It Aint Gonna Work

If there is one phrase or a sentence which OSDD is very familiar with it is this: ‘it is not going to work’. And many a time this will be followed by a highly condescending ‘drug discovery is serious business’. This was at times accompanied by ‘look, you guys don’t understand TB research’.

Well, it had started even before OSDD was launched. Prof Brahmachari used to discuss about his vision of Open Source Drug Discovery in various fora. The Mint carried an article on Open Source Drug Discovery project on September 20, 2007. It had an interesting quote: “ You’re kidding me,” said the chairman of one of India’s largest pharmaceutical companies when he heard of Brahmachari’s idea. “Open source for drug discovery?” Prof Brahmachari did not listen to such ‘sane’ advices. He obviously is made of sterner stuff to be deterred by naysayers and went ahead with his plan. OSDD was launched on September 15, 2008. Many thought that it will die of its own. It wont just work. But then they didn’t realise that there are some youngsters around the world who just don’t get it. They don’t understand the meaning of the phrase ‘it wont work’. And they are the leaders of tomorrow. Today as OSDD is nearing 3000 members, a large number by any standards, it owes to people like Prof Brahmachari and others who just refuse to listen to ‘it is not gonna work’.

We had heard it again and again. The chorus was loud when we launched Connect to Decode. ‘It will not work’. ‘You wont get people to do this’. That was one line. Well, just the day it was opened, registrations crossed 100. And it went on to reach about 800. So much for that line. But there was a more serious line: ‘you guys don’t know what you are doing, you wont get quality data’; ‘you are going to get a lot of junk’. Well, that was a serious concern, but as Connect to Decode progressed, the power of the community annotation was evident. We got wrong data of course. And sure enough, they were curated by the community. But not junk, by any means. The community power proved the naysayers wrong again. A bunch of youngsters and not so youngsters who just don’t listen to ‘it just won’t work' are at it.

These are the folks who share the audacity of hope. They are made of the same stuff as that young American who chose hope over despair and chose to dream through a difficult childhood and went on with his Audacity of Hope to be the first in many ways in this world. OSDD understands and shares this passion of hope. ‘Yes we can’ is not just a campaign slogan, but is a matter of faith! There will be many who are waiting to tell us again and again, 'it will not work'. To them, we say, it wont work!

At OSDD, this is what we believe - Yes, We Can!

Together we will!!

Together we should!!!

Audacity of Hope

Connect to Decode onsite phase is just two weeks away! I cant wait to meet the heroes who have been so far contributing online. The work done so far is impressive. But to me more impressive is the process of collaboration and the lessons learned in organising such hugely collaborative programme. You have demonstrated that OSDD can handle huge volumes of data.
More than that, you have announced before hand that the results will be made available in the open to the world on 11 April 2010. How many science projects do this? Of course, Space programme does it. The rocket has to blast off on the designated day at the appointed time. But how many science projects?
When we were discussing Connect to Decode, Dr. Sukanya Dutta asked: why are you all stretching yourself? 'Nobody works to a deadline in Science!' Well my reply to her was if we are to do what everyone does, then why OSDD? Yes, that is what sets OSDD apart. We do things differently. We do not tread the beaten path. It is a new way indeed.
Yes, your hard work demonstrates that OSDD is a new way of doing science!
Announce that the result of a project will be available on a date, even as the project is ongoing? Isn’t this the audacity of hope?!

Sakaal Times on the Connect to Decode Genome Annotation Initiative

"This is an important important step towards drug discovery for effective treatment of Tuberculosis. Between April 9 to 11 we will be able to disclose data related to Mycobacterium tuberculosis, the bacteria that causes this disease which will be of help to scientist for effective drug discovery for the disease," Dr Samir Brahmachari DG, Council of Science and Industrial Research said. Nearly 400 researchers all across the world are collaborating through Open Source Drug Discovery (OSDD) programme of the CSIR through internet to generate data about the genetic information of the bacteria which will promise an effective treatment to the disease which affects 1.8 million people in India every year.


http://www.sakaaltimes.com/SakaalTimesBeta/20100322/5282265942248678442.htm

Getting Started in Gene Orthology and Functional Analysis

The latest innovations and rapid progress in sequencing technologies have substantially enriched whole genome data. Each genome consists of a unique gene inventory, which determines the specific phenotype and interaction with the environment. After 3.5 billion years of evolution, the number of species has expanded considerably. These species originated from simple life forms and have been confronted with complicated environmental changes. These variations, as a result of natural selection, are encoded in their genomes and provide clues to their genetic divergence from a common ancestor. The inference of variations between species by analyzing compositions of gene inventories therefore opens the door to the rich branch of comparative genomics.

Link: Getting Started in Gene Orthology and Functional Analysis

Weak link in TB bacteria cell wall

Weak link in TB bacteria cell wall: "The Mycobacterium tuberculosis protein LdtM2, involved in making “nonclassical” crosslinks in the bacterial cell wall, is required for virulence and antibiotic resistance. The study results, published online in Nature Medicine, could help identify new treatment combinations to tackle chronic tuberculosis infections.

Tuberculosis is a major global health threat. Drug resistance in TB is becoming a monumental [...]...

Gupta, R., Lavollay, M., Mainardi, J., Arthur, M., Bishai, W., & Lamichhane, G. (2010) The Mycobacterium tuberculosis protein LdtMt2 is a nonclassical transpeptidase required for virulence and resistance to amoxicillin. Nature Medicine. DOI: 10.1038/nm.2120 The Mycobacterium tuberculosis protein LdtMt2 is a nonclassical transpeptidase required for virulence and resistance to amoxicillin

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Multidrug and extensively drug-resistant tuberculosis

Multidrug and extensively drug-resistant tuberculosis: "In memoriam of Sir John Crofton (1912–2009), The greatest disaster that can happen to a patient with tuberculosis is that his organisms become resistant to two or more of the standard drugs... The development of drug resistance may be a tragedy not only for the patient himself but for others. For he can infect other people with his drug-resistant organisms...

The World Health Organization (WHO)...

World Health Organization. (2010) Multidrug and extensively drug-resistant TB (M/XDR-TB):
2010 Global report on surveillance and response. WHO. info:other/978 92 4 159919 1

Gillespie, S. (2002) Evolution of Drug Resistance in Mycobacterium tuberculosis: Clinical and Molecular Perspective. Antimicrobial Agents and Chemotherapy, 46(2), 267-274. DOI: 10.1128/AAC.46.2.267-274.2002 Evolution of Drug Resistance in Mycobacterium tuberculosis: Clinical and Molecular Perspective

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TBGO Team Leaders' Meet

The TBGO Team Leaders would meet from 5th -8th to discuss the progress of the annotation activities. In addition, they would have a chance to meet scientists working on Tuberculosis and discuss scientific projects.

IPW Team Effort

The young and motivated Team of IPW has reached the final stages of whole genome annotation of Mycobacterium tuberculosis. Some members of the IPW Team are meeting in Delhi in last week of March 2010 to accomplish the task of Data QC and data integration from other Themes of C2D. This smaller team will be working with other members online. During the Data QC process, the IPW team will go through the large repertoire of reprints of full-text articles they have generated and read at the time of data annotation.

IPW team embarks on the on-site Annotation phase

The IPW team will get together tomorrow in Delhi to embark on the on-site annotation of the TB pathways. The team mentored by Dr Anshu Bhardwaj will assemble for a couple of weeks to top up the annotations and perform the QC.

Connect to Decode TBGO Team into the last round of Annotations

The OSDD TBGO team has entered into the last round of annotations. This time the team of volunteers have embarked upon doing the QC and improvements in the Annotation Evidence Codes. The team has got together and assembled a large number of reprints of full-text research articles describing the TB genes and have started using them to improve the annotations.