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 [ | 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]. | ||
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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 | * [http://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeGUI.jar InMoDeGUI.jar] -- graphical user interface (version 1.1) | ||
* [http://www.cs.helsinki.fi/u/eggeling/InMoDe/InMoDeCLI.jar InMoDeCLI.jar] -- command line interface | * [http://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeCLI.jar InMoDeCLI.jar] -- command line interface (version 1.1) | ||
* [http://www.cs.helsinki.fi/u/eggeling/InMoDe/InMoDeGalaxy.jar InMoDeGalaxy.jar] -- for integration into own Galaxy instance | * [http://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeGalaxy.jar InMoDeGalaxy.jar] -- for integration into own Galaxy instance (version 1.1) | ||
that can be started by | that can be started by | ||
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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 (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. | Both do not require a recent Java, as they automatically install the required libraries to the local machine. | ||
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== Webserver == | == 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 (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. | 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. | ||
Revision as of 12:16, 22 July 2017
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, 2017; 33(4): 580-582. doi: 10.1093/bioinformatics/btw689
Download and installation
InMoDe offers three user interfaces.
- InMoDeGUI.jar -- graphical user interface (version 1.1)
- InMoDeCLI.jar -- command line interface (version 1.1)
- 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 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 (version 1.0) 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.
