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Probabilistic Approaches to Transcription Factor Binding Site Prediction
by Stefan Posch, Jan Grau, André Gohr, Jens Keilwagen, Ivo Grosse
- Make sure that you have installed Java 1.5 or later.
- Download the binary version of Jstacs and unzip it. You obtain a folder
jstacs-1.3.jar, and additional libraries in the sub-directory
- Download the MiMBExample class as well as the data (see link below) and save these to the same directory.
- Open a shell/terminal and
- Compile the Example by calling
javac -cp .:jstacs-1.3.jar MiMBExample.javaon the command line.
- Run the example by calling
java -cp .:jstacs-1.3.jar:lib/numericalMethods.jar:lib/RClient.jar MiMBExample ./
If you want to load the data from another directory, you need to replace the argument
./by the path to that directory.
- Using a SDE, you have to add the
jars to the Java build path by changing the properties of your project.
- If you want to use REnvironment e.g. for plotting ROC and PR curves, you must have a server with a running instance of R and Rserve.
- If you want to use UserTime to measure user time instead of wall clock time during the nuemrical optimization, you must compile
de_jstacs_utils_UserTime.cand you must set the library-path (
-Djava.library.path) to the directory where the dynamic library resides. For details see the documentation of UserTime.