Friday, October 11, 2013

Open Source Drug Discovery: A Burning Illustration of Collective Endeavor at the Leading Height

Mamata Mishra

The story of OSDD is not less than that of any story of a successful family. Family is a simple term and easy to define concept. For anyone of us, I am sure; the term family gives the first visualization of parents, children, grand children and kith and kin. While talking about our own family to our friends or any other people, the discussion starts with number of family members, the members of family (right from the youngest one to the oldest one). Then gradually the talk takes account of the relationship among the members, the weak as well as the strong relations, the conflicts, the sweet as well as the bitter moments, the collectiveness to achieve certain goals, standing with each other for every weaker situation, and encourage for and to share every success. If we take an instance of a joint family, we find more than one generation, people of different mindsets, and different thoughts. In my opinion, the OSDD initiative even goes further this point in terms of collective goal attainment.

OSDD which started as a small project has taken a form of a unit. This statement sounds easy. In reality, it is not an easy task. Keeping in view the mission, vision and goals of the OSDD initiative, it is quite clear that lot of collective-minded efforts have gone into the making of the innovative way of doing science. With time, it keeps on proving its strength. It has got many helping hands, dedicated minds. It did not wait for the best to come; rather it tried its best to prepare even the average mind to be the best of all. OSDD gave a platform to all to think differently, to do things differently even sitting at one’s own space. It has completed five years of its journey and recently entered sixth year. This is a burning example of nothing is impossible. It has given opportunity to everyone who has an inner calling to do something for the society; for the nation. At the very beginning when I read that anybody can join and contribute to the project, I was wondering about this issue. As a social scientist I was quite clear that I can do a very good study of OSDD from sociological point of view, but was not clear as ‘how can I contribute’. Slowly I realized my study of OSDD itself makes me a part of the OSDD family. I felt good about it. This initiative has set an example for all of us who want to really work for our nation. In fact, latently, doing this, we not only contribute to our nation, but to those whose population is victim of such neglected-ignorable diseases. Such kind of initiatives must be encouraged by government, private bodies as well as the citizens of a nation.

Research Scholar;
Department of Sociology;
School of Social Sciences;
University of Hyderabad;
Gachibowli, Hyderabad-46;
Andhra Pradesh, India.

Monday, September 23, 2013

 Developed by Dr G P S Raghava group

 OSDDLinux  is an open source operating system for drug discovery (customize linux) that integrate most of open source or freely available computational tools required for drud discovery.In simple words, it is an in silico platform for providing enviroment for computer-aided drug design.Due to its open source nature anybody can contribute towards drug discovery using OSDDlinux, particularly those who cannot pay for commercial software (like students, researcher, academicains from developing world). Initially this operating system developed at Ubuntu platform, now we are extending it to other linux platforms.

 Challenges in Drug Discovery

 Despite major breakthroughs and tremendous progress in the field of drug discovery, there are millions of immature death every year due to lack affordable and efficient drugs. Drug discovery and development is a costly, time consuming and laborious process. It requires approximately one billion dollars and ten years to bring a new drug molecule into the market. How to bringdown cost and time required for discovering a new drug molecule is one of the major challenge in the field of drug discovery. 

Open source OSDD initiative 

 OSDD is a CSIR led team India Consortium with global partnership with a vision to provide affordable healthcare to the developing world by providing a global platform where the best minds can collaborate & collectively endeavor to solve the complex problems associated with discovering novel therapies for neglected tropical diseases like Malaria, Tuberculosis, Leshmaniasis, etc. It provides single platform for drug discovery, bringing together researchers, wet lab scientists, research organizations, clinicians, and students. The principal of OSDD is “Collaborate, Discover & Share” and motto is “Affordable health care for all”.

 Computational Resources for Drug Discovery

 Computational Resources for Drug Discovery (CRDD) is an important in silico module of OSDD. The CRDD web portal provides computer resources related to drug discovery from a single platform. The main focus of CRDD is to provide computational resources for researchers in the field of computer-aided drug design. It provides various webservers and software related to in silico drug designing, developing biological databases related to medicine and collecting and compiling various important resources for in silico drug designing. Challenges in developing in silico tools for Drug Discovery In silico tools and techniques providing an alternative for reducing cost and time in drug discovery during various experimental phases. The computational methods for in silico drug discovery have been broadly divided into two main fields: bioinformatics and chemoinformatics. 

Chemoinformatics and other in silico tools related to computer-aided drug designing are dominated by proprietary or commercial companies, where these tools are costly with stringent license conditions. Due to heavy cost of chemoinformatics resources, computer-aided drug discovery is still a costly affair. In last few years CRDD team have developed open source webservers for computer-aided drug discovery. There are number of reasons why open source are not popular in the filed of drug discovery (particularly in chemoinformatics, pharmacoinformatics, clinical informatics) that includes; i) not available from single source, ii) difficult to install, iii) lack of infrastructure. In order to overcome some of the limitations we developed OSDDLinux. It provides the popular open source software in the field of drug discovery from a single platform.

Sunday, September 15, 2013

OSDD invited for the post of a Junior Research Fellow

Date of publication  13 th September                                              last date October 5
Position of a Junior Research Fellow to Work on DST Sponsored Project

Applications are invited for the post of a Junior Research Fellow (temporary position till the project is supported) under DST funded research project.

Interested candidates can send their application with full resume / curriculum vitae. Experienced candidates, please apply with details of your present job description to mathewritta@osdd.netbefore 5rd October, 2013 mentioning in “DST project” in subject line. Selected candidates will be called for a personal interview. The decision of the interview panel will be final.

No TA/DA will be provided for attending the interview. The qualifying candidates are expected to start working within 1-2 weeks from the selection date.

Position: Junior Research Fellow
Designation and Qualification
Emoluments for first 2 years (per month)
Emoluments for 3rdyear/SRF (per month)
  1.   Post graduate degree in basic sciences and NET qualified
Graduate degree in professional courses and GATE or equivalent qualification
Rs. 16000/-
+ 30% HRA
Rs. 18000/-
+ 30% HRA
  2.   Post graduate degree in basic sciences with NET qualification for lectureship
Rs. 12000/-
+ 30% HRA
Rs. 14000/-
+ 30% HRA
  3.   Post graduate degree in professional courses
Rs. 18000/-
+ 30% HRA
Rs. 20000/-
+ 30% HRA
  4.   Post graduate degree in basic sciences without Net qualification for lectureship

AgeBelow 30 years

Duration: Two years (Each year extended based on performance after successful assessment by review committee).

Responsibilities: Gene cloning, site directed mutagenesis, mycobacterial growth analysis, invitro assay, phosphorylation studies, protein isolation and characterization by western blot analysis, extraction of mycolates, TLC, mass spectrometry. Screening of chemical molecules against M. tuberculosis. Book keeping and maintenance of stocks and consumables related to the project.
Essential Qualifications: M.Sc. in Microbiology / Medical Microbiology / Biotechnology / Biochemistry or B. Tech Biotechnology or M. Tech Biotechnology from a recognized university / institutewith a consistent first class academic record above 60% and relevant research experience as evidenced from thesis / dissertation carried out in a reputed scientific institution. Candidates should possess the extra qualifications specified by DST along with the degrees. Attach the scanned copy of the net lectureship or GATE qualification.

Desirable: Hands on experience with Mycobacterium tuberculosis and basic microbiology techniquesPractical experience in gene cloning, site directed mutagenesis and western blotting will be an added advantage.
Candidates should be comfortable and prudent working with M. tuberculosis and other microorganisms and be aware of the necessary safety and precautions required for handling it.

Wednesday, August 28, 2013

Dr  B..EKBAL  

The way in which intellectual property rights are being applied to research nowadays has created numerous encumbrances to furthering the research boundaries in Medicinal chemistry. This has resulted in making it a necessity to patent new drugs that are manufactured, introduced and distributed in the market. So to overcome these hurdles newer indigenous ways or methods are being designed world over to overcome this lacuna. Presently market capitalization is the driving mechanism which is the new world order in the field of research. Due to this method of research that is prevalent it is nearly impossible for the poorer strata of our society to access these drugs as the multinational companies have cornered a major share in the drug market. This has led to cost escalation of life saving drugs which is a stumbling block to carry out research so as to be able to bring down the cost of these life saving drugs. All this is a fall out of the prevalent patent laws that gives a near monopoly in manufacturing those drugs to the multinational companies. This leads to an inflated subsidy bill for all the governments of developing nations that try to make it possible for the poor people to access these essential drugs for their mere survival. This leads to a road block in the treatment of neglected diseases that are prevalent in developing countries.

It is in this background that newer methods and ways in pharmaceutical research have been conceived by drawing inspiration from Open Source Software movement. This in turn has led to a people’s movement in the field of pharmaceutical research. This has been made possible by replacing the Private Software Copy Right with the General Public License or Copy Left that was introduced by Richard Mathew Stallman of the Massachusetts Institute of Technology (MIT) computer department. This has made it possible to develop new knowledge and has given the right to make modifications so as to improve it without any hindrances of the prevalent copy right law.

Private Software does not allow you to share your knowledge with others. Also the Source Code is not made available to you and as a result of this you cannot make any modifications to the software.  With the General Public Licence not only is the Source Code made available to you, but you can also share the software with others and make copies of the software. The motto or the tag line of General Public License is to share and collaborate with others.

The fundamental basis has been formulated and laid down in the form of a Creative Commons by a Stanford professor of the department of law by the name Lawrence Lessig. The primary aim of introducing the Creative Commons was to publish the creative works of a person, to acknowledge him appropriately and to enable people having a genuine interest in a relevant area to make use of it in such a way that no profit is generated out of it. Through the Creative Commons the author is given a chance for distributing his work and through this way making it available to the public at large.

Creative Commons is the basis of the frame work of OSDD (Open Source Drug Discovery) that is being followed in many countries world over. Anybody who is interested in Medicinal chemistry research can make contributions in whatever way possible through sharing and collaboration which is the basic underlying principle that OSDD follows piously. The main aim of this consortium is to find newer drug able molecules for diseases that have been neglected by the multinational companies.

In India also OSDD has been started under the aegis of Council of Scientific and Industrial Research (CSIR). The first and foremost area of research of OSDD is to discover newer drug able molecules for Tuberculosis. The major health issue that most of the developing countries are facing is the prevalent character of tuberculosis. But the main issue at hand is the lack of discovery of newer drug able molecules since 1980 by the multinational companies that have a strangle hold over this area of research. Also tuberculosis bacterium has been found to be resistant to the present drugs available in the market.  With the advent of AIDS even developed nations such as USA have seen the tuberculosis disease make a comeback. Studies have proven that an AIDS patient is more susceptible to tuberculosis and if an AIDS patient contracts tuberculosis it is found that the drugs that are available in the market are ineffective in treating such patients. In India every three minutes two people die of tuberculosis. With all this said the multinational companies are least bothered in developing newer drugs to take on the newer resistant forms of the tuberculosis bacteria. It is in this back drop that CSIR through OSDD which is a social and community collaboration with the human community at large to take on this ardours endeavour in discovering newer drugs in the treatment of tuberculosis. Already around 4500 scientists and technocrats are involved in this collaborative research. Everybody who takes part in this collaborative research as well as institutions are either monetarily rewarded or are acknowledged by CSIR.

After the first phase of the research of finding the pharmacophore is finished, the requisite reward is given and in the next stage, CSIR would then collaborate with other institutions to carry out human testing. Once the drug is synthesised, CSIR would apply for the patent. Then the licence required for drug manufacturing would be given by CSIR to firms that are willing to manufacture low cost generic drugs. The point to be noted is that, CSIR would not given the license to only one firm but to a number of firms so as to prevent a particular company from garnering the whole market share.  The generation of knowledge by complying with the patent laws through collaborative research, by which drugs are developed economically in such a way that it would be affordable to the whole of humanity without any income barriers. This is what OSDD has achieved to do in a short span of time by being a model to others.

All these enlightening research activities are a glimmer of hope to the poor tuberculosis patients of not only our country but of the human community at large. Just like Open Source Software in the computer field, the problems of copy right have been overcome in the field of pharmaceutical research. Under the aegis of CSIR this new consortium would make certain tremors felt in the field of medicinal research as well as in the prevalent drug market. The discovery of a new drug for tuberculosis is the foremost task at hand. The policy of OSDD is to make available drugs at an affordable cost to all without any barriers through a collaborative research with the community at large. 

 About  author


translation  by Mr Andrew Manuel 

Monday, March 25, 2013

Need of Support for Women Scientists to Work from Home

Mamata Mishra
Department of Sociology
School of Social Sciences
University of Hyderabad

In India woman is appreciated on the name of Rani Laxmibai and on the other side is always a victim of patriarchy. Let’s speak about woman on this occasion of world TB Day.  Although some locations in this nation still observe child marriage till date, in this same nation we have witnessed many women who have crossed the ordinary boundary of the world. For instance Rani Laxmibai, Mother Teresa, Indira Gandhi, P.T. Usha, Kalpana Chawla, Lata Mangeshkar, Kiran Bedi, Bachendri Pal, Priya Jhingan, Harita Kaur Deol, Karnam Malleswari, Asima Chatterjee and so on. There is probably no area or field where women have not gained excellence.
Science is one of the key elements of an advanced society. Broadly speaking, science and technological advancement is a sign of the growth and development of a nation. The more advanced the science and technology area is, the more advanced a nation is. Coming to the under-graduation and graduation level, women[1] candidates are performing well in science education. In fact, if we look at higher studies, they even do better, but what happens after that stage? How many out of them are really able to proceed further in their career? Do they select career and job according to their qualification? What are the possible reasons behind this? The main reason according to me, is, age factor. By the time they complete their higher studies, they will reach the age of marriage. In many cases, she is forced to get married before she completes her education. Alarm will start ringing each second to get ready for marriage and leave the career at the back door. How many of these women stand firm and go ahead according to their willingness? After giving so much of effort, if her talent could not be utilized properly, then why did she study and come this far? Or can we say the other way like why her parents allowed her to study according to her choice before cutting down her legs? There are two possible answers to this. Firstly, she opted to study science as she wants to be a scientist and work for the society and herself as well. Secondly, parents have allowed her to come so far as they might get a good standard son-in-law. Is not it a matter of shame? If she has opted to take up her educational career so far, then where is her mental strength to fight for her right to progress further? Why should she stop doing science after her marriage? If it is her parent’s decision to give her higher education, then why do they want to shatter her dreams latter? When we look at these factors, one question came to my mind is that should women not get marry then, if they want to continue their research and job etc?
Marriage is not the only factor that puts a stop to women from doing science. There are other factors such as, economic status of the parents. For example, by her utmost effort, she has completed her graduation in science. She tries to get some fellowship, but remains unfortunate in getting one. Once you complete your post graduation, you have a number of fellowship options. Many parents can not even afford till that period as they have to save a huge amount for her marriage. This is one of the reasons why a girl has to stop her education in the middle. What if her talent could still be utilized in a proper way? Another ground is our rigid tradition. In many cases, a woman will have all the resources she needs to pursue her education and career such as financial assistance, no hurry at home for her marriage. Why is she still not able to work as a scientist in our society? The reason is our rigid and conservative tradition does not allow her to go for a job or work outside home.
Analyzing the above factors, one can come to certain possible solutions. Marriage should not be an obstacle for a woman scientist. After marriage her role should not be confined to a wife, a daughter-in-law and a mother. If she is willing to work, do research or job, then her willingness should be respected by her new family members. Her new family should create a familiar environment for her to work. In some cases, they do and in some they do not. Economy in a broader sense and money in a specific sense should not close the door for higher education. Above all, rigid culture should not cut he legs down and stop her from being independent to pursue her dreams. During my recent conversation with one of the scientists, he explained that it is difficult to change the system at once, rather we can create another system, and its success will bring followers. What can be possible solution for our women scientists? Marriage, economic circumstances, and culture- all these are part of all of us; our society. It may take decades to bring in a change. Here comes an alternative to this present discussed issue, that is, make those women scientists work from home itself.
This initiative is an excellent one I came to learn about. This is the concept of working from home itself, especially for women. We are of course, aware of the initiative of working from home for moms in internet. At present there is another initiative meant specifically for women is women scientists’ forum of Open source Drug Discovery (OSDD) Initiative. The main motive of this initiative is to bring together the creative talented women scientists those who are interested to work for the cure of Tuberculosis disease by working in an open space and on a common platform. As I have mentioned earlier, there are many women who can not come out for job or research for many social factors. It specially encourages them to join for this social cause. As a matter of fact, it is not limited to a particular group of women, but welcomes any woman who is voluntarily interested to join this forum and contribute. The functioning of such forums is very important and needs to be supported by the Government, society and nation in a broader sense. Here when I mentioned the word ‘support’, it implies that the ‘strength’. This strength in the sense of support will definitely lead to outstanding contributions to the OSDD initiative in general and women empowerment in particular.

[1] In this article the category of woman is specific to women scientists only. Although, the presented arguments about education, occupation, economic and other issues are presented by keeping women scientists in view, but broadly the same arguments are applicable to any area such as social sciences, arts, humanities, and so on.