allanswers.org - ACEDB Genome Database Software FAQ

 Home >  Software >

ACEDB Genome Database Software FAQ

Section 1 of 2 - Prev - Next


URL: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html
Archive-name: acedb-faq
Last-modified: 8 Dec 97
Version: 1.40

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

ACEDB FAQ

----------------------------------------------------------------------------
Curated by: Dave Matthews
----------------------------------------------------------------------------

Frequently Asked Questions about ACEDB

   * Q0 : What is ACEDB?
   * Q1 : ! What is the current version of ACEDB?
   * Q1.5 : + What's new in ACEDB 4_5?
   * 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 : What newsgroups and mailing lists are available for ACEDB?
   * 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 '+' 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.

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.

Return to List of Questions
----------------------------------------------------------------------------

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

A1:

The current Unix version is ace.4_5d/e, released 28 August 1997.

Enhancements added during the ACE97 Workshop will be incorporated in the
next release.

The very latest development version is always available at
ftp://ftp.sanger.ac.uk/pub/acedb_src/. This is unsupported and not to be
redistributed.

The Windows 95/NT version 4.5.2, 15 August 1997, corresponds to Unix
test.ace.4_5c. For current information see the WinAce Web page at
http://mendel.medgen.ubc.ca/rbrusk/winace.html.

A Macintosh version is available as version 4.1b1, August 1995.

Return to List of Questions
----------------------------------------------------------------------------

Q1.5: What's new in ACEDB 4_5?

A1.5:

At present, all documentation on new ace4_5 features is in the Proceedings
of the ACE97 workshop.

Return to List of Questions
----------------------------------------------------------------------------

Q2: Where can I get ACEDB?

A2:

Source code and Unix binaries are available in the following anonymous ftp
sites:

   * ncbi.nlm.nih.gov in repository/acedb
   * ftp.sanger.ac.uk in pub/acedb
   * lirmm.lirmm.fr in pub/acedb
   * bioinformatics.weizmann.ac.il in pub/databases/acedb

Linux binaries in ELF and a.out format, from Jeff Bryer:

   * ncbi.nlm.nih.gov in repository/acedb
   * bioinformatics.weizmann.ac.il in pub/databases/acedb

NEC EWS4800 binaries:

   * http://www.labs.nec.co.jp/freesoft/freesofte.html

Windows 95/NT 3.51, from Richard Bruskiewich:

   * ftp.sanger.ac.uk in pub/winace
   * bioinformatics.weizmann.ac.il in pub/databases/acedb
   * Documentation: http://mendel.medgen.ubc.ca/rbrusk/winace.html

MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin:
(Note: The authors are not currently able to support MacAce. Latest version
was 4.1b1.)

   * genome.lbl.gov in pub/macace
   * ncbi.nlm.nih.gov in repository/acedb/macace
   * bioinformatics.weizmann.ac.il in pub/databases/acedb

Return to List of Questions
----------------------------------------------------------------------------

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:
        o Sun/SunOS 4.x
        o Sun/Solaris
        o DEC DECstation3100, 5100 etc.
        o DEC Alpha/OSF-1
        o Silicon Graphics Iris series 4, 5, 6
        o IBM RS-6000
        o PC 386/486/Pentium with Linux
        o NEC EWS4800
        o NeXT: contact Patrick Phillips at University of Texas, NeXTmail:
          patrick@wbar.uta.edu email: phil@decster.uta.edu
        o 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/NT
   * 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.

Return to List of Questions
----------------------------------------------------------------------------

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://probe.nalusda.gov:8000/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://probe.nal.usda.gov:8000/acedocs/webace.html, and
http://probe.nal.usda.gov:8000/ace97/webace.html and the program itself at
ftp://probe.nalusda.gov/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://probe.nalusda.gov:8000/ace97/Jade.installation.html.

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

Q5: What documentation exists for ACEDB?

A5:

From Sam Cartinhour:
     The ACEDB Documentation Library 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. The ACEDB
documentation server is sponsored by the Plant Genome Database Project at
the National Agricultural Library (USDA).

The WWW documentation server is part of the Agricultural Genome Information
System, at http://probe.nalusda.gov:8000/acedocs/. Documents in Postscript,
wordprocessor, and other non-html formats are available by ftp at
ftp://probe.nalusda.gov/pub/acedocs/. Information in the ACEDB Documentation
Library includes:

   * Primary documents from the developers Durbin & Thierry-Mieg, ca. 1992.
        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 acedb -- A C. elegans Database: Syntactic Definitions for the
          ACEDB Data Base Manager
   * Tutorials, general and specific
   * Documentation written at the ACEDB Workshops
   * A repository of 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 sources of documentation:

   * The ACEDB online help, a hypertext reader for the contents of the whelp
     directory of the ACEDB software distribution.
   * Contents of the wdoc, wtools, and wscripts directories.
   * Archives of the bionet.software.acedb newsgroup (both searchable)
        o http://www.bio.net/hypermail/ACEDB/, from BIOSCI
        o 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@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
        o 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.
        o 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://probe.nalusda.gov:8000/acedocs/overview.html.
        o 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.

Return to List of Questions
----------------------------------------------------------------------------

Q6: What newsgroups and mailing lists are available for ACEDB?

A6:

The USENET/BIOSCI conference bionet.software.acedb is dedicated to
discussions of ACEDB. The newsgroup can be accessed via a newsreader like rn
or tin, a WWW browser (news:bionet.software.acedb), or e-mail. To subscribe
to the e-mail version, send the message "subscribe acedb" to
biosci-server@net.bio.net. Mail sent to acedb@net.bio.net will be
distributed to all subscribers and to the electronic conference.

Articles posted to biosci.software.acedb 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.

There is also a separate mailing list for announcements of new releases of
the ACEDB (worm) database as well as the ACEDB software. To get on or off
this mailing list send mail to rd@sanger.ac.uk or mieg@kaa.crbm.cnrs-mop.fr.
The BIOSCI newsgroup is on this list.

Return to List of Questions
----------------------------------------------------------------------------

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 Agricultural Genome Information System has a growing stock of useful
tools at http://probe.nalusda.gov:8000/acedocs/conversion.html. Some
additional ones were contributed at the ACE97 Workshop and can be found in
the Proceedings, http://probe.nalusda.gov:8000/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@informatik.uni-stuttgart.de) has written the Perl
program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/.

Return to List of Questions
----------------------------------------------------------------------------

Q8: When and where is the next ACEDB Workshop?

A8:

The next ACEDB meeting is planned for summer 1998 in England.

The ACE97 Conference and Workshop was held July 27 - August 9 at Cornell
University, Ithaca, New York, USA. See the ACE97 Proceedings Page,
http://probe.nalusda.gov:8000/ace97/proceedings.html for the results.

The Proceedings from the May 1995 ACEDB Conference are available at
http://probe.nalusda.gov:8000/acedocs/ace95/. A final summary report is
available at http://probe.nalusda.gov:8000/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

Return to List of Questions
----------------------------------------------------------------------------

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.

Return to List of Questions
----------------------------------------------------------------------------

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.

Return to List of Questions
----------------------------------------------------------------------------

Q11: What ACEDB databases exist?

A11:

In alphabetic order by Database name

[Curators, please submit changes as new paragraphs. You may include html
links.]

A repository of many of these databases is maintained by the Agricultural
Genome Information System, both for anonymous ftp at
ftp://probe.nalusda.gov/pub and for WWW access via Webace at
http://probe.nalusda.gov:8000/alldbs.html.

Database : AaeDB
Species : Aedes aegypti (yellow fever mosquito)
ACEDB_version : 4.3
WWW : http://klab.agsci.colostate.edu/
Curator : Dennis Knudson, dknudson@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
Data_updated : regularly
FAQ_updated : April 1997

Database : AalDB
Species : Aedes albopictus (Asian tiger (forest day) mosquito)
ACEDB_version : 4.3
WWW : http://klab.agsci.colostate.edu/
Curator : Dennis Knudson, dknudson@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
Data_updated : regularly
FAQ_updated : April 1997

Database : ACeDB
Species : Caenorhabditis elegans
Current version: 4-8
Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr
Curator : Richard Durbin, rd@sanger.ac.uk
Curator : Sylvia Martinelli, sylvia@sanger.ac.uk
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/
FAQ_updated : August 1995

Database : aCHEdb
Species : wide range of species
Subject : alpha/beta fold family of proteins database ESTHER. Sequences
phylogenetically related to cholinesterases (alpha/beta hydrolase,
carboxylesterases, lipases, adhesion molecules.)
Comment : Converted to ACEDB from the original ESTHER database.
ACEDB_version : UNIX 4.5, MacAce 4.0b4
Data_version : August 1997
Curator : Xavier Cousin - cousin@ensam.inra.fr
Curator : Thierry Hotelier - hotelier@ensam.inra.fr
Curator : Arnaud Chatonnet - chatonne@ensam.inra.fr
Contact : chedb@ensam.inra.fr
Availability: Unix and Macintosh versions via anonymous ftp
FTP: ftp://ftp.toulouse.inra.fr in pub/esther
WWW : http://www.ensam.inra.fr/cholinesterase
FAQ_updated : September 1997

Database : AgaDB
Species : Anopheles gambiae (malaria mosquito)
ACEDB_version : 4.3
WWW : http://klab.agsci.colostate.edu/
Curator : Dennis Knudson, dknudson@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
Data_updated : regularly
FAQ_updated : April 1997

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
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.
WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html FTP:
ftp://keck.tamu.edu/pub/agsdb/agsdb1_0_acedb3_0_solaris2.3.tar.Z
FAQ_updated : March 1994

Database : Alfagenes
Species : Medicago sativa (alfalfa)
Curator : D. Z. Skinner, dzolek@ksu.ksu.edu
Telephone : (913) 532-7247
ACEDB_version : 3.0
FTP : probe.nalusda.gov in pub/alfagenes
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
FAQ_updated : July 1995

Database : AnoDB
Species : Anopheles sp.
ACEDB_version : 4.5
WWW : http://konops.imbb.forth.gr/AnoDB/
Curator : Christos Louis, louis@konops.imbb.forth.gr
Co-Curator : Pantelis Topalis, topalis@konops.imbb.forth.gr
Contact : AnoDB-comments@konops.imbb.forth.gr
Data_updated : regularly
FAQ_updated : August 1997

Database : AtDB
Species : Arabidopsis thaliana
ACEDB_version : UNIX 4.3, MacAce 4.0b4
Data_version : 4-7
PI : J. Michael Cherry
Curator : David Flanders
Contact : arab-curator@genome.stanford.edu
Availability : UNIX and Macintosh versions via anonymous ftp
FTP : genome-ftp.stanford.edu in arabidopsis/AtDB
FTP : ncbi.nlm.nih.gov in repository/AtDB
WWW : http://genome-www.stanford.edu
FAQ_updated : December 1996

Database : AtrDB
Species : Aedes triseriatus (Eastern tree hole mosquito)
ACEDB_version : 4.3
WWW : http://klab.agsci.colostate.edu/
Curator : Dennis Knudson, dknudson@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
Data_updated : regularly
FAQ_updated : April 1997

Database : BeanGenes
Species : Phaseolus and Vigna
Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu
ACEDB_version : 4.1
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
FAQ_updated : September 1995

Database : BrassicaDB
Species : Brassica napus (Canola/Oilseed Rape) and its parental diploid
species
ACEDB_version : 4.3
Description : Genetic maps of Brassica napus, QTL analyses for agronomic
traits, literature references and B. napus-specific DNA sequences will be
incorporated. We aim to integrate with B. napus genetic maps developed
elsewhere and to produce a Java interface that will link BrassicaDB with the
AAtDB (Arabidopsis thaliana) database through gene orthologies that are
becoming established between these closely related plant genomes.
PI : Martin Trick, Martin.Trick@bbsrc.ac.uk
Curator/Developer : Mazda Hewitt, Mazda.Hewitt@bbsrc.ac.uk
WWW : http://synteny.nott.ac.uk/brassica.html
Data_updated : Under development
FAQ_updated : August 1997

Database : ChlamyDB
Species : Chlamydomonas
Curator : Elizabeth Harris
Contact : chlamy@acpub.duke.edu
ACEDB_version : 3.0
Data_version : 1.2
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/
FAQ_updated : August 1995

Database : CIMMYT (Wheat International Nursery Data)
Species : Triticum spp.
ACEDB_version : 4.0
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/
FAQ_updated : September 1995

Database : CoolGenes
Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba
Curator : Fred Muehlbauer, muehlbau@wsu.edu
ACEDB_version : 3.0
Gopher : gopher://probe.nalusda.gov:7000/11/genome.databases/coolgenes/
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
FAQ_updated : January 1996

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
ACEDB_version : 3.0
Data_version : January 1995 (version 95.1)
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/
FAQ_updated : January 1995

Database: Cruzdb
Species: Trypanosoma cruzi
PI: Wim Degrave
ACEDB_version: 4.3
Curator: Martin Aslett
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/cruzi/
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
Data_updated : In development
FAQ_updated : November 1996

Database : CSNDB
Focus : Cell Signaling Networks
Species : human
Curator : Takako Igarashi, taka@nihs.go.jp
Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp
Assistant_Curator : Masumi Yukawa, yukawa@nihs.go.jp
Assistant_Curator : Shikiko Hasegawa, shasegaw@nihs.go.jp
Contact : Takako Igarashi, taka@nihs.go.jp
ACeDB_version : 4.1
Data : molecular data of signal molecules, molecular data of signal
transductions, signal transduction pathways, domain structure and function
of signal molecules, and three dimensional structures of signal molecules.
Availability : CSNDB is on WWW. WWW-browser is required to attach molecular
viewer RasMol (ftp: colonsay.dcs.ed.ac.uk ) for displaying three dimensional
structure of protein.
WWW : http://geo.nihs.go.jp/csndb.html

Database : CupDB
Species : Culex pipiens
ACEDB_version : 4.3
WWW : currently unavailable via www
Curator : Dennis Knudson, dknudson@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
Data_updated : regularly
FAQ_updated : April 1997

Database : Cyanoace
Species : Cyanobacterium synechocystis sp. strain PCC6803
Developer : Nobuyuki Miyajima, miyajima@kazusa.or.jp
Comment : Converted to ACEDB from Sybase
FTP : ftp://ftp.kazusa.or.jp/pub/acedb/cyanoace/
WWW : http://www.kazusa.or.jp/cyanobase/
Remark : WWW interface uses Java enhanced clickable maps.
FAQ_updated : December 1996

Database : EthnobotDB (worldwide plant uses)
Species : wide range of plant species
ACEDB_version : 4.0
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/
FAQ_updated : June 1995

Database: FilDB
Species: Filarial nematodes
PI: Mark Blaxter
ACEDB_version: 4.3
Curator: Martin Aslett
Contact: Mark Blaxter, mark.blaxter@ed.ac.uk
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Brugia
WWW: http://helios.bto.ed.ac.uk/mbx/fgn/filgen.html
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
Data_updated: In development
FAQ_updated : November 1996

Database : FoodplantDB (Native American Food Plants)
Species : Over 1,100 plant species
ACEDB_version : 4.0
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

Section 1 of 2 - Prev - Next

Back to category Software - Use Smart Search
Home - Smart Search - About the project - Feedback

© allanswers.org | Terms of use

LiveInternet