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 ofcyanobacterium we published recently. 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/

Examples:
The Haemophilus influenzae RD (TIGR)
The Mycoplasma genitalium RD (TIGR)
The Methanococcus jannaschii RD (TIGR)

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.


If you have a Sybase SQL Server System 10/11, follow 1, 3(3-1), 5
                                      if not, follow 1, 2, 3(3-2), 4, 5


1. set.data preparation

   Prepare  set.data ( vars setting ) as instructed 
  in  data/README.data.


2. ORF, CLONE data preparation

   Prepare 

  orf.data   (putative ORF)
  clone.data (cosmid, phage etc. ) (optional)

 as instructed in  data/README.data.


3. Run make_files

  INSTALL.csh,  cgi/, html/ dirs and files are created.


3-1.     run   Make_Files.csh  (sybase version)

% Make_Files.csh


3-2.     run   Make_Files.csh (non-Sybase version)

% Make_Files.csh -nosyb


4.Modify CGI programs ( for non-Sybase DBMS)


 Modify cgi programs to suit for your DBMS.


5.Install cgi scripts and  html files.

You should need to have a privilage to write to CGI and html dirs to 
run this script.

  % INSTALL.csh