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Geertjan's Blog

  • August 13, 2010

Research in Metabolomics and Proteomics on the NetBeans Platform

Geertjan Wielenga
Product Manager
YANPA (yet another NetBeans Platform application) comes from Bielefeld University in Germany. There, Nils Hoffmann is a PhD student in the area of metabolomics. He's also the main author of maltcms.sourceforge.net, an application framework mostly geared towards the definition and execution of data processing and analysis pipelines for data from machinery such as gas and liquid chromatography mass spectrometers.

Nils writes:

"I have just started using the NetBeans Platform about 8 months ago, trying to code up a simple viewer application for our processing results (basically, structured directories containing output files of our pipelines). This supports opening our result directories, which already contained a workflow.xml file in the first level hierarchy, as projects and displaying all registered file types with appropriate TopComponents. Currently, we are writing additional modules and a new project type, which supports creation of processing pipelines using the Visual Library and the Wizard API. The complete application will then be available additionally to maltcms as ChromAUI."

Here are some cool screenshots he sent accompanying the description above:

Caption: Shows the aggregation support for CSV files by column, which allows to view processing results of individual files within one plot.

Caption: Maltcms uses simple configuration files to define processing pipelines and to configure each individual element. The pipeline editor and property wizard for individual processing element configuration will make this task a lot more user-friendly.

Caption: The GCxGC-MS heatmap viewer displays two-dimensional intensity surfaces and allows the user to select and inspect mass spectra within the heatmap. Additional information can also be displayed on top and to the side of the heatmap.

Caption: When comparing GC-MS, LC-MS or GCxGC-MS data, global distance or similarity values are calculated in order to cluster and compare the files to each other. In this case, red means max similarity, while blue means min similarity.

Looks like a great application and I'm hoping we'll be holding a new NetBeans Platform Certified Training at Bielefeld University in the coming months!

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