View source for InMoDe

[[File:InMoDe-test.png|100px|left]]
by Ralf Eggeling, Ivo Grosse, and Jan Grau.

InMoDe is a collection of seven tools for learning, leveraging, and visualizing '''in'''tra-'''mo'''tif '''de'''pendencies within DNA binding sites and similar functional nucleotide sequences.

For a detailed description of the functionality of InMoDe see the [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDe_userGuide-1.1.pdf user guide].





== Paper ==

If you use InMoDe, please cite

R. Eggeling, I. Grosse, and J. Grau. [https://academic.oup.com/bioinformatics/article/33/4/580/2666342/InMoDe-tools-for-learning-and-visualizing-intra InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites]. ''Bioinformatics'', 2017; 33(4): 580-582. doi: 10.1093/bioinformatics/btw689

== Download and installation ==

InMoDe offers three user interfaces. 

* [http://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeGUI-1.1.jar InMoDeGUI.jar] -- graphical user interface (version 1.1)
* [http://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeCLI-1.1.jar InMoDeCLI.jar] -- command line interface  (version 1.1)
* [http://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeGalaxy-1.1.jar InMoDeGalaxy.jar] -- for integration into own Galaxy instance (version 1.1)

that can be started by

 java -jar filename.jar

and require an existent Java installation (8u74 or later).

In addition, there are two user-friendly alternatives for installing the GUI variant of InMoDe (version 1.0), namely (i) a [http://www.jstacs.de/downloads/InMoDe-1.0.dmg DMG for installation under Mac OS X], and (ii) a [http://www.jstacs.de/downloads/InMoDe-1.0.exe Windows installer]. 

Both do not require a recent Java, as they automatically install the required libraries to the local machine.

== Webserver ==

A server with all tools of InMoDe (version 1.0) is available for public use at [http://galaxy.informatik.uni-halle.de].
The provided web-server puts a certain limit on the complexity of runnable jobs for the learning tools.
For unlimited use, please download InMoDe and install it to your local machine or own Galaxy instance.