disk1.iso/answers/acedb-faq

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From: [e-mail] (ACEDB FAQ Pseudouser)
Newsgroups: bionet.software.acedb,news.answers
Subject: ACEDB Genome Database Software FAQ
Followup-To: bionet.software.acedb
Date: 14 Dec 1993 21:30:18 GMT
Organization: Dendrome, A genome database for forest trees
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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.
Archive-name: acedb-faq
Last-modifed: 12/14/93
Version: 1.6
Xref: senator-bedfellow.mit.edu bionet.software.acedb:96 news.answers:15809

----------------------------------------------------------------------
Common Questions and Answers about ACEDB.

    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.

    There is an HyperText Markup Language (HTML) version of this
    document available on the World Wide Web (WWW). The Universal
    Resource locator (URL) for it is:
        http://probe.nalusda.gov:8000/plant/acedbfaq.html
    [Until I get more familiar with HTML, it may not be as current
     as the plain ASCII FAQ. --bks]

    The latest version of the ACEDB FAQ should be available via
    anonymous ftp at net.bio.net as:
        /pub/BIOSCI/ACEDB/ACEDB.FAQ
    and at rtfm.mit.edu as:
        /pub/usenet/news.answers/bionet.software.acedb/
        bionet.software.acedb.FAQ
    and via electronic mail from [e-mail].

    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: [e-mail]
        --Bradley K. Sherman

----------------------------------------------------------------------
The List of questions in the ACEDB FAQ.  Questions marked with
+ are new, those with ! have substantially changed answers:

Q0:  What is ACEDB?
Q1:  !What is the current version of ACEDB?
Q2:  What hardware/software do I need to run ACEDB?
Q3:  Where can I get ACEDB?
Q4:  What ACEDB databases exist?
Q5:  What written documentation exists for ACEDB?
Q6:  Where can I find further information about ACEDB?
Q7:  How should ACEDB be cited?
Q8:  Is ACEDB object-oriented?
Q9:  What's all this about Gopher/WAIS/Anonymous ftp/WWW ...
Q10: How can I get on the ACEDB announcements mailing list?
Q11: +When and where is the next ACEDB Workshop?
Q411:Who contributed to this document?

----------------------------------------------------------------------
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 [see Q4].

     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 European integrated Genome
     Project.

     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.
         Current display modes are:
             TREE   for text type objects: papers, authors, genes
             etc.
             GMAP   genetic map
             PMAP   physical map (Sulston contig style)
             SEQ    DNA sequence - symbolic, features, sequence
             and translation
             GRID   hybridisation patterns for a probe to a clone
             grid
             BIBLIO bibliography attached to any object display
             modules under development:
             CMAP   whole chromosome physical map plot
             GEL    agarose gel simulation derived from sequence

----------------------------------------------------------------------
Q1:  What is the current version of ACEDB?

A1:  1-10.  It was released Summer 1993.

     There is apparently an upcoming bifurcation in the code.
     Durbin will be releasing a 2-x version concentrating on
     the Nematode project.  Thierry-Mieg will be releasing a
     3-x version with other features.

     To be kept informed of new releases see Q10.

     [This question refers to the software not the C. elegans data.]

----------------------------------------------------------------------
Q2:  What hardware/software do I need to run ACEDB?

A2:  ACEDB currently runs on the following Unix systems, under X11:
     Unix:
         Any machine running SunOS 4.x
             e.g. Sun SPARCstation 1, 1+, 2, IPC, IPX.
         SPARCstation 10 under Solaris [Probably all Solaris, then --bks]
         DEC  DECstation3100, 5100 etc.
         DEC  Alpha/OSF-1
         Silicon Graphics Iris series
         PC 386/486 with Linux (free Unix)
        There exist, or have existed, ports onto Alliant, Hewlett-
        Packard, IBM R6000, NeXT, Convex.   You may have to contact
        the developer responsible for the port to make these real.
    MSDOS/Windows/NT:
        A port to NT is rumored to be in the works.
    Macintosh:
        A port to the Macintosh may become available by the end of 1993.

    For cost savings, a combination of a high-end Intel platform
    with Linux appears very attractive.

   [This section should be expanded to have a more thorough
    discussion of X11 interactions.  --bks]

----------------------------------------------------------------------
Q3:  Where can I get ACEDB?

A3:  All the files are available in the following public access
     accounts (anonymous ftp sites) accessible via Internet:
          lirmm.lirmm.fr         (193.49.104.10)  genome/acedb
          cele.mrc-lmb.cam.ac.uk (131.11.84.1)    pub/acedb
          ncbi.nlm.nih.gov       (130.14.20.1)    repository/acedb

    A typical session would be:
        ftp ncbi.nlm.nih.gov
        login: anonymous
        password: your email address
        cd repository/acedb
        binary
        ls
        get README
        get NOTES
        get INSTALL
        get bin.sparc.1_4.tar.Z
        quit

----------------------------------------------------------------------
Q4:  What ACEDB databases exist?

A4:  [In alphabetic order by Database name --bks]

     Database : AAnDB
     Species : Aspergillus nidulans
     PI : Leland Ellis
     Last_update : Sept. 1993

     Database : AAtDB
     Species : Arabidopsis thaliana
     Availability :
     Curator : John Morris
     Current version: 1-5
     Contact : [e-mail]
     Last_update : Sept. 1993

     Database : ACeDB
     Species : Caenorhabditis elegans
     Availability :
     Current version: 1-21
     Curator : Jean Thierry-Mieg
     Curator : Richard Durbin
     Contact : [e-mail]
     Contact : [e-mail]
     Last_update : Sept. 1993

     Database : ChlamyDB
     Species : Chlamydomonas
     PI : Elizabeth Harris
     Contact : [e-mail]
     Availability : Still under construction
     Last_update : 30 Sept. 1993

     Database : EcoDB
     Species : E. coli
     PI : Staffan Bergh
     Contact : [e-mail]
     Availability : Still under construction
     Last_update : 11 Oct. 1993

     Database : Flydb
     Species : Drosophila melanogaster
     Availability : by request only, via ftp
     Curator : Suzanna E. Lewis
     Contact : [e-mail]
     Focus : STS content mapping project summary
     PI : Gerald Rubin
     PI : Mike Palazzolo
     PI : Dan Hartl
     PI : Alan Spradling
     Last_update : Sept. 1993

     Database : GrainGenes
     Species : Wheat, barley, oats, relatives
     Availability : Gopher greengenes.cit.cornell.edu port 70
     Availability : ACEDB version by ftp, on request from the curators
     Curator : David E. Matthews
     PI : Olin D. Anderson
     Contact : [e-mail]
     Contact : [e-mail]
     Last_update : Sept. 1993

     Database : Mace
     Species : Zea mays L. ssp. mays
     Focus : Maize genome
     Comment : Mace is the front end for maizedb, a relational
               (SYBASE) database. It is updated from maizedb by
               software written by Stan Letovsky.  Maizedb is
               updated daily and will soon be accessible by
               public login.
     Curator : Ed Coe
     Curator : Pat Byrne
     Curator : Georgia Davis
     Curator : Mary Polacco
     Off-Site Curator : Marty Sachs
     Off-Site Curator : Christiane Fauron
     Off-Site Curator : Carolyn Wetzel
     Off-Site Curator : Steve Rodermel
     Off-Site Curator/Designer : Stan Letovsky
     Off-Site Curator/Designer : Mary Berlyn
     Systems Manager : Denis Hancock
     PI : Ed Coe
     Contact : [e-mail]
     Last_update: 5 October 1993

     Database : MycDB
     Species : Mycobacterium
     PI : Staffan Bergh
     PI : Thierry Garnier
     Contact : [e-mail]
     Last_update : Sept. 1993

     Database : RiceGenes
     Species : Rice (O. sative)
     Availability : under development, login at own risk
     Curator : Edie Paul
     Contact : [e-mail]
     Last_update : Sept. 1993

     Database : SolGenes
     Coverage: Solanaceae - tomato, potato, pepper (eventually)
     Availability : Beta ACEDB via login or tar file
     Curator : Edie Paul
     Contact : [e-mail]
     Last_update : Sept. 1993

     Database : SoyBase
     Species : Soybeans
     Curator :  Lisa Lorenzen
     PI : Randy Shoemaker
     Contact : [e-mail]
     Last_update : Sept. 1993

     Database : TreeGenes
     Species : Forest trees, Pinus taeda
     Availability : contact curator
     Curator : Bradley K. Sherman
     PI : David B. Neale
     Contact : [e-mail]
     Contact : [e-mail]
     Contact : [e-mail]
     Last_update : Sept. 1993

     Database : 21Bdb
     Species : Homo sapiens
     Availability : by request, via ftp, gopher
     Curator : Donn F. Davy
     Contact : [e-mail]
     Contact : [e-mail]
     Focus : STS content mapping & sequencing of Human Chromosome 21
     PI : Jasper Rine
     PI : Michael Palazzolo
     PI : Chris Martin
     PI : Jan-Fang Cheng
     Last_update : Sept. 1993

     Database : VoxPop
     Species : Populus spp.
     Availability : contact curator
     Curator : Carl G. Riches
     PI : Reinhard F. Stettler
     Contact : [e-mail]
     Contact : [e-mail]
     Last_update : Sept. 1993

     Database : ?
     Species : Bovine
     PI : Leland Ellis
     Last_update : Sept. 1993

     Database : ?
     Species : Sorghum
     PI : Leland Ellis
     Last_update : Sept. 1993

     Database : ?
     PI : Scott Chasalow
     Species : Potato
     Contact : Scottish Crop Institute, Dundee
     Last_update : Sept. 1993

     Database : ?
     PI : George Murphy
     PI : David Flanders
     Species : Arabidopsis thaliana
     Contact : John Innes Center, Norwich, England
     Last_update : Sept. 1993

     Database : ?
     Species : Homo sapiens
     Focus : Physical mapping of human chromosomes 22 and X
     Curator : Ian Dunham
     Contact : [e-mail] [e-mail]
     PI : Ian Dunham
     PI : David Bentley
     Last_update : 28 Sep 1993

     [Curators:  Please submit an entire paragraph in
      this format for inclusion or update. --bks]


----------------------------------------------------------------------
Q5:  What written documentation exists for ACEDB?

A5:  The primary documents are included in the Software
     distribution in the wdoc subdirectory:
         acedb -- A C. elegans Database: I. Users' Guide.
         acedb -- A C. elegans Database: II. Installation Guide.
         acedb -- A C. elegans Database: III. Configuration Guide.
         Syntactic Definitions for the ACEDB Data Base Manager
             --Jean Thierry-Mieg and Richard Durbin (1991-)
     You will find other interesting documents in the wdoc subdirectory.

     By anonymous ftp from ncbi.nlm.nih.gov (130.14.20.1)
     in repository/acedb:
        doc.1_9.tar.Z

     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).

     A description of ACEDB:
     Cherry, J.M. and Cartinhour, S.W. (1993) ACEDB, A tool for
     biological information. in Automated DNA Sequencing and
     Analysis, edited by M.  Adams, C. Fields, and C. Venter.
     Academic Press (in press).  [text is available through
     ftp or gopher from weeds.mgh.harvard.edu]

     Another description of ACEDB for physical mapping projects:
     Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1993)
     Physical mapping projects and ACEDB, in Guide to Human
     Genome Computing. Ed.  Bishop, M.J.  (Academic Press)
     (review, in press).  [text is available through ftp or
     gopher from weeds.mgh.harvard.edu]

----------------------------------------------------------------------
Q6:  Where can I find further information about ACEDB?

A6:  From Jean Thierry-Mieg:
         I am proposing to organize the 1994 acedb workshop
         Monday, June 6, to Saturday, June 18, in Cargese,
         Corsica.  This place is equipped and used for summer
         school from may to october every year, this is the
         only slot yet available.

         The cost is around 3000F per person including lunch
         & lodging. Dinner is taken at the local village
         restaurant, or you can cook for yourself. It is
         possible to camp on site for free.  The place is
         beautiful, nested on a private beach, with many
         trees around. And there is plenty of work space.
         I can find some funding to cover part of the
         local costs but certainly not  pay for travels.

         The return ticket to Paris is around 1500 FF so
         3000 + 1500 = 4500 FF around 900 US $.

         This can work if at least 40 people would come
         ideal is between 50 to 80.  This may be too large
         for us.

         Could you please let me know ASAP if you are
         interested. I do not need a full commitment, but I
         have to evaluate the number of participants roughly.

         I hope 2 weeks would:
              a) let us enjoy a very pleasant place
              b) give us time for actual programming
                 to take place on many problems
         There would be, I hope, plenty of cpu around.
             --Jean Thierry-Mieg, [e-mail]

     There is a Usenet/Biosci conference titled bionet.software.acedb.
     If you do not have access to the Biosci conferences via a
     newsreader (e.g. rn, trn) you can participate in the conference
     by electronic mail.  To subscribe to the e-mail version of the
     conference send email to [e-mail] (UK, European
     readers use [e-mail] 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 [e-mail] the mail will be distributed to all
     subscribers and to the electronic conference.

     Mike Cherry has set up an ACEDB Developer's archive.  For
     anonymous ftp use the hostname weeds.mgh.harvard.edu and look in
     the acedb_dev directory. If you wish to contribute you can put
     files in the incoming directory.  Send a message to Mike
     ([e-mail]) that you have put something in that
     directory then Mike will move it out for general access.
     For gopher you can connect to weeds.mgh.harvard.edu
     (132.183.190.21) and ...
        -->  N.  FTP Archives for Molecular Biology/
     then
        -->  M.  ACEDB Developer's archive/
     [N and M are integers which are subject to change.]

     The bionet.software. acedb.conference is archived and can be
     searched using WAIS.  Here is a Gopher-style link to the WAIS
     archive. (This is also courtesy of Mike Cherry.):
          #
          Type=7
          Name=ACEDB BioSci Electronic Conference
          Path=7/.index/acedb-biosci
          Host=genome-gopher.stanford.edu
          Port=70

     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 using an WWW server (really http) with the
     Universal Resource Locator (URL) http://locus.nalusda.gov.
     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. [This section will be
     expanded in the next version.  We hope to make this
     document available as hypertext on the NAL server --bks]

     Other URL's that readers with mosaic clients might want to
     examine are:
        http://moulon.inra.fr/acedb/acedb.html for C. elegans data
        http://moulon.inra.fr/acedb/mycdb.html for Mycobacterium data
     For information on how these were created see
        http://moulon.inra.fr/acedb_conf_eng.html"
        http://moulon.inra.fr/acedb_conf.html (en francais)

     The Genome Computing Group, Lawrence Berkeley Laboratory
     has an anonymous ftp service at machine genome.lbl.gov
     (131.243.224.80) which contains:
          flydb - LBL's Drosophila Acedb-style database
          21bdb - LBL's Human Chromosome 21 Acedb-style database
          querdb - LBL's query-language extensions to Acedb
          metadata - LBL's compendium of Acedb database schema variants
          macace-aatdb-demo.hqx  -  pre-release Acedb MacIntosh version
          There is also a repository of contributed software for
          data conversions and the like.

     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 [e-mail]). 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).

----------------------------------------------------------------------
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 by Anonymous FTP from ...
           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.

----------------------------------------------------------------------
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.

----------------------------------------------------------------------
Q9:  What's all this about Gopher/WAIS/Anonymous ftp/WWW ...

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.

----------------------------------------------------------------------
Q10: How can I get on the ACEDB announcements mailing list?

A10: To get on or off the mailing list send mail to
     [e-mail] or [e-mail].
     New releases of the software are announced to
     this list.

----------------------------------------------------------------------
Q11: When and where is the Next ACEDB Workshop?

Q11: From Jean Thierry-Mieg:
         I am proposing to organize the 1994 acedb workshop
         Monday, June 6, to Saturday, June 18, in Cargese,
         Corsica.  This place is equipped and used for summer
         school from may to october every year, this is the
         only slot yet available.

         The cost is around 3000F per person including lunch
         & lodging. Dinner is taken at the local village
         restaurant, or you can cook for yourself. It is
         possible to camp on site for free.  The place is
         beautiful, nested on a private beach, with many
         trees around. And there is plenty of work space.
         I can find some funding to cover part of the
         local costs but certainly not  pay for travels.

         The return ticket to Paris is around 1500 FF so
         3000 + 1500 = 4500 FF around 900 US $.

         This can work if at least 40 people would come
         ideal is between 50 to 80.  This may be too large
         for us.

         Could you please let me know ASAP if you are
         interested. I do not need a full commitment, but I
         have to evaluate the number of participants roughly.

         I hope 2 weeks would:
              a) let us enjoy a very pleasant place
              b) give us time for actual programming
                 to take place on many problems
         There would be, I hope, plenty of cpu around.
             --Jean Thierry-Mieg, [e-mail]

----------------------------------------------------------------------
Q411:Who contributed to this document?
     [Note to international readers: 411 is the phone number for
     information in the USA. --bks]

A411: Major contributions in getting this FAQ off the ground
      were made by John McCarthy and Mike Cherry.  Other
      contributors include:
        Lisa Lorenzen
        David Matthews
        Edie Paul
        Donn Davy
        Eric De Mund
        Sam Cartinhour

      To add or modify information in this document, please
      send mail to: [e-mail]

      Bradley K. Sherman
      Dendrome Project
      Institute of Forest Genetics
      P.O. Box 245, Berkeley, CA, 94701
      Phone: [phone] Fax: [phone]

      The Dendrome Project and TreeGenes are funded by the
      USDA-ARS Plant Genome Database Project.

---------------------End of file acedb-faq----------------------------