MycDB release 1-5/3-5

Staffan Bergh staffan at biochem.kth.se
Wed Mar 23 23:56:26 EST 1994


MycDB 1-5/3-5

Stockholm & Paris March 18, 1994

The third release of the Mycobacterium database, MycDB, is now
available.

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 Departement of
Biochemistry at The Royal Institute of Technology in Stockholm,
Sweden.

MycDB is available free of charge via Internet network transfer. A
complete description of the procedure to retrieve the software and
database is available (see MycDB.Retrieval). If you are impatient, see
the end of this message.

Since last release of data, the database manager software has
undergone some changes. Partly due to this fact and partly for
administrative reasons this release comes in two versions called 1-5
and 3-5, where version 1-5 is configured for ace1 and 3-5 for
ace3. Note that the two versions are NOT compatible with each
other. There are also some changes to the models, requiring a complete
reload of the database. In the future we will only support the ace3
version, so if you already have MycDB set up, consider changing to
ace3 and if you do not have the software installed, do install
ace3. Addresses and instructions are in the file MycDB.Retrieval.

MycDB uses the excellent database software written by Richard Durbin
(MCR-LMB, UK) and Jean Thierry-Mieg (CNRS, France). The ACEDB software
allows the user to browse information by simply pointing and clicking
with the workstation mouse. A variety of powerful query methods are
also available. However, our experience is that most users choose the
mouse interface to find the information they are interested in.

As far as possible all information is connected to other information
in the database. The database software presents the information in
separate windows that allow many parts of the database to be viewed at
one time.  There are also many paths to any piece of information,
allowing the user to easily navigate the connections between the
various types of information.

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://kiev.physchem.kth.se/MycDB.html. 

   The M.tuberculosis physcal 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 Departement of Biochemistry, KTH: 
       http://kiev.physchem.kth.se/MycDB.html 
   The ftp server at the Departement of Biochemistry, KTH: 
       kiev.physchem.kth.se (130.237.52.64) in pub/MycDB 
   The ftp server at Institut Pasteur: 
       ftp.pasteur.fr (157.99.64.12) in pub/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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