Saturday, August 27, 2011

At Ekalavya’s Feet 
To those who dare to go beyond….

Zakir Thomas  
OSDD is launching an e-learning initiative seeking to impart instruction in subject areas relating to drug discovery. The story of Ekalavya in the Indian epic Mahabharatha depicts the urge of a village student not having access to brilliant teachers to seek knowledge, a determination to seek knowledge that was out of bounds to his peculiar situation, the ability to learn without the physical presence of the master, and to excel at the art. Though with a tragic end, it has been inspiring example for all those who followed the path of learning through their own difficulties. 

The internet is regarded as the next biggest leap in knowledge dissemination after the invention of the printing press. If the printing press released knowledge from confines of monasteries and libraries, internet released us from the confines of physical space, from the confines of printed word, and opened up windows to the world in our homes. It is an unprecedented opportunity particularly to those in developing world to access knowledge that has so far been the privilege of few. 

OSDD is driven by the fact that the current market oriented drug discovery models fail to find solutions to problems affecting large number of patients, particularly those afflicted by diseases endemic to the tropical regions. Those who hold the power over the knowledge that could lead to find solution to these problems, fail to do so, as it is not profitable to their enterprises. A patient whether of tropical disease or otherwise should have the access to latest drugs. We refuse to accept a worldview which result in a situation where all lives do not have equal value. Rather than be passive spectators of the problem, OSDD endeavor is to find a solution to reach the unreached.

Drug Discovery has been a hallowed science, often revered only in the confines of pharmaceutical research and development centers. In the conventional drug discovery model, the job of the academic world has been to train scientists, who will then work with the industry. Most drugs developed in the 20th century were developed in this model and we owe to the pharmaceutical industry for their contribution to improving life expectancy around the world. In the recent years, as the new drug pipelines are drying up there is a general feeling that low hanging fruits are plucked. There is increasing awareness of the complexity of the task associated with drug discovery and the academia has risen to face this challenge and a large number of early stage discoveries are taking place in research laboratories of universities, which are then licensed to pharmaceutical enterprises. This points to the need and possibilities of fostering collaborations in drug discovery and the opportunities that lie in tapping the potential of student minds in solving problems. OSDD endeavors to bring drug discovery to the open, where researchers, scientists, academicians and industry can collaboratively endeavor to solve complex problems.
The convergence of computing and mathematical, statistical, biological and chemical sciences are providing reasonable predictions in a field where the basic approach followed in discovery of penicillin still rule the roost. Advances in science is throwing up large data and advances in computation is enabling analysis of this data which will feed into the drug discovery pipeline. Therefore, it is reasonable to expect bioinformatics and cheminformatics to play an important role in the drug discovery process.
While bioinformatics has been widely accepted and practiced in the academic community, with strong presence of both open and proprietary software adding value, informatics has been rather slow to take root in the discipline of chemistry. Therefore we see fewer student/researcher activity in cheminformatics, the impact is directly seen in the lesser number of open source software and tools. The OSDD community developed tools reflects our commitment to fill this gap, and this endeavor will continue. 
While OSDD is a serious drug discovery project, it has an equally important educational component.  The workforce behind OSDD community, currently around 5,500 from more than 130 countries, is the student fraternity. They are engaged in furthering the understanding of the biology of the organism, from cloning to expression to synthesis of complex molecules, to developing software tools and analyzing large volumes of data. In this activities they are guided by experienced academicians and scientists, both in public and private sector. 
At OSDD we would like to go beyond those who are actively engaged in its drug discovery activities to the wider student community, by providing an e-learning platform where they could find material on a wide array of topics, from bioinformatics to quantum mechanics, from pharmacology to medicinal chemistry, from open source to intellectual property. 
We have launched this e-learning initiative out of our firm commitment that internet provides a platform to reach the unreached. We have the conviction born out of our experience that in the distant and remote corners, far away from prominent academic institutions, there are brilliant minds capable of solving complex challenges, and they are eagerly seeking knowledge. Thomas Grey wrote in his Elegy Written in a Country Churchyard:

Full many a gem of purest ray serene
The dark unfathomed caves of ocean bear;
Full many a flower is born to blush unseen,
And waste its sweetness in desert air.

We at OSDD refuses to accept this status quo. And our e-learning initiative is a step to make knowledge free from the narrow confines of elite institutions to the wide open world of internet. It is also our little contribution to humanities’ tireless effort to create a world, as in Tagore’s words: 

Where knowledge is free
Where the world has not been broken up into fragments 
By narrow domestic walls
Where words come out from the depth of truth
Where tireless striving stretches its arms towards perfection
Where the clear stream of reason has not lost its way Into the dreary desert sand of dead habit.

What gives us confidence to launch this e-learning initiative is the large academic and scientific community, already involved in OSDD. Some of them have already been using e-learning as effective tool to train researchers in OSDD activities. They will provide lectures on various topics to the benefit of all, even those who are not even members of OSDD. This will include some well known teachers, from reputed universities, who will provide their lessons over this e-learning platform, to reach to those who are not lucky enough to be in their classrooms.
We would urge the student community to make the best of this opportunity. The power of the web is unleashing an unprecedented openness in science. Today the students, particularly in the developing world, have more opportunities for learning than the generation before them.It is for them to make full use of these opportunities. 
The following lines of Lord Alfred Tennyson’s poem Ulysses has special meaning to those who would not like to rest on what they have got in life. Ulysses, who after winning his battles and epic voyage returned to his Kingdom, but decided to abdicate his thrown in favor of his son Telemachus and start a new journey. The poem Ulysses is his farewell speech.

How dull it is to pause, to make an end, 
To rust unburnish’d, not to shine in use! 
… And this gray spirit yearning in desire

To follow knowledge like a sinking star, Beyond the utmost bound of human thought.…To strive, to seek, to find, and not to yield.
OSDD is for those who seek to go beyond the ordinary!


Wednesday, August 24, 2011


 STEP  1

                              Are u  a registered  member of  OSDD (SYSBORG )  

                              NO               JOIN OSDD   check your mail after 24 hrs

                              YES               LOGIN





 Submit  or Search 








OSDD released    New data base  SyncDB

                LOGIN              OSDD Sync DB Tutorial               JOIN OSDD

The Following Are Guidelines for Making Entry into the SyncDB

  1. Author name is automatic and reflects one's login name
  2. E-mail where the confirmation for the entry is to be posted should be entered in the e-mail box
  3. Institution can be selected from the drop down list and if not present in the list "other" can be selected
  4. Preferably the IUPAC name of the compound may be entered though it is not mandatory
  5. Organic or Inorganic may be specified. Further classification such as heterocycle (may be further to quinazoline, quinoline, indole, pyrazole, isoxazole), acyclic, alicyclic, aromatics for organic compounds and metal chelates for inorganic may be entered in the blank space
  6. Whether the structure of the compound is reported or it is new should be specified. If reported the Patent or publication of the corresponding URL may be provided for ready reference
  7. Compound can be entered in two ways. Either it may be loaded as sdf or mol file or it may be drawn in the Java applet. Compound number will be generated only if the compound is new in the database. If a structure is already present in the database which was entered by some other institute or researcher then the duplicate structure cannot be entered
  8. Preferably compounds with more than 90% purity should be submitted
  9. It is mandatory to enter the HPLC data and HPLC spectra for the organic compounds. The required fields are provided. This is considered essential for ensuring the purity of the compound. Additionally in case the compound is found active in the preliminary screening and a resubmission is required this will be used as one of the parameters for confirming the purity attributes of other batches. The HPLC data of a submitted compound should be relatively new (recorded recently)
  10. 1H and 13C NMR of the compound have to be uploaded. This can be in the form of PDF or JPEG or TIFF format
  11. The mass spectra of compounds can be uploaded in the form of PDF, JPEG or TIFF format. It is mandatory and the molecular ion peak of the compound can be entered into the provided space
  12. Solubility of the compound should be mentioned
  13. If an old/ known compound is submitted which has been investigated for any kind of biological property earlier, the activity data for the same should be provided
  14. If the synthesis of compound is a structure-based design then the preferable biochemical target may be indicated
  15. Any other information concerning molecule which is not included above may be provided in the remarks column
  16. The software works nicely on all the web browsers




Tuesday, August 23, 2011

OSDD – Awakening a Scientific Revolution
                                                                   Dr Prita Anil

Though the M. tuberculosis genome was sequenced more than a decade back, much scientific progress have not been accounted for, to find a cure for the ancient but deadly disease. At a juncture when practically there is no ongoing research for an anti-tubercular drug and multi-national pharma companies have dropped such R&D from their schema, CSIR, India has taken up this Herculean yet noble task, by creating a collaborative, co-operative, community-centered platform called OSDD of which I am also a proud member.
The saying “great things are done by a series of small things brought together”  holds true in case of this open forum where work is contributed in the form of numerous online projects by a variety of people from all walks and class of life. So great has been the endurance of the community that an incredible achievement is on the way as more and more have risen up to the challenge.
What sets us apart from other species is that we humans are driven by ambition. It gives me immense satisfaction to see that OSDD has succeeded in awakening the hitherto latent ambition and scientific temperament in the students of present day by giving them access to first hand scientific research.
This noble mission with a difference is here to stay and the world over has started taking notice of this self-sustaining innovative model of open source research.  
In the true spirit of science and in the undying quest of knowledge there is nothing more a researcher can ask for –

 “come join the national mission” - be a proud Indian, be an OSDDian
   prita anil 

Sunday, August 14, 2011

Open Source Drug Discovery is not a research project:  it is a movement .....



                                                              JOIN OSDD 


Thursday, August 11, 2011

Now in my career and research I feel  I am not alone

Swati Gandhi

In India   every higher educated girl is facing  some difficulty of choosing the direction after  her studies.
One road taking to the job where  she have to work out of field
Another road leads her to the academic career, go and teach the half and shallow knowledge.
Third road leads her to the social life where she  have to dump her  career and have to get settle with family 
Last road was leading her  to progress with research. 
I thought of opting the fourth option of rising and growing with research.
My selection was research and learning. 
to continue my passion in science .
I  passed few months thinking of what to do 
and praying to God
 to show me the correct place for my dream . 
 One day my friend called me and asked to meet in college to discuss
 some project .
I became very happy .
We met and he said that the
 is giving an opportunity to work 
and collaborative  research.
 I felt like  a rebirth, a kind  of relief .
My mom and dad sat beside me and gave me the hope . 
 I can do it.
  I   got an opportunity to use my knowledge 
For the noble cause of finding affordable drug for the
 As we are a middle class family .
to spend money for doing research 
was not at all possible 
 OSDD solved my problem as now I can work from 
anywhere and everywhere 
to learn and work ,
always  in  touch with my field
and chase my  beloved dreams.

Gradually , 
I got a chance to interact with many people
 who are contributing their knowledge  to OSDD .
Many of them are managing it with their daily jobs 
may be a scientist 
may be a college  professor 
may be a house wife
may be  a researcher .
To my surprise
the best thing 
which fascinated me about OSDD 
 that they are (now  we are ) not asking for our qualifications
but only our knowledge ,
our devotion ,
our dedication,
our willingness
 to serve the humanity.
I was devoting my whole day and night to bring out the best I could. 
This helped me to learn a lot & contribute to the 
collaborative  research  world  .
Apart from learning the subject ,it helped me to nurture my qualities by giving me the challenges like finishing a given task on time, 
working with the team, managing the groups, validating, curating

 There were times when my internet was in trouble  my system was with low resources
 low speed ,
low bandwidth.
 But my passion never got low.
 I was trying hard to manage it
My group
Helped me to overcome it
to finish the things up. 
The fellow mates and all my friends were with me always, I got the time to recover and again I got back to work.
 Super computing is the award & reward osddians got , as to experience the supercomputing facility was  like a dream.
Feeling lucky for getting great experience of it.
I am very thankful
 the one who initiated the idea of open sourcing.
It is really like a boon to me and will always keep working on it and going to contribute to the best I can in all my life. 

Monday, August 8, 2011

............Once I struggled for computer resources.................................

      Samir K. Brahmachari- OSDD Mentor(DG CSIR) 

@CDAC GARUDA  opening boot camp at   Malabar Christian College 

"Once I struggled for computer resources   and internet access; now I have access to super computing facility from my home.  OSDD project made it possible."   Swathi Gandhi  Osdd researcher from Gujarat

      Revolutionary initiative happened in the 
Indian Science  Policy


In my career journey as a teacher, the passion for  learning and knowledge, had diverted and dissipated in  different directions. Working in a college, located in a rural area, besides teaching, there were a lot of things to be involved and I did enjoy them too.  But the quest for higher learning I could not pursue much and I lost the focus in the course of time. Blame is on me, not on circumstances
 In an attempt  to be back to the stream , I joined University Department in early 90s as a researcher on  part  time basis. Commuting about 70 km. single way between  my institution, Marthoma College, Chungathara and Calicut University on vacation days and holidays, itself was not easy. Then there was also the tiring synthetic and analytical work in the Inorganic Chemistry lab.
It was mainly for literature survey and thermal decomposition studies I had to struggle for internet access and computer programs. Eventhough computers came to My Department at that time there were many constraints regarding working hours.  Fortunately one of my fellow researchers was having  inertnet connection at his home at that time, even though it was slow and also the power and connection failed intermittantly. Somehow we together did much of the work at his home. Meanwhile I also installed a system and a slow dial up connection at my home. Being employed, I could afford it. In the light of my experiene narrated here, one can easily imagine the plight of students and researchers hailing from rural backgrounds and are economically or socially backward. Their destiny has not changed much through these years.
Today, informatics and computational methods are part and parcel of all areas of knowledge. Computers have prolifirated much in our country. But  it is largely in commercial and administrative applications and to some extent for educational purposes. The initiative in the ares of  higher learning and research is very meagre. Only very few of the  institutions have enough hardware and software requirements for advanced learning and research. Young talented students from rural backgrounds and middle and lower  ranks of social strata can never hope to use it. They depend largely on public sector and Government Institutions for their education.   Reasons are easy to be identified. Lack of awareness, non availability of fecilities or non affordability of intensive training and coaching required to cross the entry barriers etc.  But this does not mean they lack talent, innovative mind and creativity. It is a fact that  vast pool of these resources remain undertrained and underutilised.
Under such circumstances, for the first time in our Nation’s scientific history super computing power reaches genuinely interested researchers throughout the length and breadth of the country.  By all means it is one of the most revolutionary initiative happened in the Indian scientific field  in this decade Until now only those belonging to the elite institutions could even dream of having access to computational fecility of this level. OSDD and Garuda has done a great service to the nation in throwing open this fecility to the OSDD researchers.

 It has already built up a community where scientists, researchers, students and others with genuine interest come together, exchange ideas and knowledge, share expertise and fecilities. It aims at involving the un-utilised or underutilised intellect of all those who can contribute.  Now students  even from rural institutions and even educated lady home makers can make their own contributions to scientific research, provided they have a genuine interest and commitment. Already such contributions are giving steam to the Open Source Drug Discovery movement. With the advent of supercomputing fecility OSDD community is looking ahead for greater strides. Sameer Brahmachari, Director General of CSIR  announced the opening of Garuda supercomputing facility on 28th of December 2010 Christian College. What a researcher requires is a broadband internet connection and a rational thinking and a genuine dedicated approach to doing science. They will now be able to design molecules with desired properties or analyze genomes or complex protein structures by accessing the super computers, the Government of India provides. This is expected to fire up hitherto untapped, unnoticed talent of Indian Rural Youth.

OSDD itself is a mission with a difference. Developing affordable drugs for neglected diseases affecting the common people of India and other third world countries is the proclaimed aim of the project. The killer disease, Tuberculosis is the first target OSDD is working on. With the appearance of drug resistant varieties the killer epidemic is looming large over the country. The common medicines used to treat this disease were developed some fifty years back or more. Hence developing a more effective affordable drug becomes an issue of great national priority. This is the rationale for OSDD. It intends to develop non -patented drugs in open source.