ACEDB Genome Database Software FAQ

ACEDB FAQ Pseudouser acedbfaq at s27w007.pswfs.gov
Fri Oct 8 17:11:58 EST 1993


Archive-name: acedb-faq
Last-modifed: 10/6/93
Version: 1.2

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Common Questions and Answers about ACEDB.

    This document will be posted monthly to the Usenet newsgroup
    bionet.software.acedb.  It is intended to be used as an index
    to ACEDB databases and to information about the database
    software.

    Errors of commission or omission are unintentional.

    Please send comments and corrections to acedbfaq at s27w007.pswfs.gov.
    Curators of ACEDB databases should take note of Question 4 and
    keep me apprised of changes.

    This FAQ has been submitted for approval for Usenet archival
    storage.  It has also been submitted to the Bionet curator.

        --Bradley K. Sherman 

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List of questions in the ACEDB FAQ:

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?
Q411:Who contributed to this document?

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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 data about diverse species [see Q4].

     ACEDB allows for automatic cross-referencing of items when loaded
     and allows for hypertextual navigation of the links using a mouse.
     Certain special purpose graphical displays have been integrated
     into the software.  These reflect the efforts 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.  The next release will be
     2.0.  (This refers to the software package.)

----------------------------------------------------------------------
Q2:  What {hardware | software} do I need to run ACEDB?

A2:  ACEDB currently runs on the following Unix sytems, under X11:
	 Any machine running SunOS 4.x.
         Sun SPARCstation 1, 1+, 2, IPC, IPX:
         SPARCstation 10 running Solaris:
         DEC  DECstation3100, 5100 etc.
         DEC  Alpha/OSF-1
         Silicon Graphics Iris series
         PC 386/486 with Linux (public domain Unix)
    Other 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.
    Macintosh:
        A port to the Macintosh may become available by the end of 1993.


----------------------------------------------------------------------
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

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Q4:  What ACEDB databases exist?

A4:  [In alpha 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 : curator at frodo.mgh.harvard.edu
     Last_update : Sept. 1993

     Database : ACeDB
     Species : Caenorhabditis elegans
     Availability :
     Current version: 1-21
     Curator : Jean Thierry-Mieg
     Curator : Richard Durbin
     Contact : rd at cele.mrc-lmb.cam.ac.uk
     Contact : mieg at kaa.cnrs-mop.fr
     Last_update : Sept. 1993

     Database : ChlamyDB
     Species : Chlamydomonas
     PI : Elizabeth Harris
     Contact : chlamy at acpub.duke.edu
     Availability : Still under construction
     Last_update : 30 Sept. 1993

     Database : EcoDB
     Species : E. coli
     PI : Staffan Bergh
     Last_update : Sept. 1993

     Database : Flydb
     Species : Drosophila melanogaster
     Availability : by request only, via ftp
     Curator : Suzanna E. Lewis
     Contact : SELewis at lbl.gov
     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 : matthews at greengenes.cit.cornell.edu
     Contact : oandersn at wheat.usda.gov
     Last_update : Sept. 1993

     Database : Mace
     Species : Zea mays L. ssp. mays
     Focus : Maize genome
     Comment : Mace is the frontend for maizedb, a relational\
               (SYBASE) database. It isupdated from maizedb by\
	       Stan Letovsky.  Maizedb is updated daily and\
	       will soon beaccessible by guest 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 : maizedb at teosinte.agron.missouri.edu
     Last_update: 5 October 1993

     Database : MycDB
     Species : Mycobacterium
     PI : Staffan Bergh
     PI : Thierry Garnier
     Contact : staffan at pasteur.fr
     Last_update : Sept. 1993

     Database : RiceGenes
     Species : Rice (O. sative)
     Availability : under development, login at own risk
     Curator : Edie Paul
     Contact : epaul at nightshade.cit.cornell.edu
     Last_update : Sept. 1993

     Database : SolGenes
     Coverage: Solanaceae - tomato, potato, pepper (eventually)
     Availability : Beta ACEDB via login or tar file
     Curator : Edie Paul
     Contact : epaul at nightshade.cit.cornell.edu
     Last_update : Sept. 1993

     Database : SoyBase
     Species : Soybeans
     Curator :  Lisa Lorenzen
     PI : Randy Shoemaker
     Contact : lorenzen at mendel.agron.iastate.edu
     Last_update : Sept. 1993

     Database : TreeGenes
     Species : Forest trees, Pinus taeda
     Availability : contact curator
     Curator : Bradley K. Sherman
     PI : David B. Neale
     Contact : Dendrome at s27w007.pswfs.gov
     Contact : bks at s27w007.pswfs.gov
     Contact : dbn at s27w007.pswfs.gov
     Last_update : Sept. 1993

     Database : 21Bdb
     Species : Homo sapiens
     Availability : by request, via ftp, gopher
     Curator : Donn F. Davy
     Contact : DFDavy at lbl.gov
     Contact : aggarwal at genome.lbl.gov
     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 : cgr at poplar1.cfr.washington.edu
     Contact : STETTLER at coyote.cfr.washington.edu
     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 : idunham at crc.ac.uk id1 at sanger.ac.uk
     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-)

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

     You will find other interesting documents in the wdoc subdirectory.

     "An Introduction to ACeDB: For MycDB a Mycobacterium DataBase"
     is available.  Try anonymous ftp at ftp.pasteur.fr (157.99.64.2)
     in pub/MycDB.  [I could not find this document at first glance,
     so it may be part of the distribution itself which is in the
     same directory.  Clarification from the curator would be helpful
     --bks.]

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

A6:  There is a Usenet Biosci conference titled bionet.software.acedb.

     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
     (cherry at genome.stanford.edu) 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:
          #
          Type=7
          Name=ACEDB BioSci Electronic Conference
          Path=7/.index/acedb-biosci
          Host=genome-gopher.stanford.edu
          Port=70
     (This is also courtesy of Mike Cherry.)

     If you do not have access to the Usenet you may receive the
     conference messages by e-mail.  To subscribe to this service send
     email to biosci at net.bio.net requesting inclusion in the
     acedb-soft list and explicitly stating the e-mail address at which
     you wish to receive the mail.

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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.

----------------------------------------------------------------------
Q411:Who contributed to this document?

A411: Bradley K. Sherman (bks at s27w007.pswfs.gov) is currently
      managing this FAQ.  Major contributions in getting it
      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: acedbfaq at s27w007.pswfs.gov

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




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