Centre for Development of Advanced Computing (C-DAC), an initiative of the Department of Information Technology (DIT), Ministry of Communications and Information Technology (MC&IT) develops solutions for bioinformatics. The Centre recently launched ‘Anvaya’, a high-throughput genome analysis pipeline which will now help biologists to unravel the ease of handling large volume data. Dr Rajendra Joshi, Group Co-ordinator and Head, Bioinformatics, Scientific Engineering and Computing Group, C-DAC, provides a glimpse of the bioinformatics industry and the centre’s future efforts to Nandita Vijay in an email interaction. Excerpts:
How would you describe the current scenario of bioinformatics in India and abroad?
In India, the bioinformatics application is yet to realize its full potential. Here bioinformatics research is carried out by a few select researchers at universities and institutes. In the US and Europe, bioinformatics has been well accepted and one can see large projects being taken up by the academia and industry.
How is the field of bioinformatics expected to evolve?
Bioinformatics technologies are currently being used for computational genome analysis and structure-based molecular modelling and design. Considering the rapid progress in the field, it is expected that systems biology based analysis would be the future of bioinformatics. The field of systems biology deals with the understanding of functioning cell along with the pathways, networks, signalling etc. This understanding would revolutionize the future of biotechnology.
How receptive is the pharma and biotech sectors towards bioinformatics?
In the countries like the US and Europe, the pharma and biotech companies have embraced bioinformatics as a technology. This is because they see this as a major enabler to reduce cost, efforts and time for developing products. Pharma companies use bioinformatics for designing better drugs, the agri-biotech companies use it for better crop varieties and the livestock industry is also using it to understand genomics of livestock for producing disease resistance varieties. In India, the biotech industry is yet to realize the potential of bioinformatics.
What according to you are the visible trends in this space?
A visible trend is the utilisation of bioinformatics for better drug discovery by the pharma sector. Even the agri-biotech companies are making the best out of bioinformatics to produce better crop varieties. A few selected groups with high level of expertise are currently working on basic research projects in the systems biology space.
Could you tell us about the challenges in this space?
Over the last few years, the biotech space has emerged from a cottage industry to a full-fledged production science. In the post-genomic era, data generation is no longer a challenge as a high level of automation and robotics are being used for data generation. As a result there is a flood of sequence data, structure data and interaction data. Mere raw data does not lead to any new science and one has to analyse this data to generate knowledge. The sheer volume and types of data make it extremely difficult for any kind of analysis. This is the biggest challenge and one has to look at new technologies for advanced computing, build better algorithms to have better data integration tools.
How difficult is it for the industry to get the right and qualified personnel ?
Bioinformatics is a highly interdisciplinary field and requires multiple skill sets in advanced areas of research. One needs a good understanding of biology as well as computers, maths and statistics. There is a severe shortage of highly skilled manpower. Though there are many short-term courses available, unfortunately the quality of manpower produced via such courses do not meet industry expectations.
How keen are the current pool of biotech engineers and science graduates looking to specialize in this segment?
Bioinformatics or computational biology has a great future. The current pool of biotech engineers and science graduates have shown a good amount of interest. However, they need to realize that this is a long-term career path and does not have short-term benefits. They also need to realize that there is a great opportunity only for highly skilled manpower with high level of specialization.
Could you give us an overview of the bioinformatics projects going on in the country?
The Department of Biotechnology (DBT) and Department of Information Technology (DIT) have special divisions to fund projects in bioinformatics. The Open Source Drug Discovery (OSDD) project of Council of Scientific and Industrial Research (CSIR) is one of major bioinformatics projects in the country. CDAC has set-up the Bioinformatics Resources and Applications Facility (BRAF), which is funded by the DIT and the facility is presently accessed by researchers. We have already released a few products to enable the researchers to utilize supercomputing clusters and grids.
Considering the number of products launched, where is C-DAC positioned in bioinformatics ?
For bioinformatics , one has to employ high-performance and high-throughput technologies to handle the vast amount of data and analyze it to generate knowledge. C-DAC has been a leader in high performance computing technologies and also has a large bioinformatics group, specializing in genomics, modelling and software development. The capability has led to a number of collaborations with eminent research organizations and industries in India and globally. These include the Institute for Animal Health (UK), Sanger Institute, UK, University of Surrey, Oregon Health & Science University (OHSU), National Institutes of Health, USA, National Centre for Cell Science (Pune), University of Pune, Nicholas-Piramal and Jubilant BioSys.
What are C-DAC’s key strengths ?
Our strengths in high performance computing and has helped interactions with global partners. The expertise in computational genomics, molecular modelling and software development has helped to develop software solutions for clusters and grids like GIPSY, GenomeGrid, iMolDock and Genopipe that can be customized. Our latest offering ‘Anvaya’ is a high-throughput genome analysis pipeline with a bioinformatics software to execute a set of analyses ‘in-series’ or ‘in-parallel’ using a workflow environment. Researchers will no longer need to view numerous web-servers to complete complex computational genome analysis. ‘Anvaya’ brings to the desktop, numerous tools that a genomics researcher would use.
How different is ‘Anvaya’ from GenomeGrid, iMolDock, Genopipe and Gypsy?
GIPSY and GenomeGrid are problem-solving environments used on the clusters and grids respectively. These have various sequence analysis and modelling applications plugged-in with user-friendly interface. Genopipe is a high throughput annotation pipeline for comparative genomics. With Anvaya , users can have the advantage of backend supercomputing cluster to handle numerous genomes at a given time resulting in a high throughput analysis.
C-DAC has initiated projects for the international and Indian companies. Could you give us an update on its progress?
Projects with Jubilant and Nicholas Piramal are complete and have resulted in new findings. With IAH and Sanger are ongoing. Genopipe software has already been installed at IAH and is used for genomics of Mycobacterium and Salmonella. With the University of Surrey, the project is on systems biology of mycobacterium. The project with OHSU is about large simulations of medically important membrane proteins and with NIH the focus is on the development of a cancer biomedical informatics grid (caBIG).
What are the concrete future plans for CDAC in this space?
With a large amount of expertise in advanced computing technologies like clusters, grids, accelerators, combined with the expertise in bioinformatics, CDAC is uniquely poised to play an important role in the computational biology scenario in the country and globally. We plan to open an advanced centre for bioinformatics which will be a nodal centre to conduct advanced research in genomics and structure based modelling. Efforts would also be to increase collaborations with leading global pharma-biotech sector.