MiMB: Difference between revisions

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


=== Abstract ===
TODO


=== Getting started ===
=== Getting started ===
__NOTOC__
__NOTOC__
We recommend to use a [http://en.wikipedia.org/wiki/Software_development_environment software development environment] (SDE) as for instance [http://www.eclipse.org eclipse].
== Basic Requirements ==
* Make sure that you have installed [http://java.sun.com/javase/downloads/index.jsp Java] 1.5 or later.
* Make sure that you have installed [http://java.sun.com/javase/downloads/index.jsp Java] 1.5 or later.
* Download the binary version of [http://www.jstacs.de/download.php?which=bin-zip&version=1.3  Jstacs] and unzip it. You obtain a folder <code>jstacs-bin-1.3</code> containing <code>jstacs-1.3.jar</code>, and additional libraries in the sub-directory <code>lib</code>.
* Download the binary version of [http://www.jstacs.de/download.php?which=bin-zip&version=1.3  Jstacs] and unzip it. You obtain a folder <code>jstacs-bin-1.3</code> containing <code>jstacs-1.3.jar</code>, and additional libraries in the sub-directory <code>lib</code>.

Revision as of 16:22, 4 December 2009

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