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(New page: == Probabilistic Approaches to Transcription Factor Binding Site Prediction == by Stefan Posch, Jan Grau, André Gohr, Jens Keilwagen, Ivo Grosse === Abstract === TODO === Links...) |
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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 == | |||
__NOTOC__ | |||
* 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 [http://www.jstacs.de/downloads/MiMBExample.java MiMBExample] class as well as the data (see link below) and save these to the same directory. | |||
* Open a shell/terminal and <code>cd</code> to the <code>jstacs-bin-1.3</code> directory. | |||
* Compile the Example by calling <code>javac -cp .:jstacs-1.3.jar MiMBExample.java</code> on the command line. | |||
* Run the example by calling <code>java -cp .:jstacs-1.3.jar:lib/numericalMethods.jar:lib/RClient.jar MiMBExample ./</code><br /> If you want to load the data from another directory, you need to replace the argument <code>./</code> by the path to that directory. | |||
* Using a SDE, you have to add the <code>jar</code>s to the Java build path by changing the properties of your project. | |||
== Additional Requirements == | |||
* If you want to use [http://www.jstacs.de/api/de/jstacs/utils/REnvironment.html REnvironment] e.g. for plotting ROC and PR curves, you must have a server with a running instance of [http://www.r-project.org/ R] and [http://www.rforge.net/Rserve/ Rserve]. | |||
* If you want to use [http://www.jstacs.de/api/de/jstacs/utils/UserTime.html UserTime] to measure user time instead of wall clock time during the nuemrical optimization, you must compile <code>de_jstacs_utils_UserTime.c</code> and you must set the library-path (<code>-Djava.library.path</code>) to the directory where the dynamic library resides. For details see the documentation of [http://www.jstacs.de/api/de/jstacs/utils/UserTime.html UserTime]. | |||
=== Links === | === Links === | ||
* [[Downloads]] | * The sources and the API of Jstacs as well as earlier versions can be found in [[Downloads]] | ||
* [[Getting started]] | * For more general remarks on the first steps using Jstacs see [[Getting started]] | ||
* [[MiMB Example]]: all code snippets of the chapter and additional comments. | * [[MiMB Example]]: all code snippets of the chapter and additional comments. | ||
* Data (available soon) | |||
Latest revision as of 10:38, 11 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-1.3containingjstacs-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
cdto thejstacs-bin-1.3directory. - Compile the Example by calling
javac -cp .:jstacs-1.3.jar MiMBExample.javaon 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.cand 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)
