A demonstration of how to use XMLDB is included in
the web application Gene Notebook. This application
allows the user to create and edit information about
genes in an XML database.
More information about the Gene Notebook may be found
in Chapter 10 of Designing
XML Databases. An older version was also presented
as a demo at the tutorial on XML Databases for Bioinformatics
at Pacific Symposium on Biocomputing, January 2002.
based on that version is also available.
The Gene Notebook is available as a web application,
download the file using IE, right-click the previous
link using "Save Target As"). A web application
is an archive that can be automatically installed
by a web application server, such as Apache
jakarta tomcat. To use the web application, the
XMLDB database that comes with Designing
XML Databases should be installed in Oracle or
IBM DB2 and the appropriate JDBC drivers included
in the CLASSPATH for Gene Notebook (such as the lib
directory). Complete instructions for installing the
latest version of the software is available at the
book's web site, http://www.phptr.com/graves/installation.html
If you already have Apache Tomcat installed and have
a JDBC driver for either Oracle or DB2 database, simplified
- Save the genenotebook.war file in the Tomcat webapps
directory. (Note that the web application must be
installed in "/genenotebook" on the web
- Place the JDBC driver jar file in either the Tomcat
lib directory or the webapp lib directory.
- Create the XMLDB schema for Oracle
or DB2. (This are
the same examples from the book and CD.)
- Expand the war file by restarting Tomcat.
- Edit the xmldb.properties file in genenotebook/WEB-INF/classes
to specify that the DBMS is Oracle or DB2 and to
set the xmldb property to the JDBC connect string
as described in the properties file.
- Edit the same xmldb.properties file to specify
the XML parser being used, if you are not using
the default parser Apache
- Point your web browser to the appropriate URL
(for example, http://localhost:8080/genenotebook).
- The index.html page for Gene Notebook has instructions
for creating a sample document.
Older Versions of Tomcat
This web application works under Apache jakarta 4.0.3
(and later). To use other versions of jakarta with
this application, a slightly different web application
file is needed, genenotebook401.war,
because of the way that Tomcat interacts with Xalan.
If using older 3.x versions of Tomcat and you get
an error message on the console about Tomcat not finding
the SAX parser, you should move the xerces.jar file
from "webapps/genenotebook/lib" to the shared
"lib" directory in $TOMCAT_HOME.
These materials are Copyright
2001, 2002 by Mark Graves and contain material Copyright
2002 by Prentice Hall PTR. All rights reserved