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Open Access Methodology article

HotSwap for bioinformatics: A STRAP tutorial

Christoph Gille1* and Peter N Robinson2

Author Affiliations

1 Institute for Biochemistry, Charité University Hospital, Humboldt University Berlin, Germany

2 Institute of Medical Genetics, Charité University Hospital, Humboldt University Berlin, Germany

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BMC Bioinformatics 2006, 7:64  doi:10.1186/1471-2105-7-64

Published: 9 February 2006

Abstract

Background

Bioinformatics applications are now routinely used to analyze large amounts of data. Application development often requires many cycles of optimization, compiling, and testing. Repeatedly loading large datasets can significantly slow down the development process. We have incorporated HotSwap functionality into the protein workbench STRAP, allowing developers to create plugins using the Java HotSwap technique.

Results

Users can load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs. Saving changes to the Java file causes STRAP to recompile the plugin and automatically update its user interface without requiring recompilation of STRAP or reloading of protein data. This article presents a tutorial on how to develop HotSwap plugins. STRAP is available at http://strapjava.de webcite and http://www.charite.de/bioinf/strap webcite.

Conclusion

HotSwap is a useful and time-saving technique for bioinformatics developers. HotSwap can be used to efficiently develop bioinformatics applications that require loading large amounts of data into memory.