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Gene Notebook

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

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. A presentation based on that version is also available.


The Gene Notebook is available as a web application, genenotebook.war. (To 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 instructions are:

  1. Save the genenotebook.war file in the Tomcat webapps directory. (Note that the web application must be installed in "/genenotebook" on the web server.)
  2. Place the JDBC driver jar file in either the Tomcat lib directory or the webapp lib directory.
  3. Create the XMLDB schema for Oracle or DB2. (This are the same examples from the book and CD.)
  4. Expand the war file by restarting Tomcat.
  5. 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.
  6. Edit the same xmldb.properties file to specify the XML parser being used, if you are not using the default parser Apache Xerces.
  7. Point your web browser to the appropriate URL (for example, http://localhost:8080/genenotebook).
  8. 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

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