MiMB

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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)
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