MycDB - mycobacterial database, release 3-6

Staffan Bergh staffan at biochem.kth.se
Wed Feb 15 19:28:08 EST 1995


Stockholm & Paris February 15, 1995

The sixth release, called 3-6, of the Mycobacterium database, MycDB,
is now available.

MycDB is a database intended to contain information on all aspects of
mycobacteria, relevant to the study of the organisms and diseases
caused by them. The focus has initially been on the molecular
biology of mycobacteria, such that the database contains data on
physical and genetic mapping, nucleotide sequences, and data on
antigens and antibodies used in the study of the immunology of
mycobacteria.

MycDB is implemented in ACEDB, a general database manager initially
developed for the C. elegans genome project by Richard Durbin
(MRC-LMB, UK) and Jean Thierry-Mieg (CNRS, France), but since adapted
for other organisms and also for totally unrelated fields. It is
'object-oriented', and easily configured for different
purposes. Objects are heavily crosslinked so that a user can call up
(e.g) the Sequence corresponding to an Antigen, and from there look up
the Antibody recognizing the antigen, and then look at the
bibliography for the antibody. Complex queries can be performed with a
built-in query language or with the TableMaker, a facility for
producing tables suitable for further processing.

MycDB is funded by the WHO and the Fondation Raoul Follereau and is
maintained jointly by the Unite de Genetique Moleculaire Bacterienne
at the Institut Pasteur in Paris, France and the Department of
Biochemistry at The Royal Institute of Technology in Stockholm,
Sweden.

MycDB is available free of charge through the World Wide Web (at URL
http://www.biochem.kth.se/MycDB.html) or through ftp. Retrieval
instructions can be found at the end of this message.

New in release 3-6:

    * 227 new DNA sequences, current up to January 31, 1995
    * Close to 500 new references, from Medline up to January 1995.
    * The M. leprae contigs have been moved to the new Map class. Most info on
     M.tuberculosis physical mapping (Clones, Clone_Grids) has been removed as
     we are working on finishing this.
    * Model changes. Strain is now a model in its own right and crossreferences
     to Strain has been added to Sequence, Locus, and others. Gene has
     disappeared, all Genes are now Loci. In the future we plan to provide a
     filter for loci connected to coding sequences.
    * The model changes unfortunately means you will have to restart the
     database from scratch. (If you have used the database for your own data,
     contact staffan for further info.)
    * The WorldWideWeb server has a new address, an alias for the old one: URL
     http://www.biochem.kth.se/MycDB.html. The old address will continue to work
     for the forseeable future.

New in release 1-5/3-5:

    * Software version. MycDB now uses ACEDB1-10 (use updates 1-1 to 1-5) or
     ACEDB3-0 (use updates 3-1 to 3-5). Note that we will in the future only
     make updates available for version 3 of the software.
    * Model changes. As a consequence of changing software and feedback from
     users the models have changed. This unfortunately means you will have to
     restart the database from scratch. (If you have used the database for your
     own data, contact staffan for further info.)
    * A WorldWideWeb server has been set up (replacing the gopher), and can be
     found at the URL http://www.biochem.kth.se/MycDB.html.
    * The M.tuberculosis physical map has been removed, as we are currently
     working on finishing it. We hope to have this ready by next release.
    * New sequences. Many new sequences from GenBank/EMBL/DDBJ, with added
     annotations and similarity search results. Also sequences from Doug Smiths
     sequencing project at Collaborative Research (Thanx Doug).
    * Bibliography and address list has been updated.

Release 1-2 of MycDB contained:

    * MycDB now uses version 1-9 of the ACEDB software with, among other
     improvements, improved query facilities.
    * The cosmid physical map of M.tuberculosis produced at the LGMB. (this is
     a working version, kindly provided by Wolfgang Philipp and Sylvie Poulet).
    * A update of the compilation of nucleotide sequences from mycobacteria in
     GenBank and EMBL.
    * An extended list of antigens and antibodies, now including the CDC/WHO
     list of antibodies available to mycobacteriologists.
    * Addresses of more than 60 researchers.

Release 1-1 of MycDB contained:

    * The cosmid physical map of M.leprae produced at the LGMB.
    * A compilation of nucleotide sequences from mycobacteria in GenBank and
     EMBL.
    * A compilation of antigens and antibodies, based on the article of Young
     et al.
    * More than 1200 references downloaded from Medline.

The database currently requires a Unix workstation running
X-Windows. A variety of precompiled versions of the ACEDB database
software are available through anonymous ftp. See the file
MycDB.Retrieval for more info. An (experimental) Macintosh version of
the ACEDB software is also available.

If you wish to obtain the MycDB database please contact us, via
e-mail, fax, mail or telephone. If you are impatient and are already
familiar with internet/ftp, all relevant information can be found at

      the WWW server at the Department of Biochemistry, KTH:
     http://www.biochem.kth.se/MycDB.html
      the ftp server at the Department of Biochemistry, KTH: ftp.biochem.kth.se
     (130.237.52.63) in pub/MycDB
      the ftp server at Institut Pasteur: ftp.pasteur.fr (157.99.64.12) in
     pub/MycDB
      or the mirror site at the Weizmann Institute in Israel (thanks Jaime!):
     bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb

The file MycDB.Retrieval describes in more detail the database system
requirements, network retrieval procedures for obtaining the database
and methods of obtaining future updates.

For more information contact Staffan Bergh or Stewart Cole.

Staffan Bergh
Biochemistry, Royal Institute of Technology, S-100 44 Stockholm, Sweden
Email: staffan at biochem.kth.se
Fax: (46 8) 24 54 52
Voice: (46 8) 790 8758

Stewart Cole
Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, F-75724 Paris
Cedex 15, France
Email: stcole at pasteur.fr
Fax: (33 1) 45.68.85.93
Voice: (33 1) 45.68.84.46



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