• New Delhi
  • 12 December 2013
  • Features
  • By Rahul

Supercomputing puts Indian agriculture on fast-track mode

Realizing the paradigm shift it can bring about, the government is focusing on increased bioinformatics intervention in agri-sciences. Currently under process, the national grid on bioinformatics is expected make much better sense out of huge genomic

supercomputing-in-agri

Nobel laureate and noted scientist, Dr Walter Gilbert once remarked that most of the biological investigations in 21st century will be in silico. Proving him right, the advent of genetic engineering and genomic approaches, have opened new vistas for increasing the productivity and quality attributes of bio-systems. During the last one decade, genomics has witnessed an information explosion and creation of databases, not amenable to traditional analytical approaches. Here came the role of bioinformatics that emerged as an inter-disciplinary programme, linking computational and mathematical sciences with life sciences.

ASHOKA is the name of India's first supercomputing hub for Indian Agriculture has been established at Centre for Agricultural Bioinformatics (CABin), that stands for advanced super-computing hub for OMICS knowledge in agriculture. The CABin is a part of the Indian Agricultural Statistics Research Institute (IASRI), New Delhi, involved in the development of partnerships at various levels among national and international organizations in the field of bioinformatics and related fields. The main centre for CABin will have dedicated high speed connectivity to domain centres working in different domains of agriculture such as crops, animals, fisheries and agricultural microbes. Further with the active support from agriculture ministry and fruitful partnership with the CDAC, Pune, the IASRI is setting up a nationwide grid of supercomputers for agri-biotech research, agricultural planning and research. Aim is to bring the biologists, statisticians and computer scientists together from the point of view of system biology approach and effective problem solving. This computational facility will not only for researchers of the Indian Council of Agricultural Research (ICAR) but all agri- scientists across the nation.

Although, activities related to bioinformatics were initiated at different ICAR institutions at small scale in isolated mode, hardly any coordinated efforts were made to integrate these activities at national level in the field of agriculture. Therefor, this supercomputing environment is being developed for high performance computing in the field of agricultural bioinformatics and computational biology under a sub-project "Establishment of National Agricultural Bioinformatics Grid (NABG) in ICAR" of the National Agricultural Innovation Project (NAIP), Indian Council of Agricultural Research (ICAR) New Delhi. The facility is set up in a state-of-art data centre and two super-computers of this hub are listed at rank 11 and 24 in the Indian Institute of Sciences (IISc) list of top super-computers of India.

This super-computing hub consists with hybrid architecture of high performance computing having (i) 256 nodes Linux cluster with two masters with 3072 cores and 38 Tera Flops computing, (ii) 16 nodes windows cluster with one master, (ii) 16 nodes GPU cluster with one master with192 CPUs + 8192 GPUs and (iv) SMP based machine with 1.5 TB RAM. Also, this hub has approximately 1.5 Peta Byte storage divided in to three different types of storage architecture i.e. Network Attached Storage (NAS), Parallel File System (PFS) and Archival. This hub also consists of super-commuting systems ( 16 node Linux cluster with one master with 40 TB storage) at National Bureaux of Plant Genetic Resources (NBPGR) New Delhi, and Lucknow, National Bureaux of Agriculturally Important Microbes (NBAIM) Mau and National Bureaux of Agriculturally Important Insects (NBAII), Bangalore which forms a National Agricultural Bioinformatics Grid in the country. Number of computational biology and agricultural bioinformatics software/workflow/pipelines along with National Biological Computing Portal are in the process of development, which will provide seamless access to these biological computing resources to the biological researchers across the country.

According to Dr Anil Rai, head and principal scientist, CABin, "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. 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 regualarly 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 (biotechnology), CABin believes that it is a right step forward."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," he mentioned in a visibly excited tone.

 

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