C2D Memories....

Its been a week, in fact more than a week but C2D memories are still fresh. We are still exchanging photographs (in fact I wanted to upload the best photograph here but I was really confused...Every photograph has its own story!!).
Waah...ahaaa these are only words that I want to use to describe C2D conference. Here I would like to mention that though I am from TBGO, this blog is for all of us. After all we are a team: TEAM OSDD. Our bosses tried hard (really hard) to separate us using the names of the two teams (My apologies to both the bosses) but hey guys we still came together and this was seen during the conference as well, when students from both the teams interacted, discussed and shared their knowledge.
After 3-4 months of online work, the onsite part started with the workshop where everyone was new and just were not more than chat friends, had lots of work pressure and deadlines (aiyoo deadlines). But finally we (at least IPW) achieved what we decided and got our annotations curated and waah gr8 job done by Dr. Anshu's students with Dr. Kitano, Dr Samik Ghosh, Yukiko and Dr. Nagasuma's guidance. The network poster needs no explanations or descriptions. It says everything itself where hardwork interwoven with several neurons resulted in such a big achievement. When IPW team's poster was one of the landmark achievement's of the conference, Team TBGO wonderful act on the stage was the one of the major topics of discussion throughout the conference. With a second special screening of the skit for SKB, and a detailed discussion with SKB, TBGO team leaders were really flying high.
Attending wonderful talks, tweeting the whole day with new netbooks, meeting different people...aaahhh I don't have many words to explain all this. Moreover I would also like to mention the gr8 performace by Sahara Band on the last day where everyone jumped on th stage and converted a decent band to a bhangra party (Yess....Saakshi we finally managed to do this....Guys, we always wanted to have a JAM session and we did that!!!)
And hey how can I miss the media coverage......We were on TV as well ...btw I hvnt seen that myself if anybody has seen that do inform me.....Anupam Me and Saurabh with Anshu mam, SKB, And our Science minister gave interviews to Aj Tak, CNBC....gr8!!
Professionally what else can you expect and when you get so many good friends...fulltooshh enjoyment then you have achieved everything......
Hope to see you all again in the second round of C2D as well!!!!

IPW Rocks!!

Today the IPW Team was delighted to see the Mtb Network on a POSTER that they have generated in past few days. There was a lot of enthusiasm and excitement. Prabhakar tried his best to pin up the poster with help from the team, and Samik and Yukiko providing full support to them. The Project Director, Zakir Thomas, was also a part of this activity and the Volunteers captured the Team with their Network :)

Look forward for more from this dynamic and talented members of IPW..

Building strong India

The exciting science journey on second day at JNU started with presentation by Kiran katoch on "The Problem of TB in India, A Clinicians Perspective". Her speech gave us a clear view about problems in diagnosing TB as well as the current methods and the developing methods in diagnosing TB. After her speech we were gathering information regarding the importance of computational technology in life sciences. Presentation by GPS Raghava, Samik Ghosh and Hiroaki Kitano on bioinformatics threw limelight on computational biology.After having a good lunch, our journey continued with the presentation of work done by IPW team. To get ourselves refreshed IPW team got game for us using cell designer software (sow & grow). Science requires collaboration of information from various disciplines and this was exemplified yesterday. We as TBGOs learnt the basics of cell designer which can be used for our future strategy.

After a number of serious lectures, we had an enjoyable interaction with our PI, our team members and ZT sir. We all got to know about each other and shared our experiences.We had a good dinner and went to YVK eagerly waiting for the dawn to continue our journey.

JNU day of C2D '10

After an interesting first day of the C2D '10 conference, with a rocking TBGO team's drama performance, IPW's funny video, the annotators looked forward to a normal day at JNU.

Kiran Kotoch talked about the problems of TB in India in a Clinicians' perspective. Some of the clinical difficulties encountered are early diagnosis of the disease, multi-system involvement, Co-infections, latent tuberculosis, Dormant infection, etc., and the prevention of the disease and vaccines administration is a challenge. It is interesting that no new drugs has been administered for the last 20 yrs.!!!
Some of the methods under program to diagnose the disease are sputum smear microscopy, radiology to a limited extent, culture diagnosis, line probe assays / PCR or biopsy, FNAC, specimen from affected organ. Sputum microscopy is relatively faster and the resports are available in 24 hours. But this can be done only when there are atleast 10000 baccilli. Moreover a dead bacilli and a live one cannot be differentiated. Other tests that are used are gamma interferon assay, chromatography – mycolic acid patterns by HPLC, macrophage based methods – viability of mycobacterium but low sensitivity, patch test with TB MPB 64 (– not evaluated in endemic countries).

GPS Raghava introduced to us the drugPedia and MycoTB which is an In silico approach. MycoTBis an open source software for managing Mysobacterium tuberculosis data exclusively. Samik Ghosh and Matsuaka Yukiko taught the participants of the conference about the software, Cell Designer. After lunch the members of the IPW team helped the other members from the Glycomics, Gene Ontology Annotation team, Protein structure/Fold Annotation team, Glycomics of Mtb team and Immunome of Mtb team. They were patient to teach all the participants even when being asked again and again.

At dinner time, the TBGO team had a round of introduction . The team leaders shared their experiences with the members and they taught the members the mistakes that they see in the members' annotated sheets. Members was recognized by their E-mail id.s rather than their names!!! Most of the members belong to the Hanger's group and he was on cloud nine whenever his name or his team members talk aloud!!! Fellow annotators thanking Swathi Gandhi's helping character, Chotu re-enacting his piece of drama, VS answering the questions from the annotators were some of the interesting happenings of the discussion. ZT joined the team later in the discussion and enquired the annotators about their experience. Most of the students agreed that their motivational factor was the thought that their work would help save millions of Tb patients across the globe!!! One of the annotators Hemant expressed his view on the Indian educational system and suggested that students shouldn't be evaluated by the marks given, but by their hardwork, innovation, intellect and commitment.

After a nice dinner, the participants returned to Vishwa Yuva Kendra for a good night sleep!

TBGOs day

Most awaited day " C2D conference " started with warm welcome by Zakir Thomas follwed by introduction of OSDD theme and the potentials of this program by our SKB.we had speakers from various parts of the world. We had an interactive session with the cheif guest hon'ble ministry of science. After a very long serious session, we the TBGO team breaked this seriousness by a comic skit (TBGO annatation club) which made everyone to sit straight. TBGO rocked the first day. TBGO GOing..........
The TBGO team after the conference went to India Gate and had very nice time with our friends.After having our dinner, we went to sleep dreaming about tomorrow's exciting science journey.

BUILDING STRONG INDIA

INDIA stands unique among other countries for its" UNITY IN DIVERSITY" and I experience it now. Number of people with different age groups, languages,custom have joined here to build a strong INDIA-FREE from poverty, disease through science. The young minds are ready for science journey to build a strong INDIA through "C2D".This will serve as a starting point for the indian economic progress with experienced minds guiding he enthusuastic young minds

TBGO Rocked.........

Woww...What a start!!!!!!
TBGO team rocked C2D...
Three Cheers for all the students. 9 Team leaders joined us almost a week before the conference. After long working sessions of curations, they practiced whole night to prepare a skit which they executed very very well on the stage.
They recieved great applause!!!! Guys the skit was in high demand and we performed the skit again.... a special screening for SKB :)
After a long, tiring day, students got to enjoy a lot at the INDIA GATE.
Ubuntu Chris, DiponLove, The Moderator, Sleeper Deeper, SS, Silent peacemakers accomapanied by other members and the managers with our very own Ekta.
But we won't stop here. There are many goals yet to be accomplished.

Higher and Higher!!

One of the Historic moments in the course of Science where all the ideas that prevailed, will change forever. The concept of Science which was considered to be closed Science will not be close anymore after this historic moment, and that was only possible because of a eminent person who came up with this brilliant idea, and he was none other than SKB. It is great to be a part of this programme. The students got very much motivated under the presence of our beloved SKB. The students are all now charged up and are ready to walk the path that our beloved sir shown us and nothing seems to be possible in the course of Science.

At last the wait is over!!! The students arrived VYK with face full of smiles and excitement.. They met their team members. They were much more excited by the surprise gifts..

In this Pleasant morning, the OSDD c2d programme started off with a welcome by ZT and the students are awaiting the most awaited moment, the Speech of the Minister of Science and Technology Dr.Prithviraj Chavan. SKB introduced the chief guest to the gathering.

Yesterday was another day of curation work. Filtering all the wrong entries was a troubling experience but we were happy about the quality of the entries that we have achieved. Though it was a long serious day, we had some laughs too. Chotu declared that he had 7 hours of sleep (which made the other members mad, as they had less than 5 hours of sleep) but added after a pause that it was for the last 3 days together, which made the team roar with laughter. Its proud to say that Chotu Lumbu has polished his linguistic skills that he is almost a tamilian in his talk (But he is from Delhi). Ubuntu also tried her speech in Hindi, only to say Bhoot (Ghost) instead of Bhookh (Hunger). We tried some telugu, kashmiri and bengali too. The day was filled with Krazzy activities, with everyone laughing at each other (there were LOTS of reasons for us to laugh). We were tweeting all the day, with some new designations (Eg. Moderator turned to Room keeper when she was trying to change the temp. of Air Conditioner and being the door-man(woman). She was also bugging the bugger bhaiya toooo much.) We even discovered that Bugger Baiya has a good talent of story telling which we enjoyed late at night. With the last day of curation work to look forward, we went to sleep.

Today, it was a lazy start (being the last day of work). We completed our curation work, had some snaps together. But altogether it was a fast day that we had to rush through. Our friends have already arrived and Bugger Baiya was having constant calls which made all of us to look forward to meet our friends!!!

Fishing to Super-Computing

With a bright sunshine, we (TBGO team) took off a good start to another day of curation work. Though a regular day, it was filled with knowledge, wisdom, fun and frolic. Chotu Lumbu's crazy heights (especially at night), the Moderator's unsuccessful attempts of peace-making, SS's constant curation, Sleeper Deeper's snore filled work, the Hunger (Bugger Bhaiya) happy-GO-lucky work, Dancing Sangeetha and Rajeshwari's moves, the Coffee Freak (Ubuntu, taking two coffee cups at a time) really freaked out. The Hanger, were some of the day's fun moments. The Moderator took on the job of moderating the AC temperature control as well! The Silent Keepers (Sangeetha and Rajeshwari) were amazingly stay-put @ the silent zone.

We did some very very serious work as well!!! Rajender introduced us to his Zebra fishes (Fishes know him better than anyone). We even asked them (fishes) to eat well and drink lots of water. We got trapped at the Orbitrap Mass Spec room for a loooooong session (Anyway we learnt a lot from Rhishi). The buzzing sound of the printer confused us with the MassSpec (& also broke Ubuntu's sleep). Solexa Man (Ashok) explained about Solexa (The famous genome sequence analyser) and we were confused who was solexa, the Man or the machine?!! We had a session with Pandey ji and his TB (terabytes) supercomputers.

We spoke to SKB via Skype. He enquired about our work and our stay here at NDelhi. He encouraged us to keep up this good work.

After the hard work, we went to our welcoming bed at night only to dream about our GOids and literature papers!!!!

BIG network

The IPW Team is eagerly waiting for the BIG network of metabolic reactions which is being generated by Cell Designer at NIPER, Mohali. Anup, a core member of the IPW Team, is working online, with Kaveri, from NIPER and closely following this job which will finish in a couple of hours.

Anupam and Ahalyaa are working really hard to reach their targets for today. Aparna and Vijaychitra are focusing on some of the difficult to annotate proteins in their set, whereas Kausik works ONLY with difficult to annotate proteins. Another interesting Group is Akanksha and Prabhakar, trying their level best to understand PPEs and lipoproteins :)

Rohit is busy making presentations and having serious discussions with Anu, who has joined us from NCL yesterday. We also have with us Samik and Yukiko from SBI and they are really excited to meet the Team. Yasha and Gayathri from Group 4 are really exhausted with too many hypothetical proteins to annotate!! And finally there is Ashwini and Priti who sit quietly during the sessions to surprise the Team with a huge number of proteins that they annotate every hour!!

IPW is all about team work and the Team is on the lawn for the evening play session......more to come after this break!

Crazy "GO"ing !!!!!

Yet another Day..........So many curations left!!!!!!!

But hey guys....we won't let the day go just like that.........

With all the doubts (with lots of arguements and fighting: Dipon and Deepa) being cleared among the team leaders and lots of entries in the final sheet, TBGO has gone off to a flying start. Converting electronic annotations to manuel literature, formating the entries, drinking coffee and tea in between, discussions with VS, planning the work with Deeksha and Saakshi, made up most of the day. But hey, we did have some fun doubled with the added members Sangeetha and Rajeshwari.

Bored??? Bugger Bhaiya (DiponLOVE: he wants this in red... his fav colour..... but guys red is for wrong annotations and how come your whole sheet is red?????????????) will entertain us with his wit! Scribling on the white board, waiting for the hanger ubuntu to hang (so we can crack some jokes), calling each others by funny pet names, were some of our pass times. The Moderator (Sham) became the moderator between The Hanger (DiponLOVE) and Sleeper Deeper (Deepa), who finds the biggest challenge is to keep the air around them calm! Chotu Lambu (Vivek - Youngest and tallest), who unfortunately doesn't like his most dearest name, laughs like a mad man whenever he is curating his entries. His madness was at its highest, especially when he started banging his head and swirling in his chair :D :D Silent Suresh (SS) is the most silent worker of this group. Peacemaker Karthi is the right hand of Bugger Bhaiya. (Bhaiya has a left hand vacancy. Lets inform VS!) Ubuntu Chris is the proudest of all cause everyone loves to use ubuntu (:Ubuntu herself) which everyone find it difficult to use (: Dipon), as it gets hanged. Chris the Great Ubuntu resolves the problem of others with her great ubuntu features and accesories. The newcomers are trying to maintain their silent image (which is really hard to keep up with the rest!!!!). We have yet another member... Yipppyyyyyyyyy none another than JADU (Ubuntu Chris)... Our own JADU from KOI MIL GAYA.... Hey aliens are also GOing.!!!! (special request from Moderator: No Red) So GOing!!!!

Happy GOing.......

P.S.: Nicknames are patented to TBGO. Copying is strictly prohibited. Terms and Conditions applied.

The Last Mile

IPW Team is pushing hard to finish the last mile of data QC before coming to the on-site phase at Teen Murti. The Team at this hour (11:14 pm) is sitting in the lounge of the Guest house concentrating on the task. They have shown unending commitment to finish this humongous task in such a small period of time!!!

But this is not all... The Team is very active when it comes to play sessions too!!! They take a 20 mins break every evening in the lawns of HRDC, playing and having fun.

As most of the selected C2D members have boarded their trains, the eagerness to meet the Virtual Team is getting more intense.

Cheers to all the members who have made C2d possible!!!!

Get Ready for the Swirl

Many of the participants of Connect to Decode must be boarding trains today and tomorrow. Do take enough rest while in train. When you are at the onsite phase your PIs have plenty of assignments for you that might keep you awake almost the whole night during your stay. The IPW and TBGO team are working without a break to meet the schedule. This is probably the most intensive QC exercise you can come across. So its work time folks. But you bet, you are going to have a ball of a time. It will be one great learning exercise – for everyone- including the Connect to Decoders, the PIs, the organisers and the rest of us. All of us are eagerly awaiting your arrival. Buckle up for the fast drive!

TBGO Workshop Day1

TBGO C2D: Gene Ontology Annotation by the students across the world. And now they are here in Delhi for the final rounds of their work.

Lets hear from them their experiences for the DAY1.

Hey, We (PSGians) landed here at the Nizamuddin Station with hand full of luggages that we can hardly carry. Mr. Sukhbir received us with a big smile and with a weird sense of direction! We finally reached IGIB Guest House. After lunch with Sukhbir and Deeksha, we went to IGIB lab, where we met our Guide, Dr. Vinod Scaria. Dr. Zakir Thomas gave us a visit. He even sneaked at Suresh's work and gave him a shock (Suresh didn't know that he was talking to ZT)! Anyway, we finally ended at the conference room with a room full of scientists and "kids" (Thats how they called us!). After surviving the questions that were bombarded at us, we got to continue our work! We returned to our rooms late at night, to a much awaited cosy bed and looking forward to tomorrow's dawn!

Sunday!!! Hurray... Its a holiday... I guess not! :( We worked! Dipon and Vivek joined us for lunch and ever since, they are stuck with us! Since it was Easter, Shamini (Sham), Dipon, Suresh and Myself went on a road trip to St. Sacred Heart Cathedral with Mr. Saurabh, late in the evening. We pushed cars (boys did this exercise and VS helped too!), jumped on the autorickshaw (which got punctured) and even trended on our footwear. We roamed the streets of Delhi to find Palika Market and we finally found a bottle of water (Bisleri Bottle)! Open Central Park was crowded but we had the time to relish our bottle of water! We found kids dancing MJ's moves on the road, woman washing her clothes, Delhi band playing some tune and the calm trees shadowing the streets at night. We got on the Metro, saw Hanuman Mandir and returned back to IGIB. Poor Deepa, Karthi and Vivek. They were stuck with small notebooks and annotation work. Dont worry, they'll get their due credit (I hope!).

Joining forces against TB

A partnership involving the US Food and Drug Administration may speed up delivery of new tuberculosis drug combinations, says Priya Shetty.

New TB drugs are desperately needed. The existing treatment is a cocktail of drugs that must be taken over 6–8 months. Often, one of the biggest challenges facing healthcare professionals is simply ensuring that their patients finish the course of treatment. Full-Text Article: http://scidev.net/en/health/hiv-aids/opinions/biomed-analysis-joining-forces-against-tb.html

TB GO on the GO

The TB GO team has moved to onsite mode. A nerve centre has started functioning at the CSIR IGIB facility at Naraina. Yes, the same centre which sequenced human genome and the one which hosts the IT infrastructure of OSDD. Amidst the hum of the machines and scientists in their coats, a bunch of Connect to Decoders has moved in today to Dr. Vinod Scaria’s lab.

It is indeed an interesting lab. One which any bio-informatician would like to be part of. A series of servers lined up in a state of the art server room gives out a regular hum and lights go on and on. Few rooms away are state of the art sequencing machines. Adjacent to the server room separated by a glass, is a row of computers.

As you walk in a bunch of Connect to Decoders are already infront of the screens and immersed in working. They had just reached New Delhi railway station two hours ago. This is what is called hitting the ground running.

In the afternoon they had an unusual visitor. Jean Marie from UK who is writing a book on innovation in China, India, South Africa and Brazil was wanting to know about OSDD. What better way to know about OSDD but to speak to Connect to Decoders.

The GO team is here to do the last bit of QC. Or, may be, they will throw a surprise when you meet them. You don’t get a bunch of bright young minds and expect nothing, right?

To Tokyo via Ghaziabad

The IPW team is working extra time to finish the QC on the IPW data. The team is led by Dr. Anshu who is at the White Board with plans, sketched and schedules. The team is gung ho and literally burns midnight oil. It is not sure if burning midnight oil is the correct term to use as they go to sleep only at 3.00 AM in the morning. Few days back they had the excitement of seeing the first network, now the effort is to make it as comprehensive and as meaningful as possible. They are online with Tokyo on all the days.
They had the Chief Mentor calling on them to see the progress. They were on skype with SBI Japan. Dr. Kitano joined from Tokyo. Discussions were on plans, networks, pathways and how to develop production level data to be readied for mapathon when the rest of the team comes in on 9th. Later the network map generated on Cell designer was seen by the Chief Mentor. Dr. Brahmachari was thrilled to be with the Connect to Decoders. Questions started flowing on all directions. What is critical or not… what is the function of the pathway, which is distinctive which is not…. And Dr. Brahmachari was most impressed by the young Connect to Decoders.
Later Dr. Nagasuma joined from IISc Bangalore on the protein structure annotation progress.
The air is abuzz with activity…technology is in full flow
You can expect an exciting scientific exploration during the onsite phase... Gears up, folks!

First Network

It is exciting and emotional to see the First Network that the IPW Team generated using Cell Designer for the first set of quality checked data !!! Samik from the Systems Biology Institute. Japan, has been interacting with the Team working from Delhi through Skype calls. Today we also interacted with The Chief Mentor and Project Director of OSDD through Skype and had interesting discussions on network analysis. Watch out for more...we are at it.

Annotating the Tb Glycome

Glycome… the fancy and less friendly cousin of the proteome and the genome is an interesting component of any organism. Comprising of the enzymes that add, lengthen, reduce, modify and change sugar residues in a protein or lipid, they actually comprise that “unknown” factor that the scientists often do not dare to look into. Glycans are difficult to study : with 9 sugars able to branch in endless possibilities and form zillions of structures, having no template driven synthesis mechanism and extremely challenging to sequence. But still, glycosylation is the most prevalent post-translational modification, often being responsible for cell-cell interaction, infection development, antigen-antibody mediation and reproductive biology to mention a few and hence cannot be disregarded. However, though their role in infection development is acknowledged, very little experimental research is actually available on it. Prokaryotic glycosylation came into the focus of scientific research only in 2002 when a N-glycosylation equivalent pathway was discovered in Campylobacter jejuni. Research has been ongoing since then to identify these genes in other bacteria.

The GlycoMtb team of the OSDD C2D initiative, focuses on the Mtb glycome, a very poorly characterized sector of the Tb genome. The existing genome annotation showed only 100 known genes for glycosylation in Mtb. But clearly, there has to be more…! In an organism that has the most complicated of the cell wall structure that comprises of glycolipids, an organism that fools the host defence mechanism and develops the deadliest of the diseases in humans definitely has more than 100 odd genes for the glycosylation pathway. Armed with this belief, the GlycoMtb team used a 2 pronged approach. The first phase was to look for homologues of bacterial glycan modifying enzymes in Mycobacterium. This gave an important lead… the answer to the genes responsible for glycosylation lay in the 1500 odd genes annotated as “hypothetical protein/conserved hypothetical protein/conserved membrane protein”. Hence bagan the long journey amidst the amino acid sequences, looking for sequence similarity, pattern matches and secondary structure matches. The team finally emerged 2 months later with a full functional prediction of the unnamed proteins…. Reducing the number of "proteins with unknown function" from 1500 to 270. As of now we have about ~400 genes which may be glycan modifying and maybe another hundred or so which are glycoproteins. This phenomenal task has only been possible due to the “nothing is impossible” belief of the team members , essentially made up of master’s students across the country.

The team is still at work incessantly, trying to make a more comprehensive list of the enzymes and proteins which they feel holds the key to a lot of unanswered questions in Mtb infection and hoping to release the data in the upcoming C2D conference in April 2010.

BBC World News on OSDD

Tuberculosis is one of the world's oldest diseases. It's been so good at surviving through the millennia that today one third of the world's population carries it. As certain strains begin to develop resistance against the commonly-used drugs the hunt is on for a new treatment – a hunt that has taken more than thirty years without success. Angela Saini reports from India - which has a fifth of the world's TB cases – on how a new online project is hoping that by pooling the knowledge of the world’s best scientists they might come up with the answer.

Listen to the Clip: http://www.bbc.co.uk/iplayer/console/p006wgns

More on the clip at Angela Saini's Blog : The Hunt for the new TB Drug

C2D Programme Update

We have just updated the Programme for C2D10. We have added a few more speakers and workshops that we feel the C2D team would enjoy.

The Programme details are also available at the C2D10 Website at URL: http://c2d10.osdd.net/programme

C2D Onsite Phase Begins

At the Ops Room
Away from the buzz of Delhi, nestled among green trees frequented by birds, is CSIR's Human Resources Development Centre at Ghaziabad. HRDC is having a bunch of unusual group. Usually frequented by scientists and leaders of CSIR, is now the hub of Connect to Decode activity. Dr. Anshu Bhardwaj has quietly started the onsite phase of Pathway Annotation project. Her handpicked team leaders are quietly doing the Quality Control (QC) check of the data annotated by the team.

As you walk into the room, you get the sense of walking into the Ops Room of a major military operation. The air is tense. Hardly any words are spoken. Work is brisk. Fingers work on the key boards like that of a skilled tabla player. You might have heard of power play in cricket. This team has devised power sessions which last for an hour. After each power session there is a lean hour, again a power session...and on and on they go till late into the night. Dr. Anshu has to drag out her team for lunch and coffee. Except on one occasion- if a peacock is dancing with full bloom, the team takes a break to peek a look and you can see Rohit running with his camera. But sensitive as they are the peacocks shy of their dance very soon and the team is back on their keyboards with their fingers dancing with double vigour.

Some photos…

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.