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

Full 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.

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Author information

Author/s: Stajich, Jason E (JE); Lapp, Hilmar (H);

Affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA. jason.stajich(-atsign-)duke.edu

Journal and publication information

Publication Type: Journal Article; Review

Journal: Briefings in bioinformatics (Brief Bioinform), published in England. (Language: eng)

Reference: 2006-Sep; vol 7 (issue 3) : pp 287-96

Dates: Created 2006/09/11; Completed 2006/11/03;

PMID: 16899494, status: MEDLINE (last retrieval date: 12/26/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Algorithms
Computational Biology - trends

Databases, Factual - trends
Software

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