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Briefings in Bioinformatics Advance Access published online on August 9, 2006
Briefings in Bioinformatics, 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
Received October 11, 2005
Accepted June 28, 2006

Original Papers

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

Jason E. Stajich * and Hilmar Lapp

* To whom correspondence should be addressed.
Jason E. Stajich, E-mail: jason.stajich{at}duke.edu


  Abstract

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.

Jason Stajich, received his PhD from Duke University in 2006 and is currently a Miller research fellow at University of California, Berkeley. He serves as the President of the Open Bioinformatics Foundation, and has authored numerous modules in BioPerl and GMOD.

Hilmar Lapp, joined NESCent as Assistant Director of Informatics in May 2006. He has served on the Board of Directors of the Open Bioinformatics Foundation since 2001, and leads development of several open source projects and modules. National Evolutionary Synthesis Center, Durham, NC 27708, USA.


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