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Is NetBeans the #1 Bioinformatics Platform?

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A few days ago Geertjan posted some screenshots of a bioinformatics application on the NetBeans Platform. I was really very excited because besides being a programmer I'm also a geneticist and I've worked for a bioinformatics company for a long time. One of my first projects with the NetBeans Platform was a bioinformatics application, ChipInspector, that we ported to the NetBeans Platform.


ChipInspector is a tool that utilizes statistical analysis of high throughput gene expression data to calculate which genes are potentially active under certain conditions, e.g., in cancerous cells, in order to help track the root causes of this activity. 

The application Geertjan showed is in a very similar field. One of my projects was an application for the creation and analysis of signal transduction networks and we were working with the same data formats and data sources that this Quantitative Biology Tool is using. The people behind these applications even collaborate with the same institutons! And, it seems that besides business applications, more and more scientific applications are using the NetBeans Platform as their basis.

I wasn't the only one to be inspired by Geertjan's blog entry. Kevin Farnham, chief editor for Java.net, blogged about this same topic today. So I asked Geertjan if he knows about more bioinformatics applications on the NetBeans Platform. He sent me info about a couple that I would like to list here:

Quantitative Biology Tool

QBT is a tool that lets you define, visualize, annotate, and simulate biological systems of interest. It utilizes SBML, a very popular XML format for defining the models.


Another interesting application is an information fusion software platform called BioCAD. It utilizes local and global optimization for bio-network inference, text mining techniques for network validation and annotation, and Web services-based workflow techniques.


The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface.

The related website already lists a massive set of Modules to reuse. So they actually have used the NetBeans Platform to create their own platform that can be used for creating other applications


BiologicalNetworks is a Systems Biology software platform for biological pathways analysis, querying and visualization of gene regulation and protein interaction networks, metabolic and signaling pathways. It is equipped with filtering and visualization tools, to provide high quality, easily understood scientific presentation of your pathway analysis results. It has recently been ported to the NetBeans platform.


Then there is Instant JChem, an application in a very related area, which can be used to query large databases of chemical structures, mainly used in the pharmaceutical industry for querying huge databases of potentially biologically active compounds.

So, it seems the NetBeans Platform is used more and more in this context as a platform and to create more platforms for applications in biological sciences. If you know of more applications in this area, let us know. It would be cool to plug all of these applications together in order to create one enormous computational biology application, the largest bioinformatics application in the world! :-).

The Java Zone is brought to you in partnership with ZeroTurnaround. Check out this 8-step guide to see how you can increase your productivity by skipping slow application redeploys and by implementing application profiling, as you code!


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