MiMB

Probabilistic Approaches to Transcription Factor Binding Site Prediction

by Stefan Posch, Jan Grau, André Gohr, Jens Keilwagen, Ivo Grosse

Getting started

• 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.

Additional Requirements

• 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.

Links

• 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)