BioconductorBuntu

BioconductorBuntu - A Linux Distribution that Implements a Web-Based DNA Microarray Analysis Server

Paul Geeleher, Dermot Morris, John P. Hinde and Aaron Golden

Bioinformatics Advance Access (23/3/09) doi:10.1093/bioinformatics/btp165

BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, and provides a user friendly web-based graphical user interface to many of the tools developed by the Bioconductor Project, whether locally or across a network. Installation is a turn-key procedure, simply based on booting off the installation CD or image file. In its current version, several microarrays analysis pipelines are supported including oligonucleotide (e.g. Affymetrix Genechips), dual or single dye (e.g. Exqion miRNA arrays) experiments, with the existing set of preprocessing methods for normalization, background correction and so on are easily expanded.

The entire system itself is designed to be extensible, by server side integration of further relevant Bioconductor modules as required, facilitated by its straightforward pipeline construction using the underlying Python scripting environment. This makes BioconductorBuntu particularly flexible as regards the development of user-friendly processing procedures to facilitate the analysis of next-generation sequencing datasets. The system is best installed on a dedicated network server, allowing any number of registered individuals connected to the same LAN to make use of its capabilities.

Availability: BioconductorBuntu is available for download under a creative commons license ISO file of full BioconductorBuntu Installation (Ubuntu + BioconductorBuntu) or BioconductorBuntu Debian package to install on an existing Ubuntu system. A zip file containing all relevant scripts is available here. A zip file containing the Estrogen datasets typically used in numerous Bioconductor tutorials may be found here.

It is recommeded that you install BioconductorBuntu on a dedicated server using the supplied ISO file. For testing purposes we recommend installing the BioconductorBuntu in a virtual machine like VirtualBox or VMWare Server. This is a very straighforward procedure and will not affect any existing installation. NOTE: THE ISO FILE MUST BE BURNED TO A DVD AS IT IS TOO BIG TO FIT ON A CD. BioconductorBuntu can now also be installed on a Ubuntu system using a Debian package. This is in a Beta stage and is not recommended for use on a production machine. If this is the case it is suggested that you set up the component required manually. To install the debian packge, open a termial window, navigate to the directory where you have downloaded the package and type: sudo dpkg -i debian.deb NOTE: YOU WILL BE ASKED FOR YOUR MYSQL ROOT PASSWORD DURING INSTALLATION. THIS IS REQUIRED TO CONFIGURE THE DATABASE. MAKE SURE YOU HAVE IT OR INSTALLATION WILL NOT BE ABLE TO FULLY COMPLETE. ALSO ENSURE THAT YOU'RE INTERNET CONNECTION IS FULLY WORKING AND PROXY SETTINGS ARE CONFIGURED TO ALLOW DOWNLOADING OF REQUIRED PACKAGES. Once the system is installed navigate to "http://localhost/cgi-bin/login.py" to login if you are connecting from the server itself, or "http://servername/cgi-bin/login.py" if connecting from a remote machine.

Documentation: Handbook [1.9 megs]
Individual Sections of Handbook: Introduction to Genomics And Microarrays, Microarray analysis, Using the System, Installation Instructions

BioconductorBuntu is the result of a collaboration between Paul Geeleher, Dr. Aaron Golden and Professor John Hinde (NUI Galway) and Dr. Dermot Morris (Teagasc), and has been supported by a Teagasc Walsh Fellowship and Science Foundation Ireland (05/RFP/CMS0001).

Feel free to contact BioconductorBuntu's author, Paul Geeleher (paulgeeleher-at-gmail.com) if you have any questions on this software.

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