Recent Posts by Geertjan Wielenga

Has the final frontier been reached for Java EE 6 tools in NetBeans IDE? In the daily builds for the upcoming NetBeans IDE 7.2, there is now code completion in calls to EntityManager.createNamedQuery of named queries defined within JPA entity classes: Above, the cursor is between the quotation marks in "em.createNamedQuery". Now all possible named queries are shown, from all entity classes in the application, and as I type the completion box narrows to match the currently...

Behind the scenes of the above is MindCite and its CiteLink product, "a ground-breaking, RDF-Native, Link-Analysis tool capable of querying, visualizing, and analyzing information from triple-stores and semantic-services. Such information may be the result of Semantic-Integration of databases, GIS systems, CDR analysis, analyzed time-series data, text and more": Further info: http://www.mindcite.com/ http://aiccse.wordpress.com/2009/04/28/mindcite-joins-aicc/

GenDB is a genome annotation system created at Bielefeld university (by Lukas Jelonek) in Germany. The application supports automatic and manual genome annotations. It is based on a client/server architecture where the client is implemented using the NetBeans Platform to enable easy integration of new modules. Currently it supports common visualizations for genome annotations. It is not restricted to the GenDB server as adata source but has a plugin mechanism and an API for...

Proteus is an application for 2D-gel-based proteomics data management created at Bielefeld university (by Konstantin Otte and Nils Hoffmann) in Germany. The software lets you manage gelelectrophoresis experiments, browse gels, plan picking on microtiter plates, and manage gel-plate connections. It also enables the planning of MALDI mass spectrometry identification experiments by planning and management of MALDI target plates and inputs of identification data. Proteus collects...

QuantiSphere is a desktop application for management, analysis, and evaluation of fluorescence microscopy images. It is developed as a part of a new protein quantification method at Bielefeld university (by Samy Slaih) in Germany. The system contains all the tools needed for the development of this method, such as cross microscope compatibility and file management, object recognition, analysis, and visualization modules. A screenshot:

Maui, the Maltcms User Interface, is an application created at Bielefeld university (by Nils Hoffmann) in Germany for interactive visualization, exploration, annotation, batch-processing and statistical analysis of raw data from GC/LC-MS and GCxGC-MS experiments in the metabolomics context. Users may define custom mass spectral databases for identification purposes and can interactively compare their spectra to those in the database. Maui includes a statistical frontend backed...

Delta2D is an advanced 2D gel analyzer, by DECODON, a bioinformatics company. Delta2D provides image warping, proteome maps, web scouts, and quantitative analysis letting you extract more information from your gels, in a fraction of the time needed by conventional packages. A screenshot:

In the IDE, a cool feature is that you can change the Font & Color profile to "Norway Today" (shown below) or "City Lights", both of which result in your code editor having a dark background with fonts rendered in different colors to the standard black: However, as NetBeans user Paul Cinnamond writes in an e-mail I received yesterday: "Put yourself in the shoes of someone that changed the editor background color and then realized they need to change the other windowcolors in...

"Who is that amazing musician?" I hear you wondering. That's Zoran, one of the members of the NetBeans governance board and also the NetBeans Dream Team. He is a lecturer at the University of Belgrade in Serbia, where he's set up the NetBeans User Group Serbia and regularly gives courses about creating Java desktop applications on the NetBeans Platform. He's also a very nice guy, if you're ever in Belgrade you should visit him and talk about... Java.