Bio-Linux

1. Bio-Linux 2.0 includes the following software: Bio-Linux Overview What is Bio-Linux? Bio-Linux is an integrated, bioinformatics-centred, computer system. By providing both standard favourite and cutting edge bioinformatics tools on a Linux-based system, it combines the benefits of being powerful, configurable, and easily updateable, 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. 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 EGTDC to enable researchers to quickly make the most of the capabilities of their Bio-Linux machine. A list of some of the bioinformatics software on the current version of Bio-Linux 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 RedHat Distribution. Thus, in addition to the core set of bioinformatics tools, Bio-Linux also contains all the security features and a wide range of general development tools (programming languages, compilers, MySQL, etc) common on Linux machines. System details: Bio-Linux 2.0 is based on RedHat 7.3 and Ximian Gnome, 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. MaxD (TRIBE-)Mcl MrBayes Mspcrunch NetBLAST (NCBI) Njplot Paml Phylip Primer3 R (stats language) Rasmol ReadSeq Seaview Splitstree T-coffee Tree-puzzle Wise ACT ARB Artemis APE BLAST (NCBI) Blixem ClustalW ClustalX Dotter, Emboss FastDNAml Fasta Forester/ATV GDE GeneSpring Hmmer Jalview The EGTDC partnership The EGTDC is committed to delivering a combination of open-source and commercial bioinformatics packages to EG awardees. Staff at this bioinformatics-based Data Centre includes 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 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 are adapting the “Nembase” system to provide EST analysis and data warehousing tools. Environmental Genomics Thematic Programme Data Centre CEH Oxford, Mansfield Rd, Oxford, OX1 3SR Website: http://envgen.nox.ac.uk Helpdesk email: helpdesk@envgen.nox.ac.uk Helpdesk phone: 01865 281976 Community Mailing list info: http://envgen.nox.ac.uk/mailinglist.html EGTDC Bio-Linux An integrated bioinformatics solution for the EG community ATV phylogenetic tree ClustalX showing DNA polymerase alignment GeneSpring showing yeast transcriptome MaxD loading probes for microarray analysis RasMol displaying 3D protein structure A Bio-Linux machine running bioinformatics applications