InMoDe: Difference between revisions

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If you use InMoDe, please cite
If you use InMoDe, please cite


R. Eggeling, I. Grosse, and J. Grau. [https://academic.oup.com/bioinformatics/article/2666342/InMoDe-tools-for-learning-and-visualizing-intra InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites]. ''Bioinformatics'', 2016. doi: 10.1093/bioinformatics/btw689
R. Eggeling, I. Grosse, and J. Grau. [http://bioinformatics.oxfordjournals.org/content/early/2016/12/28/bioinformatics.btw689.full InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites]. ''Bioinformatics'', 2016. doi: 10.1093/bioinformatics/btw689


== Download and installation ==
== Download and installation ==

Revision as of 13:40, 1 January 2017

InMoDe-test.png

by Ralf Eggeling, Ivo Grosse, and Jan Grau.

InMoDe is a collection of seven tools for learning, leveraging, and visualizing intra-motif dependencies within DNA binding sites and similar functional nucleotide sequences.

For a detailed description of the functionality of InMoDe see the user guide.



Paper

If you use InMoDe, please cite

R. Eggeling, I. Grosse, and J. Grau. InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites. Bioinformatics, 2016. doi: 10.1093/bioinformatics/btw689

Download and installation

InMoDe offers three user interfaces.

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, namely (i) a DMG for installation under Mac OS X, and (ii) a 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 is available for public use at [1]. 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.