TU Delft

Start using the program with Eclipse

This page is a short guide for compiling and running the examples provided with our framework for biofilm modeling. The program is presently available in the form of compiled Java classes that may be used in new programs to implement other biofilm models. However, knowledge of the Java programming language will be necessary, if you wish to use these libraries. If you have knowledge of other programming languages (such as C++) and wish to learn Java, there is plenty of material freely available on the internet (see our suggested links at the end of this page). No Java knowledge is required for now to follow the steps in this guide.
In order to begin creating biofilm models you will need the following:

Both the Java SDK and Eclipse are available for most popular platforms, including Microsoft Windows, Mac OS X and Linux.
The remaining instructions will assume that you installed the Java SDK and eclipse correctly in your computer. Please refer to the respective websites for assistance in installing the Java SDK or Eclipse.

Preparing the program
Create a directory in your computer to place the program. For example 'c:\framework' in the case you are using windows or '/home/$yourlogin$/framework' if you are using linux. Copy the framework.zip file to this directory and unzip the contents. Do this in a way that the original framework.zip file remains in the directory. The file listing for the directory should be


(windows screenshot)

Opening the program in eclipse
To create a new eclipse project with the biofilm modelling framework follow these steps:

The program is now imported in Eclipse in the form of a new project called "framework". You may open source code for the examples by browsing to the package nl.tudelft.bt.model.examples and clicking on the files with extension '.java'.
The javadoc documentation is located in the 'doc' subdirectory, in our example 'c:\framework\doc'. Use your web browser to view the documentation.

Running an application using Eclipse
The programs created or edited in Eclipse may be run directly from Eclipse using the 'run' command. From the package explorer, right-click on a class that has a 'main' method and select run>Java application. Try this for the "Monospecies2DGUI" application in the nl.tudelft.bt.model.examples.monospecies2D package.
Eclipse possesses many other features to assist in Java programming, including debugging. Please refer to the Eclipse documentation.

Included in the package is a distribution of the JfreeChart Java class library, used for plotting of state variables in realtime in the course of the simulations. JFreeChart is available for free at www.jfree.org.

The framework also has functions for output of biofilm structure representations using POVRAY. The POVRAY program is available for download at www.povray.org.

Java links
Sun java tutorial Start learning Java programming
Thinking in Java Learn object oriented programming in Java in this book by Bruce Eckel, available for free download

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2004 - Biofilm Modeling group at the TU Delft