InMoDe

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.

InMoDe is continuously developed further. Feel free to report bugs, make feature requests, or give other comments and suggestions to eggeling[at]cs.helsinki.fi.

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, 2017; 33(4): 580-582. doi: 10.1093/bioinformatics/btw689

Download and installation

InMoDe offers three user interfaces.

• InMoDeGUI -- graphical user interface
• InMoDeCLI -- command line interface
• InMoDeGalaxy -- for integration into own Galaxy

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 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.

Version history

Version 1.1

Minor improvements (changelog) for ISMB 2017 (poster)

• InMoDe User Guide (version 1.1)
• InMoDeGUI-1.1.jar
• InMoDeCLI-1.1.jar
• InMoDeGalaxy-1.1.jar
• Source code

Version 1.0

Initial release

• InMoDe User Guide (version 1.0)
• InMoDeGUI-1.0.jar
• InMoDeCLI-1.0.jar
• InMoDeGalaxy-1.0.jar