Wednesday, November 9, 2011

GARUDA Grid .... Helping Cross Computational Barricades !!!!!

04/11/2011: Further strengthening the collaborative endeavors, an MOU was signed between CSIR/OSDD and CDAC ,Bangalore,  providing, the Garuda grid supercomputing facility to OSDD on 4th Nov 2011.The MOU was signed at Jawahar Lal  Nehru University, New Delhi by OSDD Project Director  Mr. Zakir Thomas and  Chief Investigator, GARUDA, CDAC. Dr. Subrata Chattopadhyay. The OSDD team was represented by Project Director Mr. Zakir Thomas and principle investigators Dr Anshu Bhardwaj and Dr Andrew Lynn. 

OSDD–CDAC partnership came into existence, with the recognition of the need of high performance computing in the OSDD drug discovery process and GARUDA grid of CDAC was proposed as the possible solution for the computing problems faced by the members of OSDD community. Set up in 1988, Centre for Development of Advanced Computing (C-DAC) is the premier R&D organization of the Department of Information Technology (DIT), Ministry of Communications & Information Technology (MCIT) for carrying out R&D in IT, Electronics and associated areas. CDAC was originally founded with the aim of building Supercomputers within the country, in context of denial of import of Supercomputers by USA. Since then CDAC has been undertaking building of multiple generations of Supercomputer starting from PARAM with 1 GF in 1988.Along with its core function of providing supercomputing facilities to the country, CDAC has been functioning in various areas like building Indian Language Computing Solutions, on various aspects of applied electronics, technology and applications, Health Informatics and various education & training activities. CDAC has since it’s foundation, emerged as a premier third party R&D organization in Information Technologies and Electronics in the country working on strengthening national technological capabilities. As an institution for high-end Research and Development C-DAC has been at the forefront of the IT revolution, constantly building capacities in emerging/enabling technologies and innovating and leveraging its expertise, caliber, skill sets to develop and deploy IT products and solutions for different sectors of the economy, education and research
As the OSDD projects moved into their second phase, involving Cheminformatics group, the activities became computation intensive the need of high performance computing was recognized. The members of the Cheminformatics group involved in building computational models in order to screen molecules for anti TB activity were confronted with the issues of internet connectivity, connection speed, and power supply interruption, hassles, which were likely to slow down the progress of the work .It became mandatory to employ supercomputing power where in many CPU/ Clusters could be connected to give much enhanced computing power and GARUDA grid of CDAC came to the rescue. The GARUDA Grid is the computational grid developed by Center for Development of Advanced Computing (CDAC) which has approx 6000 CPUs and 70 teraflops computing power. It connects 45 institutes across the country through high speed NKN (National Knowledge Network) connectivity. GARUDA resources are accessed through the high-speed communication fabric and the user friendly GARUDA Access Portal provides user interface to the Grid resources thereby hiding the complexity of the Grid from the users. The GARUDA Access Portal is also accessible through Internet so that users not belonging to the GARUDA Network can submit jobs on any of the GARUDA resources. Along with the GUI, Grid resources can also be accessed through command line interface. GARUDA allows submission of both sequential and parallel jobs and also provides job submission mechanisms like Problem Solving Environments (PSE) which are specialized software for solving one class of problems, such as Bio –informatics and Work flow tools which consists of a sequence of connected steps, serving as a virtual representation of actual work.

As a flag off to this collaboration a GARUDA Boot Camp was held at Malabar Christian College, Calicut from 28th - 29th December 2010. The boot camp was aimed at providing hands on training to selected OSDD members on usage of GARUDA grid and included presentations and hands-on sessions on GARUDA Architecture, Tools, Security, and Application enablement. The boot camp was well received and OSDD members from different parts of the country attended the camp. Since then, OSDD members spread across the country, have been using the GARUDA Grid to perform data mining and modeling experiments, which otherwise would have been a very tedious task on the existing user personal computers. Over 25 fold decrease in computing time has been observed when compared to user PC’s and  GARUDA grid has enabled the users to submit multiple jobs at a time increasing the efficiency and accelerating the process of drug discovery.

GARUDA grid of CDAC, has enabled OSDD researchers and students from ordinary institutes across the country to conduct experiments requiring high computing facility without interruption and is indeed one of the most important resources of OSDD. This OSDD –CDAC collaboration will definitely yield valuable results in  the drug discovery process in future.

Acknowledgement : Pushpdeep Mishra  
                                  websites :


Saturday, October 15, 2011

OSDD molecules

click to enlarge 









Friday, October 14, 2011

OSDD – Redefining IPR in open source innovations

The monopolization of knowledge as an individual property has always been a much debated issue. The pros and cons of patent technology and award of IPR has been a long debate, dating back to 1421 when world’s first patent was arguably granted to Filippo Brunelleschi for an improved method of transporting goods up and down the river Arno in Florence, and with the most recent reforms in the patent acts by the US government the debate still continues. With the emergence of open source as a trend in technological innovations the question of the possibility of co-existence of patent rights and technological innovations in open source mode cropped up giving way to further debates and discussions. Patents and open source products have been conceived to be fundamentally incompatible and there have been numerous efforts towards the development of models that bring together patents and open source which has resulted in the development of open source licenses like the GPL.

Patenting is known to play a very crucial role in the development of new products in pharmaceutical and biotechnological industries.Both pharmaceutical and biotechnological industries are research intensive and patents play an important role in establishing market monopoly and ensuring social returns. British economists Taylor and Silberston, based on a survey of UK R&D managers, suggest that pharmaceutical R&D expenditures would be reduced by 64 percent in the absence of patent protection. While patents play a vital role in governing market monopoly, and have been instrumental in motivating pharmaceutical innovations the manufacturing interest in itself is largely governed by purchasing capacity of the consumer population and demand. This mechanism is quiet evident when one compares the existing markets for so called new age diseases like cancer and diabetes and diseases that afflict the invisible population of the developing countries like TB and malaria. Unfortunate is the fact that patents as a mechanism to ensure Return on Investment (ROI) from the market fail to play the role it plays as a driver of innovation in the pharma industry. Lack of profitable market incentives has discouraged the effort of manufacturing drugs for neglected diseases that affect the poor population of the third world.

OSDD is a multifaceted drug disocvery project that is offering a sensible and practical model that aims at converging patents and open source innovations. It is a common assumption that open source innovations and patent systems are far from co-existence OSDD through its noble quest to discover drugs in an open source mode is also a novel initiative towards recalibrating the patent systems. The current status of dry drug pipeline for neglected tropical diseases like TB, along with the understanding that in the absence of a market size that attracts the interests of the pharmaceutical industry, Intellectual Property (IP) Rights as a legal system has limited role to play in fostering innovation is the is the key motivation behind OSDD.OSDD is proving that an IP neutral approach towards drug discovery and development is in fact the  best way to ensure affordability and accessibility of drugs in market. This approach is quite Contrary to the popular perception of patents as a legal system to exercise control and as a means of monetary gain. OSDD, despite mandating the open sharing of data by the participants on the community portal doesn’t hamper the patenting of any of the original data or hinder further research on any of its patents by any group anywhere. OSDD understands that researchers may be contributing patented inventions to OSDD or there may be cases where the inventors worked in an open source environment yet would like to file patents. OSDD though an open platform of research, encourages such patenting for ensuring attribution to the inventors and for proving the non-obviousness of the research.
 OSDD has a unique view on patents and the instances were inventions are covered by patents, it is to fulfil the following objectives:

1.    Affordability and Accessibility – Most of the pharmaceutical companies don’t undertake drug discovery for neglected diseases and this task has been undertaken by OSDD. But along with discovery of new potent drugs it is also crucial to ensure the affordability and accessibility of the drugs. Patented inventions of OSDD are to ensure that the drugs are licensed non exclusively, as a generic drug, utilizing open competition in the market, removing the monopolistic nature of IP for access in developing countries

2.     The second objective of patenting in OSDD is to ensure quality control of downstream drug manufacturing, by licensing to only those entities who employs quality processes during drug manufacturing

3.    Thirdly OSDD supports patenting based on general public licence that ensures that the subsequent innovations which follow on the existing patent remain openly accessible through the OSDD community through its viral clauses.

OSDD is thus emerging as a unique healthcare model that blends together the policies of patenting and innovative open source research to make drugs for neglected diseases prevalent in developing countries easily accessible and affordable without price monopolies. It is indeed the need of the hour that we develop a balanced view towards health as a right, and health as a business (quoting Dr Samir K Brahmachari).Models like OSDD which can assimilate together the concepts of patents and open source research are required to bring out more innovative breakthroughs that can change the lives of underprivileged population across the globe.

Acknowledgements : Project Director Zakir Thomas 

Saturday, October 8, 2011

We shall start a new song for you ever/ osdd song

We shall start a new song   for you ever  more
Time will repeat the song for you ever more
It will cross fields and gavs to reach you dear
We shall  start a new song  for you  dear

Our life light  is filled with molecule  of hope
Our whisper with lover  is  teeming  your pain
Our dream is to give you ray of hope
We shall start a new song  for you  dear

We shall never switch of our lab and light 
We shall never sell our elite wisdom
We shall never sleep in the bed of flowers
Till this song reaches you dear 

We shall start a new song  for you ever  more
Time will repeat the song  you forever
It will cross fields and gavs to reach you dear
We shall  start a new song  for you  dear 


Tuesday, October 4, 2011

“Cloning and expression of selected intraphagosomal expressed genes of Mycobacterium tuberculosis” - OSDD Project at Miranda House

Miranda House College, New Delhi is one of the prestigious institutions in the country among many who have joined hands with OSDD in its noble quest for a novel drug against TB. A visit to the lab involved in OSDD’s cloning project and short interaction with the principle investigator Dr Sadhana Sharma bring home the OSDD objective of involving graduate and postgraduate students in socially relevant scientific research.

The OSDD centre at Miranda House is involved in “Cloning and expression of selected intraphagosomal expressed genes of Mycobacterium tuberculosis” with the objective to identify important intracellular genes as targets for development of inhibitors which may prove to be potential anti-tubercular drugs. Here Dr Sadhana Sharma is carrying out this project along with co-investigator Dr. Monika Sharma with a very dedicated team of undergraduate students from B.Sc. Hons Zoolgy and Biomedical Sciences and three OSDD project assistants. It is a matter of pride that one of the students Miss Iti Saarav, a research assistant in OSDD project has been selected for PhD program at Zoology department in Delhi University .In order to train the students on various aspects of cloning and expression initially a 1 month long summer workshop on cloning was conducted at the college which was attended  by 25 students from the Life Sciences department of Miranda College and students of Biomedical Science course from various other colleges 10 well trained students were shortlisted among the participants  based on their performance to  execute the cloning project. So far students of MH have been able to successfully clone 4 Mtb genes 10 more genes are in the cloning pipeline. With the cloning projects expected to be completed successfully by November, this team is planning to look into the expression of identified intracellular genes, biologically characterize the gene products and identify their inhibitors

Saturday, September 24, 2011

Gargi’s Descendants

Gargi’s Descendants

Anandibai Joshi (1865-1887)          New generation scientist

Now our nation have a lady president, a lady as president of ruling party and leader of ruling coalition and a lady opposition leader. Once we had a lady Prime Minister too, who had been sometimes referred to as the only man in her cabinet. Still, the bill for representation of women in parliament and state assemblies has fallen on stumbling blocks one after another. Things are the same or even worse in science. Women are grossly underrepresented in science and technology after all the women’s emancipation and gender sensitization. We don’t find many of them in higher levels of scientific establishments. Up to undergraduate and postgraduate level, the ratio of women is considerable and they may outnumber men in some states and regions. But the gender gap increases with increasing level of Education. Potential female researchers still hesitate at the thresholds of laboratories. Drop off factor large in going from Ph.D. to postdoctoral positions and even larger in faculty positions. Most of them drop off. In our country young ladies cannot wait much for matrimony and motherhood usually follows it. So the lady scientists have to take all the brunt of family, work and research. Even a quality child care center is a dream for most of them. And she may be in Delhi and her spouse in Hyderabad. We can identify a number of reasons for the situation. Social conditioning and prejudices play their role. It seems that, as often termed, a ‘glass ceiling’ become the stumbling block mostly. The term may be a ‘cliche’ by now. But it’s a fact there is no better term for the situation. They seems to be pushed aside even before a fair debate.  In mythology ‘Yanjavalkya’ the man of saintly wisdom, wanted to take away the prize before debate. In king Janaka’s court the great debate on wisdom was being held.  It was the greatest test of knowledge, logic and intellect and wit and theorizing skills of the time. Yanjavalkya had ordered his disciples to take away the herd of cattle offered as the grand prize for the debate. He was that confident of winning the debate. ‘Debate I will win later.’ He proclaimed. No one in the court dared to question Yanjavalkya. But the lonely voice of decent came from the down to earth lady Gargi. ‘You
have not won the debate – I am here, I will ask a few questions,’ she told him.  Eventually Yanjavalkya lost the argument. He alleged Gargi of blasphemy and told that her head will role. And her reply was that ‘now, the sword is not an argument.’ He had to concede finally. He offered not only the cattle back, but other wealth as well. Gargi,s reply was ‘You can keep them. I am not interested in cows and gold. I was interested to see how much understanding you had’

Somehow our system doesn't allow women to enter into the real debate. But here a group of young ladies are telling the scientific community that ‘you are yet to win the debate – We are here to ask a few
questions. We are not much interested in positions and fame, but to see how much understanding you had.’ They promise to be a group with solid determination to circumvent all the hurdles and inhibitions.
They include a few scientists, teachers, unemployed doctoral, post doctoral scholars and students have come under the banner of  OSDD women’s scientist forum. Their role in the open science movement and the OSDD project is really immense. They have really opened the debate. Let them prove themselves to be Gargi’s real descendants. Anandibai Joshi, who, in 1886, was the first Indian woman to obtain a medical degree in the U.S and won applauds from the British Queen, has said. “Before my marriage, I could barely read Marathi.” If she could do that much, these young and enthusiastic ladies can do much greater.

Dr. Prasad M Alex
Associate Professor in  Chemistry