InMoDe: Difference between revisions

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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.
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 [http://www.cs.helsinki.fi/u/eggeling/InMoDe/InMoDe_userGuide.pdf user guide].
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].
 
 




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 ==
== Paper ==
Line 14: Line 14:
If you use InMoDe, please cite
If you use InMoDe, please cite


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
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 ==
== Download and installation ==
Line 20: Line 20:
InMoDe offers three user interfaces.  
InMoDe offers three user interfaces.  


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


that can be started by
that can be started by
Line 30: Line 30:
and require an existent Java installation (8u74 or later).
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 [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].  
In addition, there are two user-friendly alternatives for installing the GUI variant of InMoDe, namely (i) a [http://www.jstacs.de/downloads/InMoDe-1.1.dmg DMG for installation under Mac OS X], and (ii) a [http://www.jstacs.de/downloads/InMoDe-1.1.exe Windows installer].  


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


== Webserver ==
== [http://galaxy.informatik.uni-halle.de Webserver] ==


A server with all tools of InMoDe is available for public use at [http://galaxy.informatik.uni-halle.de].
A server with all tools of InMoDe is available for public use at [http://galaxy.informatik.uni-halle.de galaxy.informatik.uni-halle.de].
The provided web-server puts a certain limit on the complexity of runnable jobs for the learning tools.
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.
For unlimited use, please download InMoDe and install it to your local machine or own Galaxy instance.
== Version history ==
=== Version 1.1 ===
''Minor improvements ([https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/changelog-1.1.txt changelog]) for ISMB 2017 ([https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/poster.pdf poster])''
* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDe_userGuide-1.1.pdf InMoDe User Guide (version 1.1)]
* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeGUI-1.1.jar InMoDeGUI-1.1.jar]
* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeCLI-1.1.jar InMoDeCLI-1.1.jar]
* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeGalaxy-1.1.jar InMoDeGalaxy-1.1.jar]
* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDe1.1_sources.zip Source code]
=== Version 1.0 ===
''Initial release''
* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.0/InMoDe_userGuide-1.0.pdf InMoDe User Guide (version 1.0)]
* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.0/InMoDeGUI-1.0.jar InMoDeGUI-1.0.jar]
* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.0/InMoDeCLI-1.0.jar InMoDeCLI-1.0.jar]
* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.0/InMoDeGalaxy-1.0.jar InMoDeGalaxy-1.0.jar]

Latest revision as of 16:50, 20 July 2018

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.


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.

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)

Version 1.0

Initial release