Tuesday Dec 01, 2009

Visual Acorn: Bioinformatics on the NetBeans Platform

Visual Acorn is a bioinformatics project on the NetBeans Platform. It is part of a larger project, called ACORN. ACORN, managed by Jacek Sroka (University of Warsaw) and Andrzej Kierzek (Surrey University), is a grid-based web server for constraint-based modeling and visualization of genome scale metabolic reaction networks.

The developer behind Visual Acorn is Mateusz Markowski, a student from one of the courses Karol Harezlak and I did in Poland, for the Warsaw JUG on 22-23 November 2008. Visual Acorn enforces authentication, after which you can draw visualizations (pathway maps) of genome scale metabolic reaction network models. You can save these visualizations in a MySQL database on a sysbio3 server at Surrey University. Furthermore, visualizations can be managed (save/edit/delete) and you can display visualization results of Flux Balance Analysis, which is a calculation of the maximal theoretical value of the objective function under media conditions specified by user-linear programming.

Below are some screenshots Mateusz sent me:

So, in addition to the rat brain analysis application, and the list of applications discussed here by Toni, this is yet another bioinformatics application on the NetBeans Platform.

About

Geertjan Wielenga (@geertjanw) is a Principal Product Manager in the Oracle Developer Tools group living & working in Amsterdam. He is a Java technology enthusiast, evangelist, trainer, speaker, and writer. He blogs here daily.

The focus of this blog is mostly on NetBeans (a development tool primarily for Java programmers), with an occasional reference to NetBeans, and sometimes diverging to topics relating to NetBeans. And then there are days when NetBeans is mentioned, just for a change.

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