Toni Epple works as a consultant for Eppleton (http://www.eppleton.de) in Munich, Germany. In his spare time he's an active member of the Open Source community as a community leader for JavaTools community (http://community.java.net/javatools/), moderator of the XING NetBeans User Group (http://www.xing.com/group-20148.82db20), founder of the NetBeans User Group Munich (http://tinyurl.com/5b8tuu), member of the NetBeans Dream Team (http://wiki.netbeans.org/NBDTCurrentMembers) and blogger (http://www.eppleton.de/blog). Toni is a DZone MVB and is not an employee of DZone and has posted 51 posts at DZone. You can read more from them at their website. View Full User Profile

Is NetBeans the #1 Bioinformatics Platform?

09.29.2009
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A few days ago Geertjan posted some screenshots of a bioinformatics application on the NetBeans Platform. I was really very excited because besides being a programmer I'm also a geneticist and I've worked for a bioinformatics company for a long time. One of my first projects with the NetBeans Platform was a bioinformatics application, ChipInspector, that we ported to the NetBeans Platform.

ChipInspector

ChipInspector is a tool that utilizes statistical analysis of high throughput gene expression data to calculate which genes are potentially active under certain conditions, e.g., in cancerous cells, in order to help track the root causes of this activity. 

The application Geertjan showed is in a very similar field. One of my projects was an application for the creation and analysis of signal transduction networks and we were working with the same data formats and data sources that this Quantitative Biology Tool is using. The people behind these applications even collaborate with the same institutons! And, it seems that besides business applications, more and more scientific applications are using the NetBeans Platform as their basis.

I wasn't the only one to be inspired by Geertjan's blog entry. Kevin Farnham, chief editor for Java.net, blogged about this same topic today. So I asked Geertjan if he knows about more bioinformatics applications on the NetBeans Platform. He sent me info about a couple that I would like to list here:

Quantitative Biology Tool

QBT is a tool that lets you define, visualize, annotate, and simulate biological systems of interest. It utilizes SBML, a very popular XML format for defining the models.

BioCAD

Another interesting application is an information fusion software platform called BioCAD. It utilizes local and global optimization for bio-network inference, text mining techniques for network validation and annotation, and Web services-based workflow techniques.

BioSPICE

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface.

The related website already lists a massive set of Modules to reuse. So they actually have used the NetBeans Platform to create their own platform that can be used for creating other applications

BiologicalNetworks

BiologicalNetworks is a Systems Biology software platform for biological pathways analysis, querying and visualization of gene regulation and protein interaction networks, metabolic and signaling pathways. It is equipped with filtering and visualization tools, to provide high quality, easily understood scientific presentation of your pathway analysis results. It has recently been ported to the NetBeans platform.

InstantJChem

Then there is Instant JChem, an application in a very related area, which can be used to query large databases of chemical structures, mainly used in the pharmaceutical industry for querying huge databases of potentially biologically active compounds.

So, it seems the NetBeans Platform is used more and more in this context as a platform and to create more platforms for applications in biological sciences. If you know of more applications in this area, let us know. It would be cool to plug all of these applications together in order to create one enormous computational biology application, the largest bioinformatics application in the world! :-).

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Comments

Chris Roberts replied on Tue, 2009/09/29 - 10:26pm

I don't know enough about bioinformatics to answer your question, and I'm not trying to start a Netbeans-vs-Eclipse flamewar, but you might want to check out the Bioclipse project at http://www.bioclipse.net/ to see what one group is doing in the bioinformatics space using Eclipse.

Toni Epple replied on Tue, 2009/09/29 - 11:13pm

Eclipse RCP is always an option, and there are many applications using Eclipse. In the scientific context with it's specific visualization needs I would personally nevertheless always prefer to work with a Swing based platform.

In my experience SWT and Eclipse RCP has it's focus on business applications with standard forms and tables, while Swing is more flexible and easier to use when you need non-standard components and visualizations, and that's why teams with such needs tend to choose Swing (like e.g. described here by Northrop Grumman: http://blogs.sun.com/geertjan/entry/netbeans_eclipse_comparison_slides_java).

But I don't want to start a flamewar about SWT and Swing either :-). I'm sure that there are some nice Eclipse RCP based applications in this field as well, and maybe Bioclipse is a good example.

Janko Diminic replied on Wed, 2009/09/30 - 8:54am

ClustScan (the Cluster Scanner) is a bioinformatics programs that takes a "top down" approach to the annotation of gene clusters encoding Thiotemplate Modular Systems (TMS).

This program is a linux server as backend and Eclipse RCP client application. Eclipse RCP has proved to be the most satisfying solution in terms of documentation and general application development.

Wai Ho replied on Wed, 2009/09/30 - 10:09am in response to: Janko Diminic

Pity though that Eclipse stuff doesn't look native (but I dont care so much about that) and that Swt is used.

Richard Adams replied on Fri, 2010/03/19 - 5:52am

At the University of Edinburgh there are several teams working on Eclipse based applications for Systems Biology: SBSI (www.sbsi.ed.ac.uk) Biopepa (www.biopepa.org) and Edinburgh Pathway Editor (www.pathwayeditor.org) Our users (at least SBSI )like the Eclipse type UI - (wizards. help/update etc, workbench etc) and since systems biology involves constructing computational models, access to IDEs is also useful for more technically minded people. For graphing we use the JFreeChart bridge which is pretty adequate for our needs. Having said this I've no experience of Netbeans - just wanted to publicize some more Eclipse based biology type projects.

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Matt Coleman replied on Mon, 2013/04/08 - 2:56am

i believe it is no.1!!

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Cata Nic replied on Mon, 2013/09/02 - 4:40pm

Which is the solution used for implementation into the bioinformatics platform? Is there a good way to find a fast answer?

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