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Briefings in Bioinformatics Advance Access originally published online on December 5, 2007
Briefings in Bioinformatics 2008 9(1):69-74; doi:10.1093/bib/bbm057
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group

Sean D. Mooney and Peter H. Baenziger

Corresponding author. Sean Mooney, Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th St, Suite 5000, Indianapolis, IN 46202; E-mail: sdmooney{at}iupui.edu

A common challenge for bioinformaticians, in either academic or industry laboratory environments, is providing informatic solutions via the Internet or through a web browser. Recently, the open source community began developing tools for building and maintaining web applications for many disciplines. These content management systems (CMS) provide many of the basic needs of an informatics group, whether in a small company, a group within a larger organisation or an academic laboratory. These tools aid in managing software development, website development, document development, course development, datasets, collaborations and customers. Since many of these tools are extensible, they can be developed to support other research-specific activities, such as handling large biomedical datasets or deploying bioanalytic tools. In this review of open source website management tools, the basic features of content management systems are discussed along with commonly used open source software. Additionally, some examples of their use in biomedical research are given.

Keywords: content management system, CMS, laboratory information management system, LIMS, website design, data management, open source software

Submitted: July 31, 2007. Received (in revised form): October 25, 2007.


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