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ACEDB Genome Database Software FAQ


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URL: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html
Archive-name: acedb-faq
Last-modified: 19 Feb 98
Version: 1.41
_________________________________________________________________

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 : 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.

New! The current Windows 95/NT version 4.5.3d, 15 January 1998,
corresponds to Unix test.ace.4_5c. For the latest documentation 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
_________________________________________________________________

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

Windows 95/NT, from Richard Bruskiewich:
* ftp.sanger.ac.uk in pub/acedb/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

NEC EWS4800 binaries:
* http://www.labs.nec.co.jp/freesoft/freesofte.html

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:
+ 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@wbar.uta.edu email: phil@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/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.
+ 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, 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)
+ 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@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://probe.nalusda.gov:8000/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.

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/.

New! Pascal Hingamp has created a tool for mirroring remote databases
to your own machine. UPace is a flexibly configurable, well documented
Perl script intended to be adaptable to any ACEDB database available
by ftp, with updating as often as you like.
ftp://ftp.hgmp.mrc.ac.uk/pub/phingamp/

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 Plants of the North American Indians. USDA Miscellaneous
Publication Number 237.
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : May 1995

Database : GrainGenes
Species : Wheat, barley, rye, oats, sugarcane, relatives
Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu
Curator : Gerard R. Lazo, lazo@pw.usda.gov
PI : Olin D. Anderson, oandersn@pw.usda.gov
ACEDB_version : 4_5 (Unix), 4.1b1 (MacAce)
Data_version : 1.8, December 1997
Availability : UNIX, Windows, Macintosh versions via anonymous ftp
Availability : Windows, Macintosh versions on CD-ROM from Dr. Baek Hie
Nahm, Korea Rice Genome Research Program, Myongji University, Yongin,
Korea.
FTP : probe.nalusda.gov in pub/graingenes
FTP : grain.jouy.inra.fr in pub/database
WWW : http://probe.nalusda.gov:8000/alldbs.html
WWW : http://wheat.pw.usda.gov/
WWW : http://grain.jouy.inra.fr
Gopher : greengenes.cit.cornell.edu
Gopher : grain.jouy.inra.fr
Gopher : probe.nalusda.gov:7002
Gopher : probe.nalusda.gov:7000/11/genome.databases/
FAQ_updated : December 1997

Database : IGD (Integrated Genomic Database)
Species : Homo sapiens
Subject : Chromosome 21
Availability : September 1994 by ftp, on-line server October 1994
Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de
Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr
Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr
Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr
Description : IGD (Integrated Genomic Database) aims to integrate
multiple public general molecular biology and human genome specific
databases into single logical database with unified interface to
existing analysis tools. From data produced by the 4th International
Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data
provided by or taken from the following databases and data
repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB.

Database : IXDB (Integrated X chromosome DataBase)
Species: Homo sapiens
Subject: Chromosome X
Acedb_version : 4.1
Data: The YAC map constructed by the Max-Planck-Institut fuer
Molekulare Genetik in Berlin, with all the attached experimental data
necessary to reconstruct the map. Information on each of 9000 YAC
clones mapped to the X chromosome, and constituting the YAC collection
assembled with clone sets from 14 different laboratories worldwide.
Latest_release:March 1996
Curator: Hugues Roest Crollius, roest@mpimg-berlin-dahlem.mpg.de
Contact: Ulf Leser, leser@mpimg-berlin-dahlem.mpg.de
PI: Hans Lehrach
FTP: ftp.mpimg-berlin-dahlem.mpg.de in directory pub/lehrach/x-map
WWW: http://www.mpimg-berlin-dahlem.mpg.de/~xteam

Database: Leishdb
Species: Leishmania major, L. infantum, L. peruviana, L. donovani and
others
PI: Jennie Blackwell
PI: Al Ivens
ACEDB_version: 4.3
Curator: Martin Aslett
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: ftp.ebi.ac.uk/pub/databases/parasites/Leish
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
WWW: http://www.ebi.ac.uk/parasites/leish/leishpage.html (in
development)
Data_updated: October 1996
FAQ_updated : November 1996

Database : LIGM-DB
Curator : Veronique Giudicelli
Focus : genetic and physical mapping of loci of Immunoglobulins and
Tcell receptors
PI : Marie-Paule Lefranc
Contact : Veronique Giudicelli, LIGM IGMM UMR CNRS 9942, BP 5051 Rte
de Mende, 34000 Montpellier, giudi@ligm.crbm.cnrs-mop.fr

Database : MaizeDB
Species : Zea mays L. ssp. mays and related species
Content : Maps, raw map data, loci, probes, genetic stocks,
variations, mutant images, agronomic traits, gene products, QTL,
bibliography, colleague addresses; hardlinks to sequence and germplasm
databases.
Latest_release : Oct 1996
Acedb_version : 4.1
Curator : Mary Polacco, maryp@teosinte.agron.missouri
PI : Ed Coe, Jr., ed@teosinte.agron.missouri.edu
Systems : Denis Hancock, dhancock@teosinte.agron.missouri.edu
FTP : probe.nalusda.gov/pub/maizedb/macedist961001.tar.gz
WWW : http://www.agron.missouri.edu
WEBACE : http://probe.nalusda.gov:8300/
Contact : db_request@teosinte.agron.missouri.edu
Comment : Data are periodically extracted into ACEDB format from
Sybase
Comment : Genera software used to maintain the Sybase database and its
gateways, except for ACEDB
Comment : ACEDB releases are announced on the MAIZE bulletin board;
http://www.bio.net/hypermail/MAIZE/
Comment : WEBACE records are hardlinked to the Sybase server where
data are curated
Funding : USDA ARS Plant Genome Research Program
FAQ_updated : Mar 7, 1997

Database : Mendel (plant wide gene names)
Species : wide range of plant species
Subject : standardized designations for sequenced genes
Comment : The purpose is to provide a common system of nomenclature
for substantially similar genes across the plant kingdom. Mendel is
maintained by the Commission on Plant Gene Nomenclature.
ACEDB_version : 4.0
Curator : Carl Price, price@mbcl.rutgers.edu
Curator : Ellen Reardon, reardon@mbcl.rutgers.edu
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : July 1995

Database : Millet Genes
Species : Pennisetum glaucum (Pearl Millet)
ACEDB_version : 4.3
Curator : Matt Couchman, Matthew.Couchman@bbsrc.ac.uk
PI : Katrien Devos, Katrien.Devos@bbsrc.ac.uk
FTP: ftp://jiio5.jic.bbsrc.ac.uk/pub/millet
WWW : http://synteny.nott.ac.uk/millet.html
WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.shtml
WWW : http://probe.nalusda.gov:8300/plant/
FAQ_updated : March 1997

DataBase : Mousedb
Species : Mus Musculus
Species : Homo Sapiens
ACEDB_version : 3.0 with extensions to define and display cytogenetic
data.
Description : Mouse genome data from the published literature,
including mouse genes with phenotypic effects, chromosome anomalies,
imprinted regions and man-mouse homologies with associated
pathological disorders. The maps are consensus ones. They use data,
such as the HIS and anomaly data, to show alignments between the
genetic and cytogenetic maps.
Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk
PI : Mary Lyon
PI : Jo Peters
Availability : Mousedb is available publicly from the UK HGMP Resource
Centre's computing service via the INTERNET. For user id. please
contact Administration, HGMP Resource Centre, Hinxton Hall,
Cambridgeshire CB10 1RQ, UK.
Tel: (+44) 1223 494520 Fax: (+44) 1223 494510
Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon
OX11 ORD
FAQ_updated : July 1995

Database : MPNADB (Medicinal Plants of Native America)
Species : Over 2,100 plant species
Curator : Daniel E. Moerman, dmoerman@umich.edu
Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB
version
Comment : MPNADB is based on a two-volume book of the same name
published in 1986 by the Museum of Anthropology of the University of
Michigan. MPNADB was first developed at the University of Michigan in
DBase II.
ACEDB_version : 4.0
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : June 1995

Database : MsqDB
Species : Interspecies Mosquito database
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 : MycDB
Species : Mycobacteria
Comment : MycDB is a collation of data on the mycobacteria, causative
agents of tuberculosis and leprosy. It is centered on the mapping and
sequencing projects under way in M.leprae and M.tuberculosis.
Curator : Staffan Bergh, staffan@biochem.kth.se
Curator : Stewart Cole, stcole@pasteur.fr
ACEDB_version : 4.3
Data_version : 4-22 (December 1996)
FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB
FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB
FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in
pub/databases/acedb/mycdb
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://www.biochem.kth.se/MycDB.html
WWW : http://probe.nalusda.gov:8300/other/
FAQ_updated : December 1996

Database : OMIA (Online Mendelian Inheritance in Animals)
Species : wide range of animal species
Subject : gene and phene (familial trait or phenotype) information
Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance
in Man (MIM) database and was developed at the University of Sydney,
Australia, in Advanced Revelation.
Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au
ACEDB_version : 4.0
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/animal/
WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html
FAQ_updated : September 1995

Database : PhytochemDB (Plant Chemicals)
Species : wide range of plant species
Subject : Consists primarily of plant chemical data, including
quantity, taxonomic occurrence, and chemical activity.
Comment : Converted to ACEDB from the original SQL database.
ACEDB_version : 4.0
Data_version : July 1994
Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov
Curator : James A. Duke, ngrljd@ars-grin.gov
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : June 1995

Database : PomBase
Curator : Sean Walsh, svw@sanger.ac.uk
Curator : Marie-Adele Rajendream
PI : Bart Barrell, barrell@sanger.ac.uk
Species : Schizosaccharomyces pombe
ACEDB_version : 4.1
FTP : ftp.sanger.ac.uk in pub/PomBase
FAQ_updated : September 1995

Database : PVP (Plant Variety Protection)
Species : Glycine max (soybeans)
Subject : Data about plant varieties that have been granted a
Certificate of Protection by the Plant Variety Protection Office.
Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB
version
ACEDB_version : 4.0
Contact: The Plant Variety Protection Office, Room. 500, National
Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705
Telephone : 301-504-5518
Fax : 301-504-5291
Email : Jeff Strachan, strachan@locus.nalusda.gov
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : June 1995

Database : Receptor Database
Species : all
Curator : Kotoko Nakata, nakata@nihs.go.jp
Co-Curator : Takako Igarashi, taka@nihs.go.jp
Co-Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp
Contact : Kotoko Nakata, nakata@nihs.go.jp
ACeDB_version : 4.1
WWW : http://impact.nihs.go.jp/RDB.html
Data_updated : regularly
FAQ_updated : October 1997

Database : RiceGenes
Species : Oryza sativa
Curator : Edie Paul, epaul@nightshade.cit.cornell.edu
PI : Susan McCouch
ACEDB_version : 4.1
FTP : probe.nalusda.gov in pub/ricegenes
Gopher : nightshade.cit.cornell.edu
Gopher : probe.nalusda.gov:7007
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
FAQ_updated : November 1996

Database : SacchDB
Species : Saccharomyces cerevisiae
Subject : Budding (common baker's) Yeast Genome
ACEDB_version : UNIX 4.3, MacAce 4.0b4
Data_version : 4.6
Data : All Saccharomyces genes contained in the Registry of Gene
Names. Results of the completed chromosomal sequencing projects have
been integrated into the database. Physical Maps based on DNA
sequencing projects, hybridization to the Olson/Riles prime filter
grids, and restriction mapping. For the completely sequenced
chromosomes the Olson prime clones have been re-mapped (on the
computer) to the DNA sequence. Saccharomyces DNA sequences contained
within GenBank are incorporated. Literature references, most including
abstracts, for the information contained within the database. Gene
protein product information obtained from the YPD database (Garrels
and Latter, CSHL) and the literature. Genetic Maps including the
underlying two point tetrad data. Including all tetrad data reported
in previous additions of the Mortimer Yeast Maps.
FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB
FTP : ncbi.nlm.nih.gov in repository/SacchDB
WWW : http://genome-www.stanford.edu/
Funding : National Center for Human Genome Research, NIH
PI : David Botstein, botstein@genome.stanford.edu
Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu
Curator : Selena Dwight, dwight@genome.stanford.edu
Curator : Cathy Ball, ball@genome.stanford.edu
Curator : Caroline Adler, adler@genome.stanford.edu
Curator : Yankai Jia, jia@genome.stanford.edu
Programmer : Gail Juvik, gjuvik@genome.stanford.edu
Programmer : Shuai Weng, shuai@genome.stanford.edu
Sys. Admin : Mark Schroeder, mark@genome.stanford.edu
Contact : yeast-curator@genome.stanford.edu
Data_Submission : yeast-curator@genome.stanford.edu
FAQ_updated : September 1996

Database: SchistoDB
Species: Schistosoma mansoni (plus other schistosomes)
PI: David Johnston
ACEDB_version: 4.3
Curator: Martin Aslett
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Schisto/
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
Data_updated: In development
FAQ_updated : November 1996

Database : SolGenes
Subject : Solanaceae - tomato, potato, pepper
Curator : Sam Beer, sbeer@nightshade.cit.cornell.edu
PI : none currently
Release : ACEDB 4.3
FTP : probe.nalusda.gov in pub/solgenes
Gopher : nightshade.cit.cornell.edu:71
Gopher : probe.nalusda.gov:7006
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
Data_updated : May 1997
FAQ_updated : May 1997

Database : SorghumDB
Species : Sorghum bicolor (L.) Moench
PI : Keith F. Schertz, schertz@tamvm1.tamu.edu
USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College
Station, TX 77843-2474
Phone : (409) 260-9252
FAX : (409) 845-0456
Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu
Southern Crop Improvement Facility, Crop Biotechnology Center, Texas
A&M University, College Station, TX 77843-2123
Phone : (409) 862-1523
FAX : (409) 862-4790
ACEDB_version : 3.0
Data_version : 2.0
FTP : probe.nalusda.gov in pub/sorghumdb
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
FAQ_updated : September 1995

Database : SoyBase
Species : Glycine max (Soybeans) and related species
PI : Randy Shoemaker, rcsshoe@iastate.edu
Curator : David Grant, dgrant@iastate.edu
Assistant_curator : Marica Imsamde, mimsande@iastate.edu
Contact : David Grant, dgrant@iastate.edu
ACEDB-Version : 3.7
FTP : probe.nalusda.gov in pub/soybase
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
WWW : http://macgrant.agron.iastate.edu
FAQ_updated : October 1995

Database : Syndb
Species : Homo sapiens, Mus musculus
Subject : STS content mapping & directed sequencing of Human
Chromosomes 21,5 with Mouse for syntenic comparison
ACEDB_version : acedb v3.3 plus moulon server
FTP : genome.lbl.gov in pub/acedb/
WWW : http://genome.lbl.gov/Genome/acepage.html
Curator : Donn F. Davy, DFDavy@lbl.gov
Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov
PI : Michael Palazzolo
PI : Chris Martin
PI : Jan-Fang Cheng, jcheng@genome.lbl.gov
FAQ_updated : October 1994

Database: ToxoDB
Species: Toxoplasma gondii
PI: David Sibley
PI: David Roos
PI: Jim Ajioka
ACEDB_version: 4.3
Curator: Martin Aslett
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: ftp.ebi.ac.uk/pub/databases/parasites/Toxo/
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
WWW: http://www.ebi.ac.uk/parasites/toxo/toxpage.html
Data_updated: October 1996
FAQ_updated: November 1996

Database : TreeGenes
Species : Forest trees
ACEDB_version : 4.3
Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov
PI : David B. Neale, dbn@s27w007.pswfs.gov
Contact : Dendrome@s27w007.pswfs.gov
FTP : probe.nalusda.gov in /pub/treegenes
Gopher : s27w007.pswfs.gov/
Gopher : probe.nalusda.gov:7508/
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
WWW : http://s27w007.pswfs.gov/
FAQ_updated : May 1996

Database: Trypbase
Species: Trypanosoma brucei
PI: Sara Melville
ACEDB_version: 4.3
Curator: Howard Cobb
Curator: Martin Aslett
Contact: Sara Melville, sm160@mole.bio.cam.ac.uk
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: ftp.ebi.ac.uk/pub/databases/parasites/brucei
WWW: http://parsun1.path.cam.ac.uk/newtryp/toppage.htm
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
Data_updated: October 1996
FAQ_updated: November 1996

Database : 21Bdb
Species : Homo sapiens
Subject : STS content mapping and sequencing of Human Chromosome 21
ACEDB_version : acedb.1-10 plus moulon server
Curator : Donn F. Davy, DFDavy@lbl.gov
Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov
PI : Michael Palazzolo
PI : Chris Martin
PI : Jan-Fang Cheng, jcheng@genome.lbl.gov
FTP : ftp://genome.lbl.gov in pub/acedb/
WWW : http://genome.lbl.gov/Genome/acepage.html
FAQ_updated : April 1994

Database : 11Db
Species : Homo sapiens
Subject : Physical and Genetic mapping of Human Chromosome 11
Description : 11Db attempts to show as full a picture as possible of
the genetic and physical maps of Human Chromosome 11. It has two new
displays, one which attempts to integrate as much of the mapping data
as possible using minimal intervals, and one which displays YAC
Contigs downloaded from SEGMAP datafiles.
Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk)
PI : Peter Little (p.little@bc.ic.ac.uk)
ACEDB_version : based on 4_1 with added map displays.
ACEDB_version : based on 3_6 with added map displays.
Data version : 1.0
Last Update : December 1995
WWW : http://chr11.bc.ic.ac.uk
FTP : ftp.cc.ic.ac.uk
Description : 11Db attempts to show as full a picture as possible of
the genetic and physical maps of Human Chromosome 11. It has two new
displays, one which attempts to integrate as much of the mapping data
as possible using minimal intervals, and one which displays YAC
Contigs downloaded from SEGMAP datafiles.

Database : 22ace
Species : Homo sapiens
Subject : Physical map of human chromosome 22, genomic sequencing and
more
ACEDB_version : 4.1
Curator : Ian Dunham, id1@sanger.ac.uk
Curator : Gareth Maslen, glm@sanger.ac.uk
PI : Ian Dunham
FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/
WWW : http://www.sanger.ac.uk/hum22/
FAQ_updated : August 1995

Database : VoxPop
Species : Populus species
Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu
PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu
ACEDB_version : 1.9
FTP : poplar1.cfr.washington.edu in /pub/
Gopher : poplar1.crf.washington.edu

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_________________________________________________________________

Q12:Who prepared this document & where is the current version?

A12:

This document is posted monthly to the BIOSCI newsgroup
bionet.software.acedb and to USENET conference news.answers. It is
intended to be used as an index to ACEDB databases and to information
about the database software.

The WWW version of this document is at:
http://probe.nalusda.gov:8000/acedocs/acedbfaq.html

A text version is available via anonymous ftp at machine rtfm.mit.edu
as pub/usenet/news.answers/acedb-faq. If you only have electronic
mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu.

Curators of ACEDB databases should take note of Question "What ACEDB
databases exist?", and keep me apprised of changes.

Errors of commission or omission are unintentional. If I have
forgotten to give you credit please let me know. Please send comments
and corrections to: acedbfaq@s27w007.pswfs.gov

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,
ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq,
http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993-1998,
approx. 70K bytes.

To add or modify information in this document, please send mail to:
acedbfaq@s27w007.pswfs.gov

The GrainGenes Project is funded by the USDA ARS Plant Genome Research
Program.

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Last Update March 27 2014 @ 02:11 PM