JMGD:Java-based User Interface to the Microbial Genome Database

Nobuyuki Miyajima miyajima at kazusa.or.jp
Fri Apr 11 02:22:24 EST 1997


Dear colleagues,

I'd like to introduce you our Java based WWW-Genome tool, JMGD.
You can see examples (Haemophilus influenzae, 
Mycoplasma genitalium, Methanococcus jannaschii) in 

http://www.kazusa.or.jp/jmgd/

Source codes are available. 
============================================================================
JMGD:Java-based User Interface to the Microbial Genome Database
============================================================================
As the rate of progress in the determination of the whole genome 
sequencing of microbial organisms increases, we will need to have 
efficient, ready-to-use tools to publicize the data through WWW as 
soon as we finish the work.  Java-based user interface to the microbial 
genome database (JMGD) can be used for almost any kind of circular 
microbial organisms. We use JMGD for the genome sequencing of 
cyanobacterium we published recently 
(http://www.kazusa.or.jp/cyanobase/map/java/cmap_small/cmap_sm.html).
Java-based highlight-image techniques that were originally developed 
y Jim Graham(Sun Microsystem) are used in JMGD. JMGD includes all the Java 
source codes, perl scripts and the cgi scripts that are also used to blink 
the selected ORFs. The platform-independent aspect of Java makes it 
easily implemented in any machines used such as UNIX 
workstations, Macintosh or Windows computers.

JMGD has been developed under Sybase, but any other database management 
systems can be applied to without substantial modifications.

JMGD is available from:

ftp://ftp.kazusa.or.jp/pub/JMGD/
http://www.kazusa.or.jp/jmgd/


0. Prerequisites:

   * software

         perl    5.003 or later
          JDK    1.02  (1.1 is not supported in the current release)
      sybperl    2.06  or later  (http://www.perl.com/perl/CPAN/authors/id/MEWP)

   * OS   

      Solaris    2.5 or later
         OSF1    3.2 or later

   * DBMS (Database Management System)

      SQL Server   10/11 or any other DBMSs can be used.

-----------------------------------------------
Nobuyuki Miyajima
Kazusa DNA Research Institute
Department of Genome Informatics,
Chief Researcher

1532-3 Yana, Kisarazu, Chiba 292, Japan
TEL:  +81-438-52-3917 FAX:  +81-438-52-3918
E-mail:  miyajima at kazusa.or.jp




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