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Geertjan's Blog

  • March 1, 2010

Plasmid Microarray Designer on the NetBeans Platform

Geertjan Wielenga
Product Manager
PLASMID is a tool for designing plasmid microarrays by using existing mixed microarray data or using virtual microarray data. PLASMID combines clustering methods, probe ranking methods, and stepwise discriminant analysis to aid in the design of optimized, mixed-plasmid microarrays. These microarrays can be used subsequently for classification and comparative genetics of plasmids.

The above information I copied from the page where you can freely download PLASMID, which is a Swing application based on the NetBeans Platform. The page claims that the application currently supports Windows only, but it seems to work fine on Ubuntu too, based on these screenshots I took after downloading the application and following the startup scenario:

First, open the sample dataset file:

Then, process the file via a wizard in the application:

Finally, view (and save) the result:

More about the application can be read in "A Java-based tool for the design of classification microarrays". Why was the NetBeans Platform used as the basis of this application, according to this document? Well, here you go:

"The NetBeans platform was chosen for development because addition of new functions is easily implemented. Also, many of the tasks common to desktop applications are provided by NetBeans. These include user interface management (e.g., menus and toolbars), user settings management, storage management (saving and loading any kind of data), window management, and wizard framework (supporting step-by-step dialogs). Each function is implemented as a NetBeans module and can be installed or removed easily without affecting existing functions. Java is a platform-independent programming language, so although PLASMID has been developed using the Windows operating system, it will be relatively easy to adapt it to other operating systems. We intend to extend PLASMID to both the Linux and Mac OS X operating systems. In addition to Java, PLASMID uses code written using the C++ programming language. C++ is needed for computationally intensive tasks that require greater speed and efficiency. The use of two different programming languages is transparent to the user."

Hurray, yet another NetBeans Platform application!

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