InMoDe - Revision history

Eggeling at 15:50, 20 July 2018

2018-07-20T15:50:15Z

← Older revision		Revision as of 15:50, 20 July 2018
Line 9:		Line 9:
	InMoDe is continuously developed further.		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.		Feel free to report bugs, make feature requests, or give other comments and suggestions to eggeling[at]cs.helsinki.fi.
	~~If you wish to be notified about news regarding the software, such as releases of a next version, send an email with the header "InMoDe subscribe" to the aforementioned address.~~

	== Paper ==		== Paper ==

Eggeling at 10:42, 26 November 2017

2017-11-26T10:42:10Z

← Older revision		Revision as of 10:42, 26 November 2017
Line 8:		Line 8:

	InMoDe is continuously developed further.		InMoDe is continuously developed further.
	Feel free to report bugs ~~reports~~, make feature requests, or other comments and suggestions to eggeling[at]cs.helsinki.fi.		Feel free to report bugs, make feature requests, or give other comments and suggestions to eggeling[at]cs.helsinki.fi.
	If you wish to be notified about news regarding the software, such as releases of a next version, send an email with the header "InMoDe subscribe" to the aforementioned address.		If you wish to be notified about news regarding the software, such as releases of a next version, send an email with the header "InMoDe subscribe" to the aforementioned address.

Eggeling at 10:35, 26 November 2017

2017-11-26T10:35:10Z

← Older revision		Revision as of 10:35, 26 November 2017
Line 7:		Line 7:


			InMoDe is continuously developed further.
			Feel free to report bugs reports, make feature requests, or other comments and suggestions to eggeling[at]cs.helsinki.fi.
			If you wish to be notified about news regarding the software, such as releases of a next version, send an email with the header "InMoDe subscribe" to the aforementioned address.

	== Paper ==		== Paper ==
Line 34:		Line 35:
	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.

Eggeling: version updates

2017-09-16T19:04:40Z

version updates

Eggeling: source code

2017-09-15T16:04:40Z

source code

← Older revision		Revision as of 16:04, 15 September 2017
Line 49:		Line 49:
	* [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/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/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 ===		=== Version 1.0 ===

Eggeling at 12:38, 22 July 2017

2017-07-22T12:38:22Z

@@ Line 20: / Line 20: @@
 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)
+* [https://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)
+* [https://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)
+* [https://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
@@ Line 39: / Line 39: @@
 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.

Eggeling at 12:17, 22 July 2017

2017-07-22T12:17:30Z

← Older revision		Revision as of 12:17, 22 July 2017
Line 20:		Line 20:
	InMoDe offers three user interfaces.		InMoDe offers three user interfaces.

	* [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/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.jar InMoDeCLI.jar] -- command line 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.jar InMoDeGalaxy.jar] -- for integration into own Galaxy instance (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		that can be started by

Eggeling: version 1.1 added

2017-07-22T12:16:59Z

version 1.1 added

Eggeling at 09:16, 14 February 2017

2017-02-14T09:16:59Z

← Older revision		Revision as of 09:16, 14 February 2017
Line 14:		Line 14:
	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/~~2938076~~/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. [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 ==

Eggeling at 11:22, 1 February 2017

2017-02-01T11:22:33Z

← Older revision		Revision as of 11:22, 1 February 2017
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/2938076/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

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

← Older revision		Revision as of 19:04, 16 September 2017
Line 20:		Line 20:
	InMoDe offers three user interfaces.		InMoDe offers three user interfaces.

	* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeGUI-1.1.jar InMoDeGUI~~.jar~~] -- graphical user interface ~~(version 1.1)~~		* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeGUI-1.1.jar InMoDeGUI] -- graphical user interface
	* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeCLI-1.1.jar InMoDeCLI~~.jar~~] -- command line interface ~~(version 1.1)~~		* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeCLI-1.1.jar InMoDeCLI] -- command line interface
	* [https://www.cs.helsinki.fi/u/eggeling/InMoDe/1.1/InMoDeGalaxy-1.1.jar InMoDeGalaxy~~.jar~~] -- for integration into own Galaxy ~~instance (version 1.1)~~		* [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 ~~(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].		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.
Line 36:		Line 36:
	== Webserver ==		== Webserver ==

	A server with all tools of InMoDe ~~(version 1.0)~~ 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].
	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.

← Older revision		Revision as of 12:16, 22 July 2017
Line 4:		Line 4:
	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].


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		* [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
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 (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.
Line 36:		Line 36:
	== 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.