Bio-Linux 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.
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

Bioinformatics: Market Review

An article reviewing the Bioinformatics Market scenario appeared on http://www.pharmaasia.com/ . The review suggests that the bioinformatics industry will be subjected to growth with different categories of firms (Biological/IT/multinationals/Domestic) entering its market. Indian bioinformatics vendors have a huge opportunity in bioinformatics services, customization of existing products and database licensing/creation/manipulation. However, they face certain challenges. By Poonam Bhana, Research Analyst, ValueNotes, India.

Key Trends

• Focus on target validation techniques – Advances in genomics and sequencing has made target identification easier through bioinformatics tools. The focus of bioinformatics in the drug discovery process has therefore shifted from target identification to target validation.



• Laboratory Information Management System (LIMS) tools – LIMS are tools that help automate collection and management of data generated in a laboratory. The market for LIMS products in India is estimated at $23 million in 2007, and is expected to grow at above 30% over 2007-2010.



• Trend towards enterprise solutions – Presently, majority of the bioinformatics revenues are derived separately from databases, services and software products. Hardly any vendor provides a complete enterprise solution. Driven by the need for integration of various databases/tools with R&D efforts, in the future, enterprise IT solutions should garner a larger share of the market.



• Long-term single vendor contracts – Companies with presence across various geographies require bioinformatics services on a global scale and often seek a single vendor that can offer a comprehensive range of services on a long-term basis, across the world. Understand and integrate a wide spectrum of emerging technologies with existing systems.



• Forward and backward integration – Pure play companies are opting for forward integration into contract research services, while pharma/Contract Research and Manufacturing Services (CRAMS) companies are also providing (or looking to provide) bioinformatics services.



• Inorganic growth – Several vendors are opting for strategic partnerships to strengthen their ability to scale, add to their service portfolio or increase client reach.



• Outsourcing of discovery informatics – Global companies were earlier outsourcing only clinical research related services to India. The implementation of Intellectual Property Rights (IPR) in India from January 2005 is gradually bringing global companies to India also for discovery services involving sensitive data.

Challenges and Critical Success FactorsIndian bioinformatics
Vendors have a huge opportunity in bioinformatics services, customization of existing products and database licensing/creation/manipulation. However, they face certain challenges like :Standardization of Service Platforms & Modular SystemsBioinformatics vendors work with varying standards and platforms. A major challenge is standardization of service platforms. Also, there is a need to offer more modular systems that can plug into other systems or well-documented application program interfaces already being used by their clients.

Problem of Market / Data Heterogeneity (Flexible tools)
Life Sciences companies may use different data formats, leading to incompatibility. Hence, it is a challenge for vendors to develop data integration tools to facilitate analysis of data sets from different sources. “Flexibility of a bioinformatics tool is essential for it to be a success. The tool should be flexible and allow for use in various applications," says Ajoy Singh, senior coordinator sales, Technoconcept (India) Pvt Ltd.Tools must be adaptable, readily configurable to support access to new data sources, instruments, tools and new functionality requirements.

Domain Knowledge and Experience
Bioinformatics is a highly specialized field where domain knowledge is more important than just cost. Lack of biological understanding can result in sophisticated computational methods being applied naively thereby leading to under-utilization of advanced tools. Hence finding the right team is vital.

For the beginners !!!!!!

Introduction

Dear Friends

I am a budding Bioinformatician and a naive blogger from the developing nation - India. I would like to use this blog as a platform to present and discuss Bioinformatics, its trends and revolutions.

Bioinformatics is a "Sangam" (meeting place) of Biology and Information technology, it is a multifacet science where biology, computational studies, Mathematics, statistics and algorithms merge. This the reason why I mention this mergence as "Horizon" .

Here I would like keep up with what is conventional as well as fresh in this area of science and research.

Visit this place to learn more about the subject.

Best wishes

Meenakshi