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.” 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 [http://www.ubuntu.com] 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 (http://nebc.nox.ac.uk/biolinux.html). Stewart Houten adds, “We make design choices in consultation 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.”
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.”
Excerpts from http://www.innovations-report.de/html/berichte/informationstechnologie/bio_linux_global_125318.html
