Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Bio-Linux goes global

13.01.2009
Release of 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 [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.”

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, “That 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.”

Barnaby Smith | alfa
Further information:
http://nebc.nox.ac.uk/biolinux.html
http://www.ceh.ac.uk

More articles from Information Technology:

nachricht Smart Computers
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

nachricht AI implications: Engineer's model lays groundwork for machine-learning device
18.08.2017 | Washington University in St. Louis

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

A Map of the Cell’s Power Station

18.08.2017 | Life Sciences

Engineering team images tiny quasicrystals as they form

18.08.2017 | Physics and Astronomy

Researchers printed graphene-like materials with inkjet

18.08.2017 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>