ColorizeMSWiki: Difference between revisions
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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 from separation experiments. | ||
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$gui2.png]] | |||
In this example, the retention time of the compounds is mapped to the x-axis and the mass-to-charge ratio is | In this example, the retention time of the compounds is mapped to the x-axis and the mass-to-charge ratio is | ||
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by rounding to nominal masses and binning the measured intensities. | by rounding to nominal masses and binning the measured intensities. | ||
[[Image:ColorizeMSWiki$ | Support for 2D Gel Electrophoresis images as well as GC- or LC-MS experimental data is provided. | ||
[[Image:ColorizeMSWiki$twod.png]] | |||
ColorizeMS provides functionality to compare measurements from up to three experimental conditions and rapidly visualize qualitative | |||
differences | 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 | The ColorizeMS Java application for different platforms can be downloaded [[ColorizeMSWiki/Downloads|here]] | ||
== Requirements == | == 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: | |||
* [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] | ||
== 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 | * 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. | |||
---- | ---- | ||
Revision as of 10:12, 29 January 2010
File:ColorizeMSWiki$logo-small.png
ColorizeMS is a Java application that allows to qualitatively compare up to three experimental conditions from separation experiments.
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.
File:ColorizeMSWiki$gui2.png
In this example, the retention time of the compounds is mapped to the x-axis and the mass-to-charge ratio is represented on the y-axis. In GC- and LC-MS measurements the time axis is discretized by the scan rate of the instrument. Each scan is represented in this visualization by one pixel and the discretization of the mass-to-charge ratio is done by rounding to nominal masses and binning the measured intensities.
Support for 2D Gel Electrophoresis images as well as GC- or LC-MS experimental data is provided.
File:ColorizeMSWiki$twod.png
ColorizeMS provides functionality to compare measurements from up to three experimental conditions and rapidly visualize qualitative 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.
Downloads
The ColorizeMS Java application for different platforms can be downloaded 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
Java Web Start
Sample Data Sets