India has launched a government-industry effort to develop indigenous portable software that will help bioinformatics research thrive across the country and help the country enter the international market on its own.
The $3 million program, funded by India’s Council of Scientific and Industrial Research, will pool the expertise of biologists across 14 publicly funded laboratories and universities, working with three software companies as industry partners, to produce inexpensive, platform-independent, and integrated bioinformatics products.
A major part of the new effort is aimed at reimplementing existing public-domain algorithms in new source code specifically designed to work across different platforms without extensive modifications, senior program officials said.
But it will also exploit domain expertise from participating biology institutions to generate new algorithms for novel products. The CSIR has set a March 2004 deadline for these products to hit the market. Funds provided to industrial partners — Tata Consultancy Services and Frontier Life Sciences of Hyderabad, and California Digital Corporation of Bangalore — are being treated as “loans” that will have to be repaid once products start moving out.
“The high cost of existing bioinformatics packages has been a major deterrent to the growth of bioinformatics in India,” said Mathukumalli Vidyasagar, executive vice president at the Advanced Technology Center of Tata Consultancy Services.
Although India’s Department of Biotechnology has established nearly 60 academic bioinformatics centers, biologists there have complained that most existing bioinformatics software comes glued to expensive and specific hardware, rendering both inaccessible.
“Take the example of molecular modeling packages — most today run on Irix and demand Silicon Graphics machines,” said Debashish Dash, a scientist at the Center for Biochemical Technology, New Delhi.
TCS has pledged to offer software developed under the new program to academic institutions at cost price. “A major objective is to make bioinformatics products accessible to a very large number of researchers,” Vidyasagar said.
TCS, Asia’s largest software company, first ventured into bioinformatics last year, committing $1.5 million over a three-year period to pursue contract research and intellectual property with the publicly funded Center for DNA Fingerprinting and Diagnosis.
In the new program, the company is creating several modules to cover sequence analysis, gene identification, protein structure analysis, molecular modeling, and quantitative structure-activity relationships.
“Unlike some existing packages, the focus will be on integration,” said a TCS program official.
But it won’t all be old algorithms in new source code.
Biologists involved in the program say novel software tools will also spring from this effort. At the Center for Biochemical Technology, New Delhi, for instance, researchers are working on a software product designed to pick out virulent sequences from the genomes of pathogenic bacteria. In a subsequent phase of development, the CBT plans to apply this to identify new virulence factors in malaria parasites.
Another package developed at the CBT, the “proteome calculator,” will allow scientists to simultaneously compare the whole genomes of dozens of organisms at the protein level. The CBT is collaborating with California Digital Corporation, to tailor these packages for Linux.
And at Pune University, a research team is trying to create software tools to represent complex metabolic pathways. The plan is to extract biochemical information from databases of enzymes and metabolic pathways and create fresh databases of metabolites and substrates. Pathway engineering could be used to seek alternate pathways to arrive at an end product in a complex biochemical sequence, even when a crucial molecule is missing.
The products might be months away, but some Indian biologists are already predicting that the country’s effort could impact international prices for bioinformatics products. “We’ve seen this in other areas of life sciences,” said Samir Brahmachari, director of the CBT. “When we developed our own low-cost products, say the hepatitis B vaccine, the price of the imported vaccine went down.”
— Ganapati Mudur, New Delhi