ACEDB FAQ

Dave Matthews matthews at greengenes.cit.cornell.edu
Mon May 21 02:27:49 EST 2001


Newsgroups: bionet.software.acedb
Subject: ACEDB Genome Database Software FAQ
Followup-To: bionet.software.acedb
Reply-To: matthews at greengenes.cit.cornell.edu
Distribution: world
Organization: USDA-ARS, Dept. Plant Breeding, Cornell University
Summary: Frequently Asked Questions about the genome database software ACEDB.

URL: htp://ars-genome.cornell.edu/acedocs/acedbfaq.html
Archive-name: acedb-faq
Last-modified: 19 May 2001
Version: 1.44
     _________________________________________________________________
   
                                   ACEDB FAQ
     _________________________________________________________________
   
   Curated by: Dave Matthews
     _________________________________________________________________
   
  Frequently Asked Questions about ACEDB
  
   
     * Q0 : What is ACEDB?
     * Q1 : ! What is the current version of ACEDB?
     * Q2 : ! Where can I get ACEDB?
     * Q3 : What hardware/software do I need to run ACEDB?
     * Q4 : Can ACEDB be networked?
     * Q5 : What documentation exists for ACEDB?
     * Q6 : Can I subscribe to the ACEDB newsgroup by mail?
     * Q7 : Is there a repository of software tools for ACEDB curators?
     * Q8 : When and where is the next ACEDB Workshop?
     * Q9 : How does ACEDB compare to commercial relational DBMS's?
     * Q10 : How should ACEDB be cited? 
     * Q11 : What ACEDB databases exist?
     * Q12 : Who prepared this document & where is the current version?
       
   Questions marked with '!' have substantially changed answers since the
   last update of the FAQ. 
     _________________________________________________________________
   
  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.
   
   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
   in 1989. 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. Durbin &
   Thierry-Mieg continue to develop the system, with contributions from
   other groups.
   
   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.
     _________________________________________________________________
   
  Q1: What is the current version of the ACEDB software?
  
  A1:
  
   New! The current version for Unix and Windows is 4_9a, 26 Apr 01.
   Updates are released ca. monthly at
   http://www.acedb.org/Software/Downloads/supported.shtml.
   These updates don't usually have different version numbers so please
   note the dates.
   
   The current version for Macintosh is 4.1b1, August 1995.
   WWW interfaces: (See "Can ACEDB be networked?".)
     * New! AcePerl -- version 1.72, dated sometime since 1.68 which was
       15 Oct 2000.
     * AceBrowser -- version 2.10, September 1999
     * webace2K (Cornell) -- May 2000
     * webace2 (Sanger) -- version 2.0a5, March 1998
     * CITA: CORBA Interface To ACEDB (UK Cropnet) -- May 2000
     * Jade: Java for ACEDB
          + version 1.0j, Apr 1998
          + New! jadex, 2001
     _________________________________________________________________
   
  Q2: Where can I get ACEDB?
  
  A2:
  
   Source code and Unix and Windows binaries are available at:
     * New! http://www.acedb.org/Software/Downloads/supported.shtml
     * ncbi.nlm.nih.gov in repository/acedb (not up to date at present)
     * http://alpha.crbm.cnrs-mop.fr/acedb/distrib/ (offline at present)
       
   MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin:
   (Note: The authors are not currently able to support MacAce. Latest
   version was 4.1b1.)
     * ftp.sanger.ac.uk in pub/acedb/macace 
     * ncbi.nlm.nih.gov in repository/acedb/macace 
     _________________________________________________________________
   
  Q3: What hardware/software do I need to run ACEDB?
  
  A3:
  
   The software is available in binary (pre-compiled) format for a
   variety of machines.
     * Unix:
          + Sun/SunOS 4.x
          + Sun/Solaris
          + DEC DECstation3100, 5100 etc.
          + DEC Alpha/OSF-1
          + Silicon Graphics Iris series 4, 5, 6
          + IBM RS-6000
          + PC 386/486/Pentium with Linux
          + NEC EWS4800
          + NeXT: contact Patrick Phillips at University of Texas,
            NeXTmail: patrick at wbar.uta.edu email: phil at decster.uta.edu
          + There exist, or have existed, ports onto Alliant, Hewlett-
            Packard, Convex. You may have to contact the developer
            responsible for the port to make these real.
     * Windows 95/98/NT/2000
     * Macintosh (not currently supported)
       
   The software is also available as source code, so you may be able to
   get it working on any machine.
   
   Memory requirements (from Richard Durbin, aug 97)
   
   The amount of memory you require for ACEDB depends very much on how
   big the database is (i.e. the disk space used by the database/
   subdirectory). Our rule of thumb is that one typically uses 5-10Mb
   plus up to 10% of the disk space size of the database. So with a 200Mb
   database perhaps 25Mb memory, and with a 500Mb database (e.g. the C.
   elegans one) up to 50-60Mb. In fact for short sessions less memory is
   used -- it is only when all classes are explored, or for example when
   parsing big files that these amounts of memory get used.
     _________________________________________________________________
   
  Q4: Can ACEDB be networked?
  
  A4:
  
   ACEDB Client / Server Computing (from Doug Bigwood, aug97)
   
   There are several client/server models for ACEDB computing and several
   more are in development. The start of the ACEDB client/server age
   began with the inclusion of aceclient and aceserver in version 4.0.
   These are C - based and use the RPC protocol for communication. These
   executables can be made from the standard ACEDB distributions.
   
   Starting in version 4.5 an xaceclient is also included with ACEDB.
   Xaceclient provides remote read/write access to an aceserver while
   providing the user with the same X displays that are found in xace. To
   use it, you create an empty database with the appropriate models and
   start xaceclient. It will automatically retrieve data from the server
   declared in wspec/server.wrm (the Montpellier server in the
   distribution server.wrm). The data will be saved locally and can then
   be viewed with a normal xace.
   
   A perl extension which provides aceclient functionality to Perl 5.x
   was developed at ACE95. The files necessary for this perl extension
   are now (ACEDB 4.5 and later) included in the wrpc directory of the
   ACEDB directory hierarchy. Documentation about how to extend perl is
   found at
   http://ars-genome.cornell.edu/acedocs/ace97/perlace/perlacecl.html.
   
   WWWAce and its successor webace were developed to provide a World Wide
   Web interface for ACEDB. Webace instructions can be found at
   http://ars-genome.cornell.edu/acedocs/webace.html, and
   http://ars-genome.cornell.edu/acedocs/ace97/webace.html and the
   program itself at
   ftp://ars-genome.cornell.edu/pub/tools/webace.tar.gz.
   
   A Java-based client called Jade allows communication via sockets to an
   aceserver. Jade installation instructions and information on
   downloading can be found at http://stein.cshl.org/jade/.
   
   There are now development efforts underway to provide additional
   client/server functionality to ACEDB including a CORBA server and
   socket-based communications. These will likely be included in future
   versions of ACEDB. A new C library interface to ACEDB internals will
   greatly ease the development of new clients and servers that will
   support additional protocols.
   
   Subsequent developments (from Dave Matthews, jul00)
   
   A new version of webace, sometimes called webace2, was developed at
   the Sanger Centre. It makes use of the new gifaceserver instead of
   aceserver to improve interactive response of the graphical displays,
   Javascript, Java, and a new Aceclient.pm module which can be installed
   into Perl without recompiling. It also supports the ACEDB ?URL class.
   The home page is at http://webace.sanger.ac.uk/. Its authors currently
   consider it "deprecated", preferring AceBrowser.
   
   AcePerl, from Lincoln Stein, is an object-oriented Perl interface to
   ACEDB. It can connect to remote ACEDB databases, perform queries,
   fetch ACE objects, and update databases. The programmer's API is
   compatible with the Jade Java API. Home page at
   http://stein.cshl.org/AcePerl/.
   
   AceBrowser, from Lincoln Stein, is a ready-to-use WWW gateway to ACEDB
   databases built on AcePerl. It has most of the functionality of
   webace. http://stein.cshl.org/AcePerl/AceBrowser/.
   
   webace2K is an enhancement of webace2, from Maria Nemchuk.
   http://ars-genome.cornell.edu/webace/webace_install.html
   
   CITA is a CORBA Interface To ACEDB, from UK CropNet.
   http://jic-bioinfo.bbsrc.ac.uk/BrassicaDB/CITA/
     _________________________________________________________________
   
  Q5: What documentation exists for ACEDB?
  
  A5:
  
    At the Sanger Centre, www.acedb.org
    
     * Current documentation and news, including:
     * Proceedings of the ACEDB2000 Conference
     * A "quick quide" tutorial for users, http://www.acedb.org/Tutorial/
     * Archive of the monthly ACEDB User Group Newsletter from Ed
       Griffiths, http://www.acedb.org/winfo/Newsletters/
     * WebDDTS for ACEDB bug reporting and tracking
     * WWW copies of the ACEDB online help (see below),
       http://www.acedb.org/Software/whelp/TOC.html
       
    In the ACEDB Documentation Library, http://ars-genome.cornell.edu/acedocs/
    
     * Archive of many still interesting documents, including:
     * The original documentation from the developers Durbin &
       Thierry-Mieg, ca. 1992.
          + acedb -- A C. elegans Database: I. Users' Guide
          + acedb -- A C. elegans Database: II. Installation Guide
          + acedb -- A C. elegans Database: III. Configuration Guide
          + acedb -- A C. elegans Database: Syntactic Definitions for the
            ACEDB Data Base Manager
     * Tutorials and technical guides, for users, curators and
       programmers
     * Documentation written at the ACEDB Workshops
     * Documents in Postscript, wordprocessor and other non-html formats,
       at ftp://ars-genome.cornell.edu/pub/acedocs/.
     * Some curator tools
     * A selection of models.wrm files from various databases
     * SampleDB, a sample database to demonstrate some ACEDB features,
       1995
     * This FAQ in html format
       
    Other
    
     * The ACEDB online help, available from the Help buttons in xace. A
       context-sensitive hypertext reader for the contents of the whelp
       directory of the ACEDB software distribution.
     * Contents of the wdoc, wtools, and wscripts directories.
     * Searchable archives of the bionet.software.acedb newsgroup
          + http://www.bio.net/hypermail/ACEDB/, from BIOSCI
          + http://genome-www.stanford.edu/cgi-bin/biosci_acedb, from the
            Saccharomyces Genome Database site
     * ACEDB User's Guide in Japanese, from Tohru Sano, NEC,
       sano at exp.cl.nec.co.jp,
       http://www.cbi.or.jp/~sano/. (Postscript at
       http://www.labs.nec.co.jp/ . Follow the prompts to register and
       "download the software".)
     * Paper publications
          + Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992).
            AAtDB, an Arabidopsis thaliana database. Plant Molecular
            Biology Reporter 10: 308-309, 409-410.
          + Cherry, J.M. and Cartinhour, S.W. (1994). ACEDB, A tool for
            biological information. Pp. 347-356 in: Automated DNA
            Sequencing and Analysis, M. Adams, C. Fields, and C. Venter
            (Eds.). Academic Press. Online version:
            http://ars-genome.cornell.edu/acedocs/overview.html.
          + Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994).
            Physical mapping projects and ACEDB. Pp. 111-158 in: Guide to
            Human Genome Computing. Bishop, M.J (Ed.). Academic Press.
     _________________________________________________________________
   
  Q6: Can I subscribe to the ACEDB newsgroup by mail?
  
  A6:
  
   Yes! Just send the message "subscribe acedb" to
   biosci-server at net.bio.net.
   
   You can also post to the newsgroup by mail, write to
   acedb at net.bio.net.
   
   Or you can access it with a standard newsreader like rn or tin at
   bionet.software.acedb, or with a WWW browser at
   news:bionet.software.acedb.
   
   The articles are archived by BIOSCI at
   http://www.bio.net/archives.html and by Mike Cherry at
   http://genome-www.stanford.edu/cgi-bin/biosci_acedb. Both archives are
   indexed for searching. This is the place to find the Questions that
   really are Frequently Asked!
     _________________________________________________________________
   
  Q7 : Is there a repository of software tools for ACEDB curators?
  
  A7:
  
   Not really, but there are several partial ones. The main tools
   available are for converting data from other formats to .ace format.
   
   The USDA-ARS Center for Bioinformatics and Comparative Genomics has
   some useful tools at
   http://ars-genome.cornell.edu/acedocs/conversion.html. Some additional
   ones were contributed at the ACE97 Workshop and can be found in the
   Proceedings, http://ars-genome.cornell.edu/acedocs/ace97/tools/.
   
   Mike Cherry maintains an archive of tools at
   ftp://genome-ftp.stanford.edu/pub/acedb_dev/utilities/
   
   For a general tool for converting data to ACEDB format input files,
   Joachim Baumann (joachim.baumann at informatik.uni-stuttgart.de) has
   written the Perl program TextConvert, available at
   ftp.informatic.uni.stuttgart.de/pub/DART/.
     _________________________________________________________________
   
  Q8: When and where is the next ACEDB Workshop?
  
  A8:
  
   The ACEDB2000 Workshop was held June 10-16 at Simon Fraser University,
   B.C., Canada. The Proceedings are at
   http://www.acedb.org/winfo/Conferences/acedb2000/.
   
   The ACE97 Conference and Workshop was held July 27 - August 9 at
   Cornell University, Ithaca, New York, USA. See the ACE97 Proceedings
   Page, http://ars-genome.cornell.edu/acedocs/ace97/proceedings.html for
   the results.
   
   The Proceedings from the May 1995 ACEDB Conference are available at
   http://ars-genome.cornell.edu/acedocs/ace95/. A final summary report
   is available at
   http://ars-genome.cornell.edu/acedocs/ace95/ace95.final.html. Also
   available online are collections of snapshots taken during the
   conference by Frank Eeckman and by Dave Matthews.
   
   For pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers,
   see the online collections:
     * by Mike Cherry at
       http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ;
     * by John Morris at
       http://weeds.mgh.harvard.edu/ace94/ace94.image.html ;
     * and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html
     _________________________________________________________________
   
  Q9: How does ACEDB compare to commercial relational DBMS's?
  
  A9:
  
   From Jean Thierry-Mieg, 4/97:
   
   Obviously, i have a biased opinion, but i would say that acedb is to
   be recommended if the following criteria are met:
   
   1) A very complex schema, that cannot be developed at once, but will
   need continuous refinement in parallel with the accumulation of the
   data
   
   2) The type of questions that will be asked are rather complex, with
   rather fuzzy answers, that one tries to refine progressively. The
   acedb browsing capacities are useful in this case and have no
   equivalent in a relational dbms
   
   ______________
   
   I would rather recommend sybase in the following case
   
   1) Simple schema, that can be designed from the start and does not
   contain too many n.n relations and does not need recursivity
   
   2) The type of questions that will be asked is: succession of
   de-correlated simple questions with simple answers
   
   ____________________
   
   Within this context, i would then list the following goodies of acedb:
   
   1) The ace file format, which is a powerful system to prepare and
   exchange data between data curators.
   
   2) The existence of an easy graphic browsing interface
   
   3) The availability of a biology-layer, if the application is about
   genetics
   
   4) Portability (any unix machine), mac (with some limitations),
   windows (in development) and price (ace is a freeware). This implies
   that you can actually redistribute the complete system, say on a CD,
   something impossible with sybase.
   
   5) Ease of use, i seriously believe that ace is much easier to
   configure and use than sybase.
   
   _____________________
   
   Finally one should consider the following question: concurrency.
   
   Sybase has a well designed transaction system, which will allow roll
   backs and refined lockings. This is essential for an application like
   a booking agency, with many users in simultaneous write access.
   
   Ace is much simpler minded. The graphic acedb creates a global lock
   allowing a single user with write access at the time, and the
   modifications are not echoed to the other "read access" users in real
   time.
   
   The non graphic client server system allows parallel downloading of
   data by many users, it is intended for example for collection of
   robots sending their independent data in parallel. This is now well
   tested.
   
   A graphic client system is being developed and now runs in our hands,
   but is not yet released.
   
   --
   
   Therefore, if you do need real time simultaneous write access with
   partial locks, and roll backs, use sybase/oracle
   
   ________________
   
   Last issue is speed and quantities of data. In principle,
   sybase/oracle is unlimited, whereas acedb needs to keep around 5-10%
   of the data in ram. But this apparent difference is misleading.
   
   On a 32 Meg machine, you can run ace with around 300.000 objects with
   a complex schema at high speed. With say 1M objects, you will need
   more memory or the performance would totally degrade because of
   swapping. However, this is really a lot of data.
   
   On a similar machine, your sybase oracle will work with that amount or
   more data only if you do not perform too many joins. This implies that
   you are asking simple questions from a simple schema which was indeed
   our first criterion to choose sybase. If you start asking complex
   questions and make joins, acedb is actually much more powerful.
   
   During tests run on a big dec alpha server by Otto Ritter in decembre
   1995 on several million biological objects with a complex schema,
   acedb was about 10 times faster than sybase, both to load the data and
   to answer queries.
   
   I would therefore conclude that the quantity of data is not a
   criterion pushing one way or the other, it is the complexity of the
   schema that matters.
     _________________________________________________________________
   
  Q10: How should ACEDB be cited?
  
  A10:
  
   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.
     _________________________________________________________________
   
  Q11: What ACEDB databases exist?
  
  A11:
  
   Too many to maintain an up-to-date listing. A list as of mid-1998 is
   available at http://ars-genome.cornell.edu/acedocs/acedbfaq.dbs.html
   
   A repository of many of these databases is maintained by CBCG, both
   for anonymous ftp at ftp://ars-genome.cornell.edu/pub and for WWW
   access via Webace at http://ars-genome.cornell.edu/.
     _________________________________________________________________
   
  Q12: Who prepared this document & where is the current version?
  
  A12:
  
   This document is posted monthly to the BIOSCI newsgroup
   bionet.software.acedb.
   
   The WWW version is at
   http://ars-genome.cornell.edu/acedocs/acedbfaq.html.
   
   This FAQ was created and maintained from 1993 - 1996 by Bradley K.
   Sherman. Major contributions in getting it off the ground were made by
   Mike Cherry, John McCarthy, and Doug Bigwood. Other contributors
   include:
     * Lisa Lorenzen
     * David Matthews
     * Edie Paul
     * Donn Davy
     * Eric De Mund
     * Sam Cartinhour
       
   It is currently maintained by Dave Matthews.
   
   Please cite as:
   Matthews, D.E., and B.K. Sherman, ACEDB Genome Database Software FAQ,
   http://ars-genome.cornell.edu/acedocs/acedbfaq.html, 1993-2000,
   approx. 30K bytes.
   
   To add or modify information in this document, please send mail to:
   matthews at greengenes.cit.cornell.edu 
   
   The GrainGenes Project is funded by the USDA ARS Plant Genome Research
   Program.
     _________________________________________________________________

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