ColorizeMSWiki - Revision history

Admin: 28 revisions

2011-10-26T06:17:23Z

28 revisions

← Older revision	Revision as of 08:17, 26 October 2011
(No difference)

imported>HeikoNeuweger at 10:38, 23 February 2010

2010-02-23T10:38:02Z

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 __NOTOC__
   [[Image:ColorizeMSWiki$logo-small.png]]
 == Downloads ==

imported>HeikoNeuweger at 10:33, 23 February 2010

2010-02-23T10:33:23Z

← Older revision		Revision as of 12:33, 23 February 2010
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	ColorizeMS is a Java application that allows to qualitatively compare		ColorizeMS is a Java application that allows to qualitatively compare
	up to three experimental conditions ~~from separation experiments~~.		up to three experimental conditions measured via hyphenated mass spectrometry (MS).

	~~Single GC-MS datasets can be visualized as heatmaps. the intensities measured for individual ion channels at~~		[[Image:ColorizeMSWiki$gui2.png]]
	~~individual scans are represented using a color mapping as shown in the previous image~~.

	~~[[Image:ColorizeMSWiki$gui2~~.~~png]]~~		Single hyphenated MS datasets can be visualized as contour plots. The intensities measured for individual ion channels at
			individual mass spectral scans can be represented using a color mapping as shown in the following image.

	In this example, the retention time of the ~~compounds~~ is mapped to the x-axis and the mass-to-charge ratio is		In this example, the retention time of the measurement is mapped to the x-axis and the mass-to-charge ratio is
	represented on the y-axis. In GC- and LC-MS measurements the time axis is discretized by the scan rate of the instrument.		represented on the y-axis. In GC- and LC-MS measurements the time axis is discretized by the scan rate of the instrument.
	Each scan is represented in this visualization by one pixel and the discretization of the mass-to-charge ratio is done		Each scan is represented in this visualization by one pixel and the discretization of the mass-to-charge ratio is done
	by rounding to nominal masses and binning the measured intensities.		by rounding to nominal masses and binning the measured intensities.

	~~Support for 2D Gel Electrophoresis images as well as GC- or LC-MS experimental data is provided.~~

	[[Image:ColorizeMSWiki$twod.png]]		[[Image:ColorizeMSWiki$twod.png]]

imported>HeikoNeuweger at 13:28, 29 January 2010

2010-01-29T13:28:14Z

← Older revision		Revision as of 15:28, 29 January 2010
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	== Downloads ==		== Downloads ==

	The ColorizeMS Java application for different platforms can be downloaded [[ColorizeMSWiki/Downloads\|here]]		The ColorizeMS Java application for different platforms can be downloaded [[ColorizeMSWiki/Downloads\|here]].
			A Java Web Start link for ColorizeMS is available [[ColorizeMSWiki/WebStart\|here]].

	== Requirements ==		== Requirements ==
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	[[ColorizeMSWiki/UserDocu\|User documentation]]		[[ColorizeMSWiki/UserDocu\|User documentation]]

	~~[[ColorizeMSWiki/WebStart\|Java Web Start]]~~

	[[ColorizeMSWiki/DataSets\|Sample Data Sets ]]		[[ColorizeMSWiki/DataSets\|Sample Data Sets ]]

imported>HeikoNeuweger at 13:23, 29 January 2010

2010-01-29T13:23:45Z

← Older revision		Revision as of 15:23, 29 January 2010
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	* Apply the visualization methods to various data sources, images from 2D gel electrophoresis measurements, GC-, LC-, or GCGC-MS contour plots.		* Apply the visualization methods to various data sources, images from 2D gel electrophoresis measurements, GC-, LC-, or GCGC-MS contour plots.
	* ColorizeMS makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences in the measured samples.		* ColorizeMS makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences in the measured samples.
	* Through the use of OpenGL functionality, the rapid zooming, scrolling and color blending of high resolution textures is delegated to the Graphics		* Through the use of OpenGL functionality, the rapid zooming, scrolling and color blending of high resolution textures is delegated to the Graphics Processing Unit and allows to interactively visualize high resolution images representing the described experimental data.
	Processing Unit and allows to interactively visualize high resolution images representing the described experimental data.

	----		----

imported>HeikoNeuweger at 08:12, 29 January 2010

2010-01-29T08:12:11Z

← Older revision		Revision as of 10:12, 29 January 2010
Line 4:		Line 4:
	ColorizeMS is a Java application that allows to qualitatively compare		ColorizeMS is a Java application that allows to qualitatively compare
	up to three experimental conditions from separation experiments.		up to three experimental conditions from separation experiments.

	~~Support for 2D Gel Electrophoresis images as well as GC- or LC-MS experimental data is provided.~~

	~~[[Image:ColorizeMSWiki$twod.png]]~~

	Single GC-MS datasets can be visualized as heatmaps. the intensities measured for individual ion channels at		Single GC-MS datasets can be visualized as heatmaps. the intensities measured for individual ion channels at
	individual scans are represented using a color mapping as shown in the previous image.		individual scans are represented using a color mapping as shown in the previous image.

			[[Image:ColorizeMSWiki$gui2.png]]

	In this example, the retention time of the compounds is mapped to the x-axis and the mass-to-charge ratio is		In this example, the retention time of the compounds is mapped to the x-axis and the mass-to-charge ratio is
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	by rounding to nominal masses and binning the measured intensities.		by rounding to nominal masses and binning the measured intensities.

	[[Image:ColorizeMSWiki$~~gui2~~.png]]		Support for 2D Gel Electrophoresis images as well as GC- or LC-MS experimental data is provided.

			[[Image:ColorizeMSWiki$twod.png]]

	~~The~~ ColorizeMS ~~application~~ provides functionality to ~~map~~ up to three experimental conditions and rapidly visualize qualitative		ColorizeMS provides functionality to compare measurements from up to three experimental conditions and rapidly visualize qualitative
	differences ~~between the measurements~~. ColorizeMS is realized as web-start application which has been tested on Microsoft Windows, Mac OS X,		differences. ColorizeMS is realized as web-start application which has been tested on Microsoft Windows, Mac OS X,
	Linux and Solaris . The project is licensed under the GNU Public License 3.0.		Linux and Solaris . The project is licensed under the GNU Public License 3.0.

	== Downloads ==		== Downloads ==

	Java ~~applications~~ for ~~the~~ can be downloaded [[ColorizeMSWiki/Downloads\|here]]		The ColorizeMS Java application for different platforms can be downloaded [[ColorizeMSWiki/Downloads\|here]]

	== Requirements ==		== Requirements ==

	~~There~~ software requirements are specified in the JNLP description of ColorizeMS and will be installed upon start of the application ~~suing~~ Java Web Start technology. The application relies on Java3D with OpenGL bindings:		The software requirements are specified in the JNLP description of ColorizeMS and will be installed upon start
			of the application using Java Web Start technology. The application relies on Java3D with OpenGL bindings:
	* [http://java.sun.com/javase/technologies/desktop/java3d/ Java3D technology]		* [http://java.sun.com/javase/technologies/desktop/java3d/ Java3D technology]
	* [https://jogl.dev.java.net/ OpenGL Bindings for Java]		* [https://jogl.dev.java.net/ OpenGL Bindings for Java]

	~~Please follow the instructions for installing a current version of Java3D on your Mac OS X machine if you experience any problems with the~~
	~~ColorizeMS application.~~

	~~----~~

	== Features ==		== Features ==
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	* Interactively correct drifts in separation (e.g. retention time in GC- or LC-MS experiments).		* Interactively correct drifts in separation (e.g. retention time in GC- or LC-MS experiments).
	* Adjust the intensity of individual measurements to compensate for e.g. different amounts of sample that were analyzed.		* Adjust the intensity of individual measurements to compensate for e.g. different amounts of sample that were analyzed.
	* Apply the visualization methods to various data sources, images from 2D gel electrophoresis measurements, GC-, or LC-MS contour plots.		* Apply the visualization methods to various data sources, images from 2D gel electrophoresis measurements, GC-, LC-, or GCGC-MS contour plots.
	* ColorizeMS makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences in the measured samples.		* ColorizeMS makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences in the measured samples.
	* Through the use of OpenGL functionality, the rapid zooming, scrolling and color blending of high resolution textures is delegated to the Graphics Processing Unit and allows to interactively visualize high resolution images representing the described experimental data.		* Through the use of OpenGL functionality, the rapid zooming, scrolling and color blending of high resolution textures is delegated to the Graphics
			Processing Unit and allows to interactively visualize high resolution images representing the described experimental data.

	----		----

imported>HeikoNeuweger at 08:05, 29 January 2010

2010-01-29T08:05:55Z

← Older revision		Revision as of 10:05, 29 January 2010
Line 22:		Line 22:
	differences between the measurements. ColorizeMS is realized as web-start application which has been tested on Microsoft Windows, Mac OS X,		differences between the measurements. ColorizeMS is realized as web-start application which has been tested on Microsoft Windows, Mac OS X,
	Linux and Solaris . The project is licensed under the GNU Public License 3.0.		Linux and Solaris . The project is licensed under the GNU Public License 3.0.

			== Downloads ==

			Java applications for the can be downloaded [[ColorizeMSWiki/Downloads\|here]]

	== Requirements ==		== Requirements ==

imported>HeikoNeuweger at 14:05, 17 July 2009

2009-07-17T14:05:15Z

imported>HeikoNeuweger at 14:51, 20 May 2009

2009-05-20T14:51:11Z

← Older revision		Revision as of 16:51, 20 May 2009
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	to integer values.		to integer values.

	[[Image:ColorizeMSWiki$~~gui~~.png]]		[[Image:ColorizeMSWiki$gui2.png]]

	The ColorizeMS application provides functionality to map up to three experimental conditions and rapidly visualize qualitative		The ColorizeMS application provides functionality to map up to three experimental conditions and rapidly visualize qualitative

imported>HeikoNeuweger at 14:49, 20 May 2009

2009-05-20T14:49:59Z

← Older revision		Revision as of 16:49, 20 May 2009
Line 43:		Line 43:
	* Apply the visualization methods to various data sources, images from 2D gel electrophoresis measurements, GC- or LC-MS heatmaps		* Apply the visualization methods to various data sources, images from 2D gel electrophoresis measurements, GC- or LC-MS heatmaps
	* Colorize MS makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences of		* Colorize MS makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences of
	* Through the use of OpenGL functionality, the rapid zooming, scrolling and color blending of high resolution textures is delegated		* Through the use of OpenGL functionality, the rapid zooming, scrolling and color blending of high resolution textures is delegated to the Graphics Processing Unit and allows to interactively visualize high resolution images of the described experimental data.
	to the Graphics Processing Unit and allows to interactively visualize high resolution images of the described experimental data.

	----		----
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	[[Image:ColorizeMSWiki$meltdb.png]]		[[Image:ColorizeMSWiki$meltdb.png]]

	We have realized the exchange of experimental data form the metabolomics software suite MeltDB to the ColorizeMS ~~[[WebStart]]~~ application using on the fly generation of JNLP files which describe the input parameters of the software. We are therefore able to directly export 2D representations of chromatograms generated by MeltDB to ColorizeMS.		We have realized the exchange of experimental data form the metabolomics software suite MeltDB to the ColorizeMS Web Start application using on the fly generation of JNLP files which describe the input parameters of the software. We are therefore able to directly export 2D representations of chromatograms generated by MeltDB to ColorizeMS.

	[[Image:ColorizeMSWiki$meltdb-form.png]]		[[Image:ColorizeMSWiki$meltdb-form.png]]

← Older revision		Revision as of 16:05, 17 July 2009
Line 14:		Line 14:
	In this example, the retention time of the compounds is mapped to the x-axis and the mass-to-charge ratio is		In this example, the retention time of the compounds is mapped to the x-axis and the mass-to-charge ratio is
	represented on the y-axis. In GC- and LC-MS measurements the time axis is discretized by the scan rate of the instrument.		represented on the y-axis. In GC- and LC-MS measurements the time axis is discretized by the scan rate of the instrument.
	Each scan is represented in this visualization by one pixel and the discretization of the mass to charge ratio is done by rounding		Each scan is represented in this visualization by one pixel and the discretization of the mass-to-charge ratio is done
	to ~~integer values~~.		by rounding to nominal masses and binning the measured intensities.

	[[Image:ColorizeMSWiki$gui2.png]]		[[Image:ColorizeMSWiki$gui2.png]]

	The ColorizeMS application provides functionality to map up to three experimental conditions and rapidly visualize qualitative		The ColorizeMS application provides functionality to map up to three experimental conditions and rapidly visualize qualitative
	differences between the measurements. ColorizeMS is realized as web-start application and is licensed under the ~~Gnu~~ Public License 3.0.		differences between the measurements. ColorizeMS is realized as web-start application which has been tested on Microsoft Windows, Mac OS X,
			Linux and Solaris . The project is licensed under the GNU Public License 3.0.
	~~Currently the program has been tested on Windows, Mac OS X and Linux systems~~.

	== Requirements ==		== Requirements ==

	There ~~are several~~ requirements ~~which~~ are specified in the JNLP description of ColorizeMS and will be installed upon start of the application suing Java Web Start.		There software requirements are specified in the JNLP description of ColorizeMS and will be installed upon start of the application suing Java Web Start technology. The application relies on Java3D with OpenGL bindings:
	* [http://java.sun.com/javase/technologies/desktop/java3d/ Java3D technology]		* [http://java.sun.com/javase/technologies/desktop/java3d/ Java3D technology]
	* [https://jogl.dev.java.net/ OpenGL Bindings for Java]		* [https://jogl.dev.java.net/ OpenGL Bindings for Java]
	~~For further details check the Web Start definition page~~

	Please follow the instructions for installing a current version of Java3D on your Mac OS X machine if you experience any problems with the		Please follow the instructions for installing a current version of Java3D on your Mac OS X machine if you experience any problems with the
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	== Features ==		== Features ==

	* Visualize and compare up to three experimental conditions		* Visualize and compare up to three experimental conditions.
	* Interactively correct drifts in separation (e.g. retention time in GC- or LC-MS experiments)		* Interactively correct drifts in separation (e.g. retention time in GC- or LC-MS experiments).
	* Adjust the intensity of individual measurements to compensate for e.g. different amounts of sample that were ~~analyze~~		* Adjust the intensity of individual measurements to compensate for e.g. different amounts of sample that were analyzed.
	* Apply the visualization methods to various data sources, images from 2D gel electrophoresis measurements, GC- or LC-MS ~~heatmaps~~		* Apply the visualization methods to various data sources, images from 2D gel electrophoresis measurements, GC-, or LC-MS contour plots.
	* ~~Colorize MS~~ makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences of		* ColorizeMS makes use of the additive color mapping in the RGB color space and allows to intuitively grasp the main differences in the measured samples.
	* Through the use of OpenGL functionality, the rapid zooming, scrolling and color blending of high resolution textures is delegated to the Graphics Processing Unit and allows to interactively visualize high resolution images of the described experimental data.		* Through the use of OpenGL functionality, the rapid zooming, scrolling and color blending of high resolution textures is delegated to the Graphics Processing Unit and allows to interactively visualize high resolution images representing the described experimental data.

	----		----
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	[[Image:ColorizeMSWiki$meltdb.png]]		[[Image:ColorizeMSWiki$meltdb.png]]

	We have realized the exchange of experimental data form the metabolomics software suite MeltDB to the ColorizeMS Web Start application using on the fly generation of JNLP files which describe the input parameters of the software. We are therefore able to directly export 2D representations of chromatograms generated by MeltDB to ColorizeMS.		We have realized the direct exchange of experimental data form the metabolomics software suite MeltDB to the ColorizeMS Web Start application using on-the-fly generation of JNLP files which describe the input parameters of the software. We are therefore able to directly export 2D representations of chromatograms generated by MeltDB to ColorizeMS.

	[[Image:ColorizeMSWiki$meltdb-form.png]]		[[Image:ColorizeMSWiki$meltdb-form.png]]