Geertjan's Blog

  • January 12, 2014

Life Sciences Platform on the NetBeans Platform

Geertjan Wielenga
Product Manager

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.

Join the discussion

Comments ( 1 )
  • Sean Phillips Sunday, January 12, 2014

    One of the points I think you are making and one that I personally like is that the software developers here are treating the problem of working with Genetic material similarly to how developers work with code. There appears to be a level of complexity in information sources including searching and linking them together. These are the problems that developers have had and solved for years with Integrated Development Environments.

    Clearly if your problem set can be treated like a document/data set workflow like this then something like the NetBeans Platform is ideal.

Please enter your name.Please provide a valid email address.Please enter a comment.CAPTCHA challenge response provided was incorrect. Please try again.