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Bioinformatics Advance Access originally published online on January 3, 2008
Bioinformatics 2008 24(3):450-451; doi:10.1093/bioinformatics/btm602
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Automated programming for bioinformatics algorithm deployment

Gil Alterovitz 1,2,3,*, Adnaan Jiwaji 2 and Marco F. Ramoni 1,3

1Children's Hospital Informatics Program at the Division of Health Sciences and Technology, Harvard University and Massachusetts Institute of Technology, 2Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology and 3Harvard Partners Center for Genetics and Genomics, Harvard Medical School, Boston, USA.

*To whom correspondence should be addressed.


  Abstract

Summary: Many bioinformatics solutions suffer from the lack of usable interface/platform from which results can be analyzed and visualized. Overcoming this hurdle would allow for more widespread dissemination of bioinformatics algorithms within the biological and medical communities. The algorithms should be accessible without extensive technical support or programming knowledge. Here, we propose a dynamic wizard platform that provides users with a Graphical User Interface (GUI) for most Java bioinformatics library toolkits. The application interface is generated in real-time based on the original source code. This platform lets developers focus on designing algorithms and biologists/physicians on testing hypotheses and analyzing results.

Availability: The open source code can be downloaded from: http://bcl.med.harvard.edu/proteomics/proj/APBA/

Contact: gil{at}mit.edu

Associate Editor: Chris Stoeckert

Received on July 28, 2007; revised on December 1, 2007; accepted on December 1, 2007

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