Sunday Jan 12, 2014

Life Sciences Platform on the NetBeans Platform

GenBeans is a tool for DNA sequence analysis created in San Diego, California, for molecular biologists. Research scientists working with DNA molecules face the dilemma of manipulating DNA sequences, often represented as simple text strings, and integrating vast amounts of sequence-dependent features at the same time. For genome-wide analysis, both are rather unchangeable static entities that can be easily represented together.

On the other hand, sequence editing is complicated by an ever-changing set of features, some wanted, some desirable, some not. Design errors may translate in months of work. A fascinating aspect, from that point of view, of NetBeans IDE is its language support with its automatic annotation as you type and rich set of meta-information because DNA sequence is comparable to a language where features and motifs are the words, it is interesting to approach DNA sequence editing & analysis in the same way NetBeans IDE handles programming languages. 

In the first screenshot, you see GenBeans during the analysis of a primer (short sequence used to amplify or sequence DNA), while the second screenshot shows some restriction enzyme analyzes.

Later, a second intermediate application named BioBeans became necessary to bring together all biology-related modules and offer a branching point for people interested in deriving works under an open-source license. Below you see a composition showing multiple BioJava demos at the same time, including sequencing trace, BLAST result (sequence homology search in sequence database) and sequence alignment in the output.

Therefore, GenBeans is a close-source suite build on top of BioBeans. Beneath BioBeans is StarBeans, which serves as a foundation for the BioBeans and GenBeans projects. StarBeans offers a standard look and feel, a project-free file management system, file editing using the NetBeans editor, and an embedded web browsing based on DJ Native Swing. StarBeans is written in Java and is fully open source.

StarBeans accumulates around 200 valid downloads per months, both sources and binaries, while BioBeans and GenBeans are newer and have smaller set of users, probably less than 100.

Future developments will be focusing on automatic annotation and annotation through varied web-based services to query public databases, and on polishing of the BioBeans layer (mainly basic DataObject for the multitude of sequence data formats). Also JavaFX is likely to make its appearance, surely to replace the current implementation of the embedded browser. The incoming release will be based on NetBeans Platform 7.4 and will concentrate on stability and usability.

The plan is to make an official release of BioBeans on the BioJava mailing list. Potential users are basically the entire community of Java programmers in life sciences. There are several open source platforms out there. Ugene is a sophisticated sequence editor (http://genome.unipro.ru) written in C++, while Bioclipse (http://www.bioclipse.net/) is an ambitious project based on Eclipse, more oriented toward drug development and chemistry. So, the ambition for BioBeans is very relative at this time but if a few small projects were to integrate with the BioBeans platform, that would be already a success.

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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