MiMB

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-bin-1.3 containing jstacs-1.3.jar, and additional libraries in the sub-directory lib.
Download the MiMBExample class as well as the data (see link below) and save these to the same directory.
Open a shell/terminal and cd to the jstacs-bin-1.3 directory.
Compile the Example by calling javac -cp .:jstacs-1.3.jar MiMBExample.java on 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.c and you must set the library-path (-Djava.library.path) to the directory where the dynamic library resides. For details see the documentation of UserTime.

The sources and the API of Jstacs as well as earlier versions can be found in Downloads
For more general remarks on the first steps using Jstacs see Getting started
MiMB Example: all code snippets of the chapter and additional comments.
Data (available soon)