December 17, 2013

Supercomputing Bolsters Agricultural Science in India

Tiffany Trader

A paradigm shift is occurring within the agricultural sciences, owing to the genomics-based data explosion and concurrent computational advances. In India, leaders are intent on furthering the burgeoning genomic supercomputing discipline through the establishment of a supercomputing center and a nationwide grid to support bioinformatics and agricultural science.

A recent article in BioSpectrum explores this transformation, noting that data-intensive nature of genomics is such that it is not well-suited to traditional analytical approaches. Thus “the role of bioinformatics emerged as an inter-disciplinary programme, linking computational and mathematical sciences with life sciences,” observes the article’s author Rahul Koul.

In New Delhi, ASHOKA – short for Advanced Super-computing Hub for OMICS Knowledge in Agriculture – was established at the Centre for Agricultural Bioinformatics (CABin) as the first supercomputing hub for Indian agriculture. CABin, part of the Indian Agricultural Statistics Research Institute (IASRI), fosters collaborative bioinformatics pursuits at the national and international levels. The center has dedicated high speed connectivity to multiple domain-centric research organizations relating to crops, animals, fisheries and agricultural microbes.

IASRI is working with the agriculture ministry and CDAC, Pune, to build a nationwide grid of supercomputers for agri-science and agricultural planning. The goal of the effort is to have biologists, statisticians and computer scientists working together with a system biology approach geared toward problem-solving. This facility will be open to Indian Council of Agricultural Research (ICAR) members as well as agricultural scientists across India.

The author notes that bioinformatics projects have been underway at ICAR institutions, but these were small scale, isolated efforts. The current initiatives seek to integrate these activities at the national level with an additional emphasis on the field of agriculture. The supercomputing environment that will undergird the research was developed to support the requirements of agricultural bioinformatics and computational biology science.

The subproject “Establishment of National Agricultural Bioinformatics Grid (NABG) in ICAR” is overseen by the National Agricultural Innovation Project (NAIP), part of ICAR. The state-of-art datacenter hub, ASHOKA, includes two supercomputers that rank at numbers 11 and 24 in the Indian Institute of Sciences (IISc) list of top supercomputers of India. The hub has approximately 1.5 petabytes of storage divided in to three different types of storage architecture: Network Attached Storage (NAS), Parallel File System (PFS) and archival.

This hub connects to supercomputing systems to form a National Agricultural Bioinformatics Grid that includes the National Bureaux of Plant Genetic Resources (NBPGR) in New Delhi, and Lucknow, the National Bureaux of Agriculturally Important Microbes (NBAIM) in Mau, and the National Bureaux of Agriculturally Important Insects (NBAII) in Bangalore. There are a number of computational biology and agricultural bioinformatics software/workflow/pipelines currently in development. The goal is to provide seamless access to these biological computing resources to scientists across the country.

Head and principal scientist at CABin Dr. Anil Rai explains the impetus for the computational grid and access portal. “We are trying to build this system so that scientists don’t have to come here every-time for the analysis but to ensure that they can carry out the same while sitting on their desktops,” he states. “For that we are building national bioinfomatics portal which is almost 80 percent ready. There is a provision for monitoring of the data results by respective scientists regularly and even sms alerts to provide quick info on progress is also there. This system will support computational requirements of the biotechnological research in the country. This will also bridge the gap between genomic information and knowledge, utilizing statistical and computational sciences. Further, this will help in establishment of large genomic databases, data warehouse, software & tools, algorithms, genome browsers with high-end computational power to extract information and knowledge from cross-species genomic resources.”

Dr. Dinesh Kumar, senior scientist in biotechnology at CABin, adds his support.”It will open up new vistas for downstream research in bioinformatics ranging from modelling of cellular function, genetic networks, metabolic pathways, validation of drug targets to understand gene function and culminating in the development of improved varieties and breeds for enhancing agricultural productivity to many folds.”

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