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NEBC Bio-Linux Version 5.0 - a one-stop shop for bioinformatics tools in a Linux context

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.

Bio-Linux is 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. 

The growth of molecular data from the fields of genomics, metagenomics and related ‘omic disciplines calls for ever improving methods of data collection, storage and analysis.  The field of bioinformatics is rich in software and fast, economical computing environments are becoming essential components of almost all research labs pursing scientific questions using these data-rich technologies.

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 looking to use the existence of freely available customised distributions to build and maintain computational infrastructure quickly and effectively.

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 but from today 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.

Dawn Field adds, “We need to foster a highly collaborative community that can make use of a network of computers throughout the UK.  NEBC Bio-Linux provides a powerful framework for delivering support, minimizing duplication of effort and most importantly, empowering researchers to take on their own analyses using a large suite of tools.”

The more visionary role of NEBC Bio-Linux is to build electronic networks of researchers with shared interests, using a shared platform.  This is already happening with a recent application of Bio-Linux in Africa. Peter Dawyndt, Professor of Computing at the University of Ghent found Bio-Linux on the web.  He comments, “Bio-Linux is a terrific solution to our need to bring state-of-the-art bioinformatics computing platform to students in Africa.  With just a set of  DVDs in our luggage, we are able to install a top-notch computing environment in which to deliver our entire bioinformatics course.  Most importantly, the entire infrastructure stays behind and remains available to interested students.”

Bio-Linux is a derivative of Ubuntu Linux customised for bioinformatics analysis and development work. Approximately 60 bioinformatics packages (providing around 500 individual programs) are installed on Bio-Linux, including open-source packages developed at the NEBC. In addition, Bio-Linux comes with comprehensive, categorised documentation for the bioinformatics packages installed. Users can install a full NEBC Bio-Linux system or just add some or all packages to already installed Debian or Ubuntu Linux systems. 

Lead Developer, Stewart Houten, says “Bio-Linux 5.0 retains the added-value features of Bio-Linux 4.0, but is now based on the highly popular and user-friendly Ubuntu distribution and the Gnome desktop.  The system is available as an installable DVD or USB memory stick, making it readily accessible to a wide audience.”

The open source GNU/Linux computing system is progressively being seized upon as the preferred choice in addressing researcher computing needs. Despite Linux distributions becoming easier  to use, the task of configuring the system for a specific purpose and collecting, compiling and setting up the academic software remains challenging. Bio-Linux provides a solution to this challenge.

Researchers and developers alike are welcome to join the NEBC Bio-Linux project and more information about the project can be found on the NEBC Bio-Linux homepage. Stewart Houten adds, "We make design choices in consulation with our community and continually adapt NEBC Bio-Linux to meet their needs. This release responds to the growing skills in our community in the use of Bio-Linux and the striking increase in the number of users downloading Bio-Linux or its packages from locations outside the UK."

Supporting quotes from the genomics community

NEBC Lead Bioinformatician, Bela Tiwari says, “The NEBC Bio-Linux network accelerates research through improved electronic communication and support. I can log into a remote machine when requested, allowing me to directly troubleshoot or undertake collaborative analysis.  Likewise, researchers can make use of a range of mechanisms for securely sharing data.  Having many users able to access a single well-maintained machine also makes effective use of NERC funds and research time alike.”

Tony Travis of the NuGO consortium says, “The NEBC Bio-Linux package repository has been an essential element of the success of our NuGO Black box project, designed to equip our community of researchers with integrated bioinformatics solutions.”

Researcher Keith Jolley, of the University of Oxford, adopted Bio-Linux to deploy a specialist set of software for genetic tracking of pathogens in a clinical setting. He says, “The availability of Bio-Linux has made it possible to distribute and maintain our software network with minimum effort”.

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 says, “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, says, "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 continues to say, “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.”

ENDS

Notes for editors

Contacts:

1. Stewart Houten (NEBC Bio-Linux Developer), Centre for Ecology & Hydrology – Tel: 01865 281630, email: helpdesk@nebc.nox.ac.uk

2. Dawn Field (NEBC Director), Centre for Ecology & Hydrology – Tel: 01865 281630, email: dfield@ceh.ac.uk

3. Bela Tiwari (NEBC Lead Bioinformatician), Centre for Ecology & Hydrology Tel: 01865 281975, email: btiwari@ceh.ac.uk

4. Press Office, Centre for Ecology & Hydrology – Barnaby Smith – Tel: 07920 295384, email: cehpress@ceh.ac.uk

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).

The Centre for Ecology & Hydrology (CEH) is the UK's Centre of Excellence for research in the land and freshwater environmental sciences. CEH is a research centre of the Natural Environment Research Council and employs 500 staff at six major sites in England, Scotland and Wales with an overall budget of about £35m. CEH science covers three core areas of expertise: Biodiversity, Water and Biogeochemistry with a major cross-cutting activity focusing on Environmental Information. CEH tackles complex environmental challenges through integrated research, aiming to deliver practicable solutions to help preserve the environment for future generations. 

The Natural Environment Research Council funds world-class science, in universities and its own research centres, that increases knowledge and understanding of the natural world. It is tackling major environmental issues such as climate change, biodiversity and natural hazards. NERC receives around £400m a year from the government's science budget, which is used to provide independent research and training in the environmental sciences.

Further information:

a) 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 is based at the Centre for Ecology & Hydrology’s research site in Oxford, and is a collaboration between research groups at the NERC Centre for Ecology & Hydrology, the University of Manchester and the European Bioinformatics Centre (EBI). 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). NEBC has recently won a contract to provide a NERC Environmental Bioinformatics Facility as part of the NERC Molecular Genetics Facility (MGF).  It is now possible to cost Bio-Linux and associated bioinformatics support into (NERC) grants. Bio-Linux will continue to be the underpinning computational environment for all activities within this new MGF-Oxford node.

b) 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.

Related links

1. Centre for Ecology & Hydrology research activities - Environmental Genomics

2. NERC Environmental Bioinformatics Centre (NEBC)

3. NEBC Bio-Linux project

4. Bio-Linux for MLST analysis

5. Ubuntu

6. Bio-Linux explained on Wikipedia