Skip Navigation


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
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
7/3/287    most recent
bbl026v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (5)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Stajich, J. E.
Right arrow Articles by Lapp, H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Stajich, J. E.
Right arrow Articles by Lapp, H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
G. Alterovitz, A. Jiwaji, and M. F. Ramoni
Automated programming for bioinformatics algorithm deployment
Bioinformatics, February 1, 2008; 24(3): 450 - 451.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. J. Mungall, D. B. Emmert, and The FlyBase Consortium
A Chado case study: an ontology-based modular schema for representing genome-associated biological information
Bioinformatics, July 1, 2007; 23(13): i337 - i346.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.