How to start
From BioWeka
Contents |
Introduction
BioWeka is an environment for the analysis of biological data and for knowledge discovery in biological data. It is based on the Weka framework, an Open Source software for data mining. Weka offers a graphical workbench as well as a command line and a programming interface (API) and contains dozens of powerful machine learning algorithms and useful visualization tools. Before you continue this tutorial, please get familiar first with Weka, especially read the documentation about the Weka Explorer and about Weka's Attribute-Relation File Format. Further articles and web sites about Weka are listed under External links.
Preparation
Prerequisites
To use BioWeka within Weka, please check, whether your computer fulfils the following prerequisites:
- Java 1.4.2 or later is installed
- Weka 3-4-4 or later is installed
Installation
Next download the latest version of BioWeka (bioweka-X.Y.Z.zip) and extract the content of the ZIP file to a directory of your choice, e.g. ~/bioweka-X.Y.Z on Linux or C:\bioweka-X.Y.Z on Windows.
Configuration
If you want to use BioWeka with an existing installation of Weka, because you already have installed additional Weka extensions and configured these extensions for the use with Weka, please read this.
Otherwise copy the file weka.jar from the Weka installation directory (e.g. C:\Program Files\Weka-3-4-4 on Windows) into the lib subdirectory of your BioWeka installation directory. That's it.
A third option is to include the original path of the file weka.jar into Java's CLASSPATH environment variable on the command line:
On Windows
SET CLASSPATH=$CLASSPATH;C:\Program Files\Weka-3-4-4\weka.jar
On Linux
export CLASSPATH=%CLASSPATH%:~/weka-3-4-4/weka.jar
Finally, if you are using Linux, make the file bioweka.sh in the BioWeka installation directory executable, e.g.:
chmod a+x bioweka.sh
Application
Start the GUI
To start BioWeka, change the current directory to the BioWeka installation directory (e.g. cd ~/bioweka-X.Y.Z) and execute the file BioWeka.bat on Windows or bioweka.sh on Linux:
On Windows
BioWeka.bat
or double/single click on the file in the Windows Explorer.
On Linux
bioweka.sh
This shows the Weka GUI Chooser.
If you like to start the Weka Explorer with an existing ARFF file, use this syntax:
On Windows
BioWeka.bat data.arff
or drop the ARFF file onto the BioWeka.bat file.
On Linux
bioweka.sh data.arff
This opens the ARFF file in the Weka Explorer.
Next steps
Read these tutorials:
