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Briefings in Bioinformatics Advance Access originally published online on August 9, 2006
Briefings in Bioinformatics 2006 7(3):287-296; doi:10.1093/bib/bbl026
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Open source tools and toolkits for bioinformatics: significance, and where are we?

Jason E. Stajich and Hilmar Lapp

Corresponding author. Jason E. Stajich, Department of Plant and Microbial Biology, University of California, Berkeley, 321 Koshland Hall Berkeley, CA 94720, USA. Tel: (919)684-2720; Fax: (919)681-1035; E-mail: jason.stajich{at}duke.edu

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2–3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

Keywords: bioinformatics, open source, software, genomics


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