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 | ||
=== Getting started === | === Getting started === | ||
__NOTOC__ | __NOTOC__ | ||
* 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
containingjstacs-1.3.jar
, and additional libraries in the sub-directorylib
. - 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 thejstacs-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
jar
s 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