ColorizeMSWiki: Difference between revisions

Latest revision as of 08:17, 26 October 2011

File:ColorizeMSWiki$logo-small.png

Downloads

The ColorizeMS Java application for different platforms can be downloaded here. A Java Web Start link for ColorizeMS is available here.

Requirements

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:

Features

Visualize and compare up to three experimental conditions.
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.
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.
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.

Integration with MeltDB

File:ColorizeMSWiki$meltdb.png

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.

File:ColorizeMSWiki$meltdb-form.png

Up to three measurements from any given experiment can be directly submitted to the ColorizeMS application.

Further information

User documentation

Sample Data Sets

@@ Line 2: / Line 2: @@
   [[Image:ColorizeMSWiki$logo-small.png]]
-ColorizeMS is a Java application that allows to qualitatively compare
+== Downloads ==
-up to three experimental conditions from separation experiments.
-Support for 2D Gel Electrophoresis images as well as GC- or LC-MS experimental data is provided.
+The ColorizeMS Java application for different platforms can be downloaded [[ColorizeMSWiki/Downloads|here]].
+A Java Web Start link for ColorizeMS is available [[ColorizeMSWiki/WebStart|here]].
- [[Image:ColorizeMSWiki$twod.png]]
-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.
-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.
-Each scan is represented in this visualization by one pixel and the discretization of the mass to charge ratio is done by rounding
-to integer values.
- [[Image:ColorizeMSWiki$gui.png]]
-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.
-Currently the program has been tested on Windows, Mac OS X and Linux systems.
 == 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.
+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]
 * [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
-ColorizeMS application.
-----
 == 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-, LC-, or GCGC-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
+* 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.
-to the Graphics Processing Unit and allows to interactively visualize high resolution images of the described experimental data.
 ----
@@ Line 52: / Line 29: @@
   [[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 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]]
@@ Line 63: / Line 40: @@
   [[ColorizeMSWiki/UserDocu|User documentation]]
- [[ColorizeMSWiki/WebStart|Java Web Start]]
   [[ColorizeMSWiki/DataSets|Sample Data Sets ]]