New release of MycDB
staffan at pasteur.fr
Fri Apr 2 03:01:04 EST 1993
The second release of the Mycobacterium database, MycDB, is now
MycDB, a Mycobacterium DataBase, uses the excellent database
software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg
(CNRS, France). MycDB is funded by the WHO and the Fondation Raoul
Follereau and is maintained by the Unite de Genetique Moleculaire
Bacterienne at the Institut Pasteur.
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 below).
The ACeDB software allows the user to browse information by simply
pointing and clicking with the workstation mouse. A powerful query
facility is also available. However, our experience is that most users
choose the mouse interface to find the information they are interested in.
New in release 1-2:
- 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.
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
The database has now also been converted to Gopher format and can be
searched on keywords. If you have a gopher client, point it at
ftp.pasteur.fr, port 70, and look for the MycDB directory.
This is just the starting point. Just as the known Mycobacterium
information is always being expanded MycDB will also be extended and
enhanced via periodic updates. There is much more information that we
are working to include in subsequent updates of MycDB, and we also hope
that the users of the database will be willing to share their data by
the medium of the database.
The database currently requires a Unix workstation running X-Windows.
Versions of the ACeDB database software are available for Sun
Microsystems SPARCstations, Digital Equipment's DECstation, Silicon
Graphics Iris series and 386/486 PC computers running the freeware Unix
version Linux. A Macintosh version of the ACeDB software is under
development, and a public release version is expected shortly.
A printed manual "An Introduction to ACeDB: For MycDB, a Mycobacterium
DataBase" is available from the UGMB group. While this manual is not
required to use the database it might be very useful as a beginning
tutorial for the ACeDB software.
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
ftp.pasteur.fr (220.127.116.11) 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 at one of the
addresses below or via electronic mail to staffan at pasteur.fr.
Royal Institute of Technology
S-100 44 Stockholm, Sweden
Fax: (int+46)8-24 54 52
Unite de Genetique Moleculaire Bacterienne
F-75724 Paris Cedex 15, France
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