ColorizeMSWiki: Difference between revisions

Latest revision as of 07:17, 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 1: / Line 1: @@
 __NOTOC__
-= ColorizeMS =
+ [[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 ColorimzeMS 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.
+The software requirements are specified in the JNLP description of ColorizeMS and will be installed upon start
-- [http://java.sun.com/javase/technologies/desktop/java3d/ Java3D technology]
+of the application using Java Web Start technology. The application relies on Java3D with OpenGL bindings:
-- [https://jogl.dev.java.net/ OpenGL Bindings for Java]
+* [http://java.sun.com/javase/technologies/desktop/java3d/ Java3D technology]
+* [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
+== Features ==
-ColorizeMS application.
-== 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.
-- 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 analyze
-- Apply the visualization methods to various datasources, 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
-- 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.
 == Integration with MeltDB ==
-[[Image:ColorizeMSWiki$meltdb.png]]
+ [[Image:ColorizeMSWiki$meltdb.png]]
-We have realized the exchange of experimental data form the Metabolomics software suite MeltDB to the ColorizeMS [[WebStart]] application using web services technology and the modular generation of JNLP files which describe the input parameters of the software. We are therefore able to export information on chromatogram alignments generated by the various tools in MeltDB to the ColorizeMS images which renders the linear interpolation of aligned features between thje individual raw data representations.
-== User documentation ==
-Select your png files representing experimental results and map them to the three color channels in ColorizeMS
-[[Image:ColorizeMSWiki$filechooser.png]]
-Navigate and zoom the visualization using the right mouse button and the scroll wheel. Users may adjust the position of the three different texture layers to compensate drifts using the buttons to the right.
- [[Image:ColorizeMSWiki$mover.png]]
-To compensate differences between the amount of sample measured, the intensity of individual channels can be modified. It is also possible to completely
-remove the influence of individual layers by setting the intensity to zero.
- [[Image:ColorizeMSWiki$alpha.png]]
-ColorizeMS allows to rapidly identify common characteristics and features of the experimental dataset.
- [[Image:ColorizeMSWiki$main.png]]
-== Sample Data ==
-D representation of GC-MS measurements on Thermo Finnigan [[IonTra]] GC-MS measurement of ''Xanthomonas campestris'' pv. campestris grown under
-the three different carbon sources Glucose, Succinate and Mannitol.
- [[Image:ColorizeMSWiki$gcred.png]]
- [[Image:ColorizeMSWiki$gcblue.png]]
- [[Image:ColorizeMSWiki$gcgreen.png]]
-Three 2D gel electrophofesis scans of the separated proteome of the organism Xanthomonas campestris pv. campestris. The two dimensional gel electrophoresis
-allows to separate the proteins by weight and polarity and the coloring of the spots has been achieved by Coomassie Blue.
- [[Image:ColorizeMSWiki$gered.png]]
- [[Image:ColorizeMSWiki$geblue.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.
-  [[Image:ColorizeMSWiki$gegreen.png]]
+  [[Image:ColorizeMSWiki$meltdb-form.png]]
-== Java Web Start ==
+Up to three measurements from any given experiment can be directly submitted to the ColorizeMS application.
- [[Image:ColorizeMSWiki$ws.png]]
+----
- - [https://meltdb.cebitec.uni-bielefeld.de/colorizems-mac.jnlp ColorizeMS WebStart (MAC)]
+== Further information ==
- - [https://meltdb.cebitec.uni-bielefeld.de/colorizems.jnlp ColorizeMS WebStart]
-== Download jar archive of ColorizeMS ==
+ [[ColorizeMSWiki/UserDocu|User documentation]]
-  - [https://meltdb.cebitec.uni-bielefeld.de/colorizems.jar ColorizeMS Application]
+  [[ColorizeMSWiki/DataSets|Sample Data Sets ]]