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NEBC Bio-Linux - a one-stop shop for bioinformatics tools in a Linux context – version 5.0 released
The NERC Environmental Bioinformatics Centre (NEBC), based at the UK Centre for Ecology & Hydrology, has released the latest version of NEBC Bio-Linux, a specialised computing system designed for the environmental genomics research community.
The rapid growth of molecular data from the fields of genomics, metagenomics and related ‘omic disciplines requires ever improving methods of data collection, storage and analysis. NEBC has addressed these needs by providing a freely available computing platform designed to provide a one-stop shop for accessing a wide range of standard and cutting-edge bioinformatics tools in a Linux context. Intended users of NEBC Bio-Linux 5.0 range from students entering the field of bioinformatics and new users of Linux to institutional teaching labs and expert computational biology groups well versed in Linux.
Previously NEBC Bio-Linux was only easily accessible to NERC funded researchers through an application process. With the release of version 5.0, this system is available online for easy download. The simplified access means researchers worldwide can also benefit from the opportunities offered by Bio-Linux. Researchers in North America, Europe, New Zealand, India, Iran, Africa and China have already taken advantage of Bio-Linux and many more users are anticipated as the field of bioinformatics continues to grow rapidly.
Dawn Field, Director of NEBC said,“ To apply information technology to the field of molecular biology researchers need access to multi-user, networked machines that are fast and contain a large suite of software. The NEBC Bio-Linux project has distributed the specialist skills and expertise needed to build this type of infrastructure within the UK. The result is a new generation of PhD students and postdocs in this community with more sophisticated computing skills. With the release of version 5.0 we aim to allow the rest of the world to take advantage of these developments.”
NEBC’s main funder, the UK Natural Environment Research Council is further supporting the implementation of Bio-Linux by funding a new NERC Environmental Bioinformatics Facility at the Centre for Ecology & Hydrology. This new facility, the fifth node of the NERC Molecular Genetics Facility (MGF), will become fully operational later in 2009 and it will be possible for reseachers to cost Bio-Linux and associated bioinformatics support into NERC grant applications. The intention is that Bio-Linux will become the underpinning computational environment for all activities within the MGF-Oxford node.
NEBC Bio-Linux was conceived in 2002 as part of the data management plan of the NERC Environmental Genomics Science Programme. Dr Pamela Kempton, of NERC said, “The Bio-Linux project has fully delivered against our expectations for the project. We are pleased to see this new development and the potential for Bio-Linux to reach a wider user audience”.
Dr Jason Snape, based within AstraZeneca UK Ltd. and the Science Co-ordinator of the two NERC Environmental Genomics Programmes, said, “NEBC and Bio-Linux were established at the outset of the NERC investment in genomics. This was a highly strategic investment aimed at building a community of environmental scientists at the forefront of genomics research that had access to the most sophisticated informatics infrastructure, technical support, advice and training that was available.” Dr Snape added, “The global success of Bio-Linux and the efforts of the NEBC team in promoting high quality training and data management standards has delivered above and beyond the original vision of the Environmental Genomics Steering Committee. NEBC truly adds value to the NERC environmental genomics research community.”
Additional information
A press release was issued to coincide with the release of NEBC Bio-Linux 5.0.
A description of the NEBC Bio-Linux system can be found in Field et al. (2006) Bioinformatics for Biologists: from Famine to Feast, Nature Biotechnology, 24, 801 - 803. (subscription required)
Links to more information on the Bio-Linux system:
- Centre for Ecology & Hydrology - Environmental Genomics research activities
- The NERC Environmental Bioinformatics Centre (NEBC) (external link)
- NEBC Bio-Linux project (external link)
- Bio-Linux on Wikipedia (external link)
The NERC Environmental Bioinformatics Centre (NEBC)
NEBC is a dedicated bioinformatics and data management centre that works to develop and implement solutions for NERC environmental ‘omics researchers. NEBC was originally based at the Centre for Ecology & Hydrology’s research site in Oxford before moving to the CEH site at Wallingford, and is a collaboration between research groups at the Centre for Ecology & Hydrology, the University of Manchester and the European Bioinformatics Centre. The NEBC team of bioinformaticians and data managers are responsible for the development of a variety of open source projects including NEBC Bio-Linux, EnvBase, HandleBar, Omixed, Terminizer, the MIBBI standards portal, and the Environment Ontology (EnvO).
Bio-Linux
The Bio-Linux (Bioinformatics on Linux) Project is an initiative promoting the use of Linux in biological and bioinformatics research. The Bio-Linux project has been developed and is maintained by the NERC Environmental Bioinformatics Centre (NEBC) at the Centre for Ecology & Hydrology. Begun in October 2002, this project is now supported by online course materials, extensive documentation and an established user-community both in the UK environmental genomics community and beyond.
Bio-Linux currently contains over 60 cutting-edge and standard bioinformatics software packages in addition to a full-featured office suite (word programming, spreadsheet, and presentation software), programming, modeling, and web-development environment core to the current Ubuntu system. Bio-Linux is suitable for the creation of teaching labs, training suites, compute clusters, and bioinformatics servers. All Bio-Linux software packages are available from the Bio-Linux repository and are compatible with both Debian and Ubuntu.
