Bio-Linux 3.0

An integrated bioinformatics solution for the EG community

ClustalX showing DNA polymerase alignment

GeneSpring showing yeast transcriptome

ATV phylogenetic tree

MaxD loading probesfor microarray analysis

RasMol displaying 3D protein structure

A Bio-Linux machine running bioinformatics applications

Bio-Linux Overview

What is Bio-Linux?

Bio-Linux is an integrated, bioinformatics-centric, computer system. By providing both a standard base and set of cutting edge bioinformatics tools on a Linux-based system, it combines the benefits of being powerful, configurable, and easily updated, with the ease of use and potential for software integration required for the handling and analysis of biological data being produced by EG-funded labs. In addition Bio-Linux comes with Condor pre-installed, simplifying the creation of loose compute clusters within a laboratory or department.

From the biology side:

Bio-Linux gives biologists access to many bioinformatics programs and packages in a user-friendly computing environment. In addition, a high level of support and help is available from the Environmental Genomics Thematic Data Centre (EGTDC) to enable researchers to quickly make the most of the capabilities of their Bio-Linux machine. A list of some of the categories of bioinformatics software on Bio-Linux 3.0 can be found on the right hand side of this poster.

From the computing side:

Bio-Linux makes it easy to get started working on the Linux platform by offering a custom designed version of Linux based on the stable and well developed Red Hat Distribution. Thus, in addition to the core set of bioinformatics tools available on Bio-Linux, it contains all the security features and a wide range of general development tools (programming languages, compilers, MySQL, etc) common on Linux machines. Condor is now preinstalled making it a simple task to create loose clusters to harness the CPU and RAM of computers that are not in use at the time.

System details:

Bio-Linux 3.0 is based on Red Hat 9.0 and Gnome 2.2, giving users a stable, flexible and proven distribution of Linux.

The Bio-Linux hardware, supplied to PI's and Co-I's on EG grants is a Dell Precision 650, dual Xeon CPU (2.4 Ghz) workstation with 1Gb RAM and 160Gb of internal storage. The machine comes with a 17'' flat panel display. The system is shown in the main figure.

The EGTDC partnership

The EGTDC is committed to delivering a combination of open-source and commercial bioinformatics packages and support to the EG community. Staff include bioinformaticians, database programmers and computing experts at three locations: CEH Oxford, the University of Manchester and the University of Edinburgh. The EGTDC also has a strong partnership with the commercial group Silicon Genetics.

The bioinformatics solutions provided include licenses for the GeneSpring transcriptomics software for all EG funded researchers and access to a GeNet microarray repository. Partners at the University of Manchester are contributing an open source microarray analysis and database system, maxd, and partners at the University of Edinburgh provide an EST analysis pipeline which includes trace2dbest and PartiGene.

Bio-Linux 3.0 includes pre-installed software for:

•sequence analysis•phylogenetics•sequence alignment•genome annotation•QTL analysis•EST pipelines•transcriptomics

System features

•based on Red Hat 9.0•automatic updates using yum•ready for clustering using Condor•many development tools including BioPerl, BioJava, BioPython, BioRuby and the Eclipse IDE

Website: http://envgen.nox.ac.ukHelpdesk email: helpdesk@envgen.nox.ac.ukHelpdesk phone: 01865 281976Bio-Linux mailing list:http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linuxCommunity Mailing list info: http://envgen.nox.ac.uk/mailinglist.html

Environmental Genomics Thematic Programme Data Centre

CEH Oxford, Mansfield Rd, Oxford, OX1 3SR

EGTDC