Bio-wise and otherwise

On post-it notes

This week and a bit o' the last one have been chock full of discussions on content, content and more content. One would expect that to happen when a bunch of tech writers get together under the Californian Sun.

Literally. 

My routine over the last  couple of weeks has been somewhat on these lines: Come morning, down that breakfast, up and run to the conference room, catch my breath to hear the boss speak, and fight that szzzzzleep that seems to take over. Cups of coffee and muffins to go. Catch a few chat sessions with new found friends and smile into the lens. Make notes, notes and more to go.

Amidst all this intellectual flurry, nobody thought about thanking the post-it note  , which seemed to be pasted on white boards in generous numbers, during our lively sessions. The finished boards had tiny yellow sails popping out of every square inch of space, creating remarkable patterns in third dimension.

This little sticky note in yellow has turned the world upside down to have those ideas come tumbling out of the deeper recesses of the human brain. Notes in psychology journals say that these notes have a strange touchy-feely-sticky appeal to the users. They have an attention gaining aspect and  render a personalized touch to any study or idea or a collaborative effort. Research has also gone to show that surveys papers with sticky notes attached elicited a better response than those without 'em, mostly due to all these attributes.

Sticky notes have been shown to have a variety of uses which could include:

The Post-up—Provides methods for getting information into chunks
The Swap Sort—Shows listing and organization methods
The Top-down Tree—Works when the nature of the problem is unknown
The Information Map—Maps messy problems and complex relationships
The Action Map—Plans actions or maps an existing process

And who'd have ever thought that sticky notes and spiders had something in common as well?

It's not surprising then, that for the past few days, I have been dreaming yellow post-it notes (no, thankfully they did not have spiders in them). A few stuck to my bag (notes, not spiders), a few on my forehead, a few on the mirror. I see post-it notes everywhere now.

So when a well-meaning colleague advised me to start a wiki page to record all my meetings, I just dipped into my handbag and brought out a wad of post-it notes. Slowly, painstakingly, laboriously, I began to write.

He gave up.

The swanky new Web 2.0 generation was not for me.

I swear by my post-it notes.

Posted at 12:20PM Jun 21, 2007 by Manju in Sun  |  Comments[2]

Sister Act

I made a beeline to the Art of Living ashram today.

The second International Women's Conference was starting and I just wasn't going to pass up an opportunity to volunteer. Firstly, I love Guruji and the values he stands for and for just being there for folks like me.

Secondly, I love mah' sisters all.

And the sisters came with their knapsacks from 50 odd countries. Women from Africa dressed in the brightest of turbans, women in cool white, women in resplendent saris, women in jeans and tee'. This event was a confluence of women from all walks of life and organizations that support the cause of women.

The list of chief guests was a star studded one- of course the biggest star and the only man was Gurudev, beaming at the bevy of women surrounding him. Banu didi, his sister (and our sister) welcomed the guests warmly and there was not a trace of stress on her beautiful face, despite the fact that she was also the driving force of this conference.

Guruji Sri Sri Ravishankar urged the audience to Save Mother Earth by finding ways to improve the degrading environment. Women need not demand rights, they simply have to assume them- was his simple yet powerful message. He urged the sisters gathered to have fun and work as well- 'because you can find solutions to problems only when you are relaxed.'

Shukria Barakzai worked as a teacher in a school under cover ten years ago. Now, she is the editor for 'Women's Mirror', a journal meant for women in Afghanistan. She is also a Member of Pariament in the country. A perfect role-model for the occasion, Shukria talked about the women of her country not having to face one particular problem, but ever so many problems. According to her, self-confidence is the bottom-line, irrespective of the religion that a woman belonged to. 'Believe in your goals' was her message.

Shukria Barakzai (file photo) 

The First lady of Sri Lanka, Madam Shiranthi Rajapakse, spoke about the various social activities going on in the war-torn Sri Lanka. Interestingly, she was crowned Miss Sri Lanka-1978 and also qualified for the Ms World pageant that year. She is the principal of a group of schools called Carlton schools, in Colombo and southern Sri Lanka. According to Madam Rajapakse, women in Sri Lanka face all kinds of problems. But women empower the family and the nation by preserving old values. She is also running an organization called Sriliya Saviya for self employment of war widows.

 Madam Sriranthi (blue saree) during the International Women's day celebrations

In her opening speech, the first lady of Mauritius, Sarojni Jugnauth emphasized the need for for health, education and sustainable development.

Ms Latha Usendi, Minister for Women and Child Welfare, Chhattisgarh, India pointed to the close bond between a woman and a tree and praised Guruji for being the binding spirit for the world.

Other guests included the lady governor of Jordan and Amman who urged women to dream big and work towards their goals.

Noted actor, Member of Parliament and danseuse Hema Malini released a book called 'Shringara' or beauty.

Ms Hema Malini (file photo) 

Ms Kiran Bedi (IPS officer and currently Director- General, Bureau of Police Research and Development, Ministry of Home Affairs) gave a which clearly rocked. She said soft skills, so important in administration, do not have to be taught to women, but men need special training to acquire them. When women assume higher positions of power, they often exchange soft skills for hard skills, losing their innate qualities. Ms Bedi urged women not to lose these wonderful quality while learning new skills. According to the articlulate Ms Bedi, men have three qualities- muscle, money and mobility. Women have yet another three- heart, humaneness and humility. The two sets are complementary.

Ms Kiran Bedi (file photo) 

 In a telecast message, Ms Diane Watson,  Congresswoman LA, spoke about the cultural and ethnic diversity of her district where folks from both the poorer and richer (Hollywood) strata lived close to one another. In a world which is made smaller by transnational activities and communication, the need of the hour was to empower women in all walks of life and lend a feminine touch.

Many brave women, strong women, artistic women were given awards during the conference. If it was not for the battle against Tsunami, it was for helping war widows of Iraq, or building toilets in villages, educating children, excelling in art, music and the like. The 'Pizza grannies' of Bangalore were recognized for their hard work and undying spirit.

There was song and dance, laughter and celebrations. There were vibrant faces, pensive faces, smiling faces and determined faces. All nuances of the same  feminine beauty.

The conference was organized by the International Association for Human Values (IAHV) and Ved Vigyan Maha Vidya Peeth (VVMVP). The conference objectives are to educate 500 girl children in India and to touch the lives of a thousand women prisoners world over with the AOL Part One course.

The conference was beautifully compered by Ms Kavitha Khanna. Kavitha is a barrister turned marketing professional for a pharma company.

She herself considered the ashram to be her home where she felt so much at ease. These words held  much comfort for the audience.

Come to think of it, when I got to the ashram early morning all set to run around with chores, I was asked to relax under the steps of the Mantap (the venue) and someone would come and let me know my duties. So there I sat, enjoying the cool breeze, taking in the serene surroundings, watching the trees sway gently in the wind. A famliar ashramite with a broom in tow, smiled at me as he went on sweeping the corridor. I sat there, and waited, in no apparent hurry.

And then in the middle of the inaugural session, when a chair on the dais (where all the dignitaries were already seated) gave way, I simply did not hesitate to run up and replace it with another. After the first session ended, I ran past Guruji to meet my hero, Kiran Bedi and have a word with her. 

Yes, the sisters had come home. The rich, the famous, the powerful, the simple. From remote villages in India to far off lands.

They all came to rest a bit and to take on the world.

Posted at 11:11AM Jun 08, 2007 by Manju in Sun  |  Comments[2]

Bangalore goes Scot'ish!

On May 18, Sun Technology Summit '07 saw over 800 developers and students gather at Taj West End, Bangalore. The enthu was palpable and the conference halls were brimming with delegates throughout the 5 hour long summit.

The keynote address was rendered by Scott McNealy. Scott captivated and enthralled the audience right from his opening statement. Alluding to Web x.y, Scott emphasized that we now live in the Participation Age where everybody is an editor, publisher, blogger, mash-up-er, and what not. The web today is clearly by the user and for the user. India itself, according to Scott, currently has 12 million bloggers. Citing the example of a bunch of youngsters who made over a billion dollars by creating the Youtube and later selling it to Google, Scott urged the developers and students to think innovatively, and out -of -the- box to create valuable solutions.

But innovation alone would not help bridge the digital divide. The spirit of sharing in the open source space will narrow the yawning digital divide and bring the power of the computer to each and every person on the planet. Scott further added that 90% of cellphones have Java programs running and that signifies the ubiquity of Java technology.

With the advent of Java FX, users can watch a movie on a phone. “No suing, no arresting, no billing. It's free!” was Scott's refrain to every Sun technology he took the name of. 'Click and wait' was the only mantra for availing all these freebies, he added. Needless to say, along with these words of assurance, Scott also urged developers to contribute code to the Open community. “Twenty five percent of the SDN is in India. Now 25% of code should be donated from India”.

To the rhetorical question on how free translates to money, Scott explained: Open drives volume and volume drives value.

India now has access to www.network.com, a Sun grid technology, where the first 200 CPU hours are free.

Not being new to Bangalore, Scott has already won the popularity vote for his charisma and wit. He seems to enjoy a celebrity status, as could be seen by the fact that several youngsters had gathered around him after his talk, to seek his autograph.

The rest of the day had talks on many interesting topics such as AJAX and Web 2.0, Java SE language features- today and tomorrow, Web Services and SOA applications using Java EE, Java EE and Glassfish. At the All Hands, which followed in the afternoon, Scott answered many questions posed by the IEC employees.

The message was quite clear to those of us who had been sitting all day in the talks: Kick butt and have fun.

Fun we did have aplenty- over chat sessions, ice cream and cookies and an occasional cup of Java.

Posted at 08:08AM May 18, 2007 by Manju in Sun  |  Comments[0]

The 'dead'ly paradox

It's a given that a person is clinically dead when the oxygen supply is cut off to the vital organs like the heart and the brain. 

Here's the thing then- doctors can  pronounce a person clinically dead based on vital signs. But are all the cells dead when clinical death happens? How and when do we pronounce cellular death? 

There are  two types of cell death- the unprogrammed and the programmed. Unprogrammed cell death happens due to cell aging, or cell damage.

During programmed cell death (or  'Apoptosis')  a cell actually commits 'suicide' under circumstances like stress or disease (like cancer). Mitochondria (tiny bean-shaped structures contained in cells) have the remarkable ability to distinguish a cancerous cell from a normal one- and when that happens, there is a chemical trigger sent by mitochondria to the cancerous cell ordering it 'to die'.  When viewed under a microscope, cells that have been subjected to programmed cell death look different than cells that have undergone normal death. Apoptotic cells are shrunken with  fragmented chromosomes, whereas cells having undergone normal death are swollen and turgid. At the biochemical level too, certain proteins (called 'Caspases') are selectively  'switched on' during programmed cell death.

A recent article (which got voted its way into Slynkr) points to an astonishing finding- that hours after a person is clinically pronounced dead, the cells are still alive. 

Doctors often give doses of epinephrine, do a CPR or apply  paddles to jolt the near-dead person back to life.  These procedures are said to 'reoxygenate' the tissues with the hope of bringing the person back to life.

But while these procedures are what the doctor ordered, how do the cells behave under these procedures?

The recent study has indicated that when doctors pump up (reperfuse) the oxygen levels into the cells of a near dead person (using CPR and other techniques), the body is somehow unable to distinguish these re-oxygenated cells from cancerous ones. The mitochondria respond to such cells in exactly the same way they respond to cancerous cells. They trigger programmed cell death. 

So is it such a good idea to hyperoxygenate the body? Or is it better to send in some salt and  ice through the blood vessels and reduce the metabolic rate, while doctors start working on the heart? In a few trial experiments, doctors found that the salt-and-ice method had astonishing results- showing better recovery among patients.

There are clearly different layers to viewing life forms. The gross can include viewing the whole body, specific  tissues, cellular states, etc.

The subtle delves into deeper layers through metaphysical studies. The heart rate has been shown to  go down remarkably during a meditative state.  Meditation is also said to be linked to a change in one's consciousness. So if life (or death) can be defined physiologically, psychologically and biochemically, why can't there be another state of definition- namely, consciousness?

Physicist Roger Penrose of the University of Oxford, UK, and psychologist Stuart Hameroff of the University of Arizona in Tucson took this complexity one step further by explaining away consciousness through physiology. They proposed that consciousness might arise from wave-like quantum-mechanical effects involving protein filaments called microtubules in nerve cells.

Many theories exist to support or dispute the phenomenon of consciousness.

Nevertheless, science cannot dispute that there are different states like sleep, wakefulness, dream state and the unconsciousness state. Metaphysicists say that these are indeed the different states of 'consciousness'.

So then, is body consciousness the same as cellular consciousness? What happens to this collective consciousness when death happens?

If body death and cellular death are not happening in synchrony, is there a  'pause-ible' state between life and death?

If life is complex, so is death, it seems. 

Posted at 05:10AM May 08, 2007 by Manju in Sun  |  Comments[0]

IISc to hold a global conference

If there are any IIScian alumni tuning into blog-land, here's an interesting piece of news. On June 22-24, 2007, the Indian Institute of Science Alumni Association of North America (IISc AANA) is holding the first ever global conference in Silocon Valley. Eminent scientists, Nobel Laureates, industrialists will gather at the conference and interact in a unique manner. It is believed that this conference will be a platform to build relationships and business partnerships between the academia, alumni, industry both in India and the US and between the two countries.

Registrations are open online and the cost is $ 150 uptil May 17. Thereafter, the registration fee increases by $50.

Once an IIScian, always an IIScian. Guyz wear your badges proud and proper. Join in the conference and meet up with ol' friends and foes, and settle those sweet scores. :-)

Posted at 06:49AM May 05, 2007 by Manju in Sun  |  Comments[0]

Women and society

Seventy odd years ago, Thimmakka, a poor yet spirited woman, was born in Gubbi, a remote village in Karnataka, India. At a very young age, she was married off to Chikkanna, a landless labourer from another nearby village. Apparently, it was not Nature's plan for them to have a child. But then perhaps Nature chose her to become a mother, in quite a different way.

One fine day 45 years ago, Chikkanna and Thimmakka simply decided to plant trees. It was no small goal. This spunky couple chose to plant saplings along a whole 4 km stretch of road between Hulikal and nearby Kudur. Thimmakka reckoned that shade along the parched land would provide succor to many a weary traveler.

They first planted saplings in a nursery before transfering them onto the road, always managing to maintain a proper distance between two adjacent saplings. Today, the trees stand proud, having been nurtured by the couple's gentle hands. Thimmakka received awards many years later, but surely her biggest trophy must be the green canopy lining the dusty road.

Between June 8-10, 2007, the International Association for Human Values, an international NGO in special consultative status with the Economic and Social Council of the United Nations and Ved Vignan Maha Vidya Peeth are organizing a conference to highlight the achievements of women in bringing about positive social change with a focus on values and ethics.

The main aim of the conference is to educate 500 girl children in India and to empower 1000 women prisoners across the globe. But it is also to recognize the wonderful contribution of women like Thimmakka.

In his speech at the previous conference held in 2005, Gurudev Sri Sri Ravishankar said: Women bring human beings to the planet…and teach us how to live. Women teach us our first behaviour, our first step in life. Women can glue the differences and bring people of diverse nature together. These qualities are inherent in a woman. For a woman, it is quite natural to relate from the level of the heart. It is necessary that women bring together the finest aspects of society; the feminine, and the ability to create, with the transformational ability to make a difference in society - these two should go hand in hand...

Many women are given awards for making a significant, positive contribution to society.  Thimmakka was one of the proud awardees at the last conference.  Shyama Sondhi was given an award for her unwavering commitment in Jammu and Kashmir to create an  Art of Living Youth movement and bringing about trauma relief and rehabilitation for youth and  prisoners. 

The conference will be attended by women all over globe, from all walks of life.  Her Highness Susan Al Said (Sultanate of Oman reflected thus:  I am very blessed that I was invited to thsi conference...We also have empowerment of women and various women ministers in the Sultanate of Oman...the future looks very bright.

This year's topics at the conference include: Women with a vision, A Vision for Governance: Democratic Governance,  A Vision for Business Leadership, Action for Awareness, Action for Empowering Women, Action for Environmental Sustainability, Action for Economic and Social Development and Action for Campaigning against female foeticide.

We as women, often have so many ideas, hopes and ideals that we carry in our hearts. But then, these dreams often remain frozen inside, because we are afraid that we hope to achieve too much.  Something beyond our capacity. Perhaps it's just a starting problem, a small bump on the road. Once we plant the first sapling, surely the second one should be easier? And so the third.

It is conferences such as these that will allow our dreams to blossom, when we note that other like-minded and equally shy women exist in this world. Holding hands, we can empower, inspire one another and move on. 

I just might join in as a (woman!) volunteer to help out at the conference. So I definitely  hope to share the conference highlights with my friends out here @ Sun. (Yet another feminine dream!)

Posted at 11:11PM Apr 29, 2007 by Manju in Sun  |  Comments[1]

Yours 'moin' and ours

Was checking out Ubuntu community documentation and stumbled upon  MoinMoin - one of the whackiest, wikiest words I have heard. It's derived from a German word which means 'Good'. Moin is  tantamount to saying 'Good day', so Moinmoin is 'A very good day'.

WikiClone

PikiPiki

You have MoinMoin questions, MoinMoin tips, MoinMoin bugs, MoinMoin mailing lists and so on. You get to edit the text on the page and feel real good when you do this coz you get a note of appreciation. You can also send suggestions about the wiki gui. Plus your ideas.

Check it out, it's real fun.

It follows the spirit of open sourcing to a tee- yours, moin and ours.

Oh, and by the way, there's a cool MoinMoin mug too in the etymology space.

Posted at 04:17AM Apr 27, 2007 by Manju in Sun  |  Comments[0]

Sun smiles on these kids

April 14-22nd was Sun Volunteers' week, a time for us to render service with a smile.  April 19 was the day we invited children from the Spastic society over to our  campus.

It was coincidental that both Sun and the Spastic society celebrated their 25 birthday so this turned out to be a great theme for the painting session.

                                             Pic: Kids paint   'Sun'ny side up!

 What flagged off this fun-filled day was the ice-breaker- passing the parcel. The one who was out had to say a lil' something about himself or herself. Among the enthusiastic students were dancers, singers, cricketers, basketball'ers and even computer game addicts.  Young Pooja, confined to a wheelchair watched the game with avid interest. There was one volunteer who stood steadfastly by her side to ensure that she got to hold the ball before it was passed on.

Pic: When Pooja wants to chat

Amidst all this camaraderie, I noticed Bala who is in his thirties, completely confined to a wheelchair, cannot speak coherently, goes into shaking spasms and needs assistance with most tasks.  Bala wanted to paint along with his group, judging by the gleam in his eyes. He finally drew a meandering river and gurgled with delight.

Pic: Bala draws a river

One the medical front, Cerebral Palsy (CP) refers to a group of conditions that affect control of movement and posture due to damage to one or more parts of the brain that control movement. An affected child cannot move his or her muscles normally, while symptoms range from mild to severe.  With treatment, some children improve their abilities gradually.

CP is usually diagnosed only when a child is about 2-3 years of age. In about 70% of the cases, CP results from events occuring before birth that can disrupt normal development of the brain.

In Feb 2006, the UCP Research and Educational Foundation reviewed advances in brain imaging techniques that may lead to very early detection of brain abnormalities in infants. Early detection is important for prognosis and for providing opportunities for early intervention to improve the chances of better outcome in children at risk.

At the biochemical level, proteins like the pathological Tau protein have been identified to be involved in the development of neurodegenerative diseases like Alzheimer's disease and progressive supranuclear palsy (PSP). Mutations (small and sudden changes in the protein read-out) in the Tau gene (which codes for the Tau protein) cause a kind of dementia with Parkinsoniasm linked to Chromosome 17. Variations in gene organization can cause differnent neurodegenerative pathways leading to disease.

While biomedical research is on full swing to identify disease loci and possible cure or therapy, it is really the homes and schools that have to bring these children to a level of self-sufficiency and dignified life.

Sheeba, a young lady of 20 odd years, is all of 2 and a half feet, and confined constantly to a wheel chair. Her disability also includes a completely bald head and stunted limbs. But there is no dearth of talent. The Society has brought this latent talent out and now Sheeba makes a modest living by painting on jute bags.

Pic: Sheeba watches the merrymaking

Surely many of us felt quite proud to be involved in community service and almost wore an 'invisible ribbon' to  show off to this world. But as the day went by, we watched Hema, Bala's mother  stand patiently behind Bala's wheelchair, attending to his every need, soothing his occasional cries and whimpers, with a gentle smile on her face. 

And then we knew.

She didn't need a ribbon. She wore a halo.
 

Pic: Bala and mommy dearest

* These beautiful pictures were taken by Manu Samuel from the IEC IPG group.

Posted at 04:31AM Apr 20, 2007 by Manju in Sun  |  Comments[4]

Sun @Bio-IT World conference

It's great to know that Sun Microsystems is a Gold sponsor for the forthcoming Bio-IT World conference being held in Boston (April 30- May 2nd, 2007). According to the program available online, Ari Shamash, Director, Sun Grid Engineering, is giving a talk on network.com.

There is a growing need of IT solutions to cater to the increasing automation and sophistication in the tools for the lifesciences and the healthcare industry. With the 'omics'* science growing in leaps and bounds, the data that is being churned out by state- of -the- art machines has to be massaged, managed and integrated for scientists and the medical fraternity to make sense out of it all. The Bio IT conference presents a wide gamut of topics brought to one podium by leading scientists and IT engineers who do cutting edge research in this amalgamated field.

Next generation sequencing technologies enable major advances in the field of genomics and biomedical research. One needs to generate orders of magnitude of more data at minimum cost. It is anticipated that using next generation technologies such as 454 and Solexa, one would soon be able to acquire, manage and analyze several trillion bases and tens of petabytes of sequence data, annually.

The $1000 genome project has spawned many innovative strategies in nucleic acid sequencing.  Data processing and management have as a result, seen more challenges in meeting the requirements in these new strategies. At the conference this year, Harvard Medical School will present the Polony sequencing technology, the IT challenges it presents and how they are being met in the Cancer Genome Atlas project.

The biomarker project is an integral part of the bio-pharmaceutical industry and the aim of this project is to identify critical gene or protein sequences that are associated with a particular diseases. Biomarkers serve as 'tags' which, when picked up as signals in a human blood/bone/tissue sample, can indirectly identify the associated underlying disease. Such biomarkers signals can be screened by using standard imaging technologies, and once this is achieved, it is possible to prescribe drugs or even design new drugs that can combat the disease. The IT challenge here is to improve imaging technologies, integrate imaging data with clinical and genotypic data and target (selective) data to external sources.  IBM Healthcare and Lifesciences division will be presenting a paper on integrated data models and architectures which combine different data onto a single platform.

Enabling High throughput screening,  the need to integrate disparate data on to multiple platforms, data management on a growing scale, simulation of complex biological processes, and growing need for data security and privacy are some of the challenges in the Bio IT research.

*omics- genomics, propteomics, metabolomics.

Posted at 11:36PM Apr 11, 2007 by Manju in Sun  |  Comments[0]

Network.com- a unique site

Utility Computing is a business model in which resources (CPU power, storage space, etc.) are made available to the user on demand. The goal of the utility computing model is to maximize the efficient use of computing resources and minimize user costs.

The Sun Grid Compute Utility is a simple to use and access data center-on-demand. Sun Grid delivers enterprise computing power and resources over the Internet, enabling developers, researchers, scientists and businesses to optimize performance and accelerate innovation without investment in IT infrastructure.

Rathna's blog  describes network.com,  a Sun site which has listed out many applications running on Sun grid. Many among these applications are used in lifesciences.

Open the Network.com pages and click on a link like BLAST (Basic Local Alignment Search Tool)
BLAST finds regions of local similarity between nucleotide (nucleotides are basic building blocks of deoxy ribonucleic acid or DNA. Our  genes are made up of several hundred nucleotides strung together in a specific sequence) or protein sequences (amino acids are the basic building blocks for proteins). 

                                                                       The DNA double helix

BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Blast is a free licence and detects local as well as global alignments in nucleotide or protein sequences needed for various biological and medical studies.

ClustalW is a fully automatic program for global multiple alignment of DNA and protein sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via graphical representations.

One very key chemical reaction that takes place in the human body is drug-protein interaction- a hot topic in biotech arena. Certain proteins are said to have key 'buttons'  on their surface called receptors. A target drug (also called a 'ligand') is said to bind to these receptors and thereby cause a chemical cascade of events- ultimately leading to cure of a disease.  The calculation of receptor binding affinity (strength) for each newly generated derivative ligand remains the most challenging aspect of drug design. eHiTS, by SymBioSys,  is a fully automated and easy to use application which does not require any manual preprocessing, pre-modelling of input receptors or ligands. It breaks up ligands into logical bits, docks each bit into the receptor and scores for binding ability.  This is a very useful tool used during rational drug design.

The network.com catalog gives information such as category, publisher, key features of the application, description, and technical information with respect to the infrastructure and configuration needed to support the application. It also gives pricing and support mechanism.

Users of network.com can demo an application, build or share an application.  Publishing to the application catalog is easy. Once approved,  a user can share the application for free or for a fee with all the users on Sun Grid. Developers and Open source communities can now share their applications at Network.com allowing users to just “Click and Run” these applications going beyond downloads.

Network.com also has customer case studies presented in the Industry examples section.

One wonders why  such a valuable site is named 'network.com' with no hint whatsoever, of being a Sun brand?

Strangely, a click on the  FAQ section does lead a user to http://www.sun.com/service/sungrid/faq.jsp#q.
The Missing Link? :-)

Posted at 08:52AM Mar 23, 2007 by Manju in Sun  |  Comments[0]

Fun and Folklore

On March 15, our IPG group at IEC took off in a bus to visit a place called 'Janapada Loka' situated on the Bangalore-Mysore Highway. The word 'Janapada' means folklore and this can relate to dance, dress, habits and lifestyle of the native people.

Janapada Loka is a 15 acre complex which is a treasure trove of Karnataka's folk heritage.  For just a few hours, our group was transported into an entirely different world of tribal people and villagers who are often forgotten in the mad race of modernity. The serene stillness of the place was akin to the quiet lifestyle of these people.

The place itself was established by HL Nagegowda, a man who took to popularizing rural traditions and customs and reviving some of this quaint and rustic charm. Apparently, he had visited hundreds of rural households and learnt of their customs so that he could exhibit these through custom built museums.

      Swords displayed in the museum 

 We were first taken around the Lokamahal museum of folk culture by an enthusiastic guide. The museum had exhibits of folkcrafts such as baskets, 'basingas' (head-dress worn by a bride and bridegroom), costumes of tribes and village dancers, and even cooking vessels used by the rural folk.

                                                                      Statues of Yakshagana dancers

At some point in the conversation, our guide had mentioned that he came from a family of singers, so we managed to persuade him to sing an old ballad which depicted a wife's sorrow for her husband leaving her for another woman. If we could understand the lyrics well enough, we'd have probably gone misty eyed.

 
But there was simply no time for mist of any sort whatsoever!

The pinnacle of our idyllic morning was the live drum dance by tribesmen of Karnataka. We sat alongside what seemed like a godzillion schoolkids whose eyes gleamed collectively like lighthouses of a vast beach. The beat of the drums was tantalizing as we watched in amazement the synergistic movement of the drummers. Starting with a slow drumroll, the drummers would end each pattern with a crescendo, beating the leather membrane in a frenzy.

                 The tantalizing drumroll 

Towards the end of the show, the drummers hoisted a few lucky kids onto the drums, and paraded them sitting thus, around the ground. The adrenaline levels must have been pretty high among the kids, coz' the flushed faces would have made Rudolph  shop for rouge.

Lunch was  at Kamat hotel, served in a traditional manner. This meant that we had to sit cross-legged on a low stool, even if it made some of us go cross-eyed trying to bend our knees. We ate a sumptuous meal served on banana leaves. But I suspect that some of us ate less than our normal quota for fear of falling off the stool!

After a heavy meal, one would have normally reclined against a good-natured tree and snooze the hours away. But the organizers had us play a game of lies, toss a ball against a stack of stones and run for cover, and finally chase our opponents crying out 'kho'!

We returned to office and back to the future. But even the stuffed up mailboxes with all the the reminders could not take our minds off the fantastic experience. The best reminder of the day happened to be that of roots, revelery and reverberating drumroll.

Acknowledgement: I'd like to thank Manu Samuel (IEC IPG), for the wonderful pictures displayed in this blog.

Posted at 03:03AM Mar 16, 2007 by Manju in Sun  |  Comments[3]

She rocks the world

Today is International Women's day and I woke up with a song in my heart. Bought a few roses to for the lovely ladies in my team. Started attending Gita classes in the morning- somewhere in one's life charter, it suddenly seems a good time to start a chat session with the Headquarters.

The average Hindu reveres Goddesses with as much devotion as the Gods. We have days of the week dedicated to  Lakshmi, the Divine Mother who passes down wealth and happiness to those who seek it sincerely. Of course, many believe in the the non-dualistic philosophy, where God and Man are One. Nevertheless, everybody gets to choose an 'image' to worship, from the generous pantheon of Gods and Goddesses.

Strange then, that in a land where Goddesses are exalted in their position, a widow is placed in the bottom rung of the societal ladder.

Deepa Mehta's movie 'Water' has brought to light one such tradition wherein widows are discriminated against in a heart-wrenching fashion.

'Water' takes us back to the year is 1938, when India was ruled by the British, and it was around this time that Gandhiji started his battle with the British, as well with the traditions that bind the Hindus. Young Chuyia is married to a much older and sickly male, who dies soon after. Chuyia is returned unceremoniously to her parents' house and from there she is taken to the holy city of Banaras to be left in the care of a group of widows who live at "the widows' house," shunned by the rest of the community. Chuiya meets several elderly women and Kalyani, a beautiful young widow.

Innocent Chuyia does not know that according to Holy Hindu Scriptures she has been destined to live here for the rest of her life, for when a woman's husband dies, she has three options: One, to marry her husband's younger brother, if his family permits; two, to kill herself on his funeral pyre (a ritual called Sati); three, to live a life of celibacy, discipline, and solitude amongst her own kind. Widow remarriage was a law that was just coming into force. In the movie, Kalyani meets and falls in love with young Narayan, a follower of Mahatma Gandhi, who wants to marry her, despite his mother's protests. The story weaves on and opens our eyes and hearts to the world of these tormented women. In a land where the pure water of the river Ganges flows on ever so gently, it is ironical that widows who live around the holy river are treated so harshly.

Cut to real life. I vividly recall my grandmother insisting on shaving her head when grandfather died. Thankfully, we prevented her from getting rid of her lovely silver locks, but we could not stop her from giving away all her beautiful clothes and taking to plain white in a big way.  Grandmum may have tried to adhere to meaningless rituals such as these, but she was also a woman of great integrity. She supported the Gandhian philosophy and wore only homespun cotton. She traveled third class, in trains, just to keep a spirit of equanimity with the poorer strata. She'd have the courage to intervene to stop a man battering his wife at a nearby slum. Oh yes, grandmum was a great role model. She never had an earning to speak of, but she had guts aplenty.

Times are rapidly changing today, in India. A woman can earn her money and speak her mind. She can balance her career and marriage. She can be the role model for millions of girls who need guidance along the meandering path of life. She can let go of dogmas and reinvent her spirit to suit changing times.

So let's celebrate this freedom. Freedom of making relevant choices. Not so much to burn bras but to burn meaningless beliefs and prejudices. And let's hope that more and more women join this Freedom wagon.

Every woman deserves roses and chocolates, diamonds and dinners, for it is SHE who rocks the world with her charm and compassion.

Happy Women's Day.

 * I would like to thank Rahim for taking the time to edit this piece.

Posted at 02:24AM Mar 08, 2007 by Manju in Sun  |  Comments[3]

We are the World (Wide Web)

Jay Leno talked about at a recent show.

True enough, the Person of the Year, says TIME magazine, is "You. Yes, you. You control the Information Age."

Most of the companies claim to be racing into the Web 2.0 generation even as the 3.0 generation is being  'innovated' upon.

Welcome to the age of Innovation. Companies are now judged by their  'I' appeal.

Innovations happen practically everywhere, even when you least expect it.

You can even be sitting on one. The Aeron chair is said to be functionally, orthopedically, anthropometrically,  ergonomically, economically, superior.  To put it rather bluntly, it appeals to everybody's base-ic instinct. Ask Marvin the cat, who seems to have lent immense grace to the chair.

In matters of the heart(h) too, women in rural India grow more  innovative day by day, just to save time and effort they spend on housework. Earlier on,they churned yogurt with a long wooden stick to bring out the butter. It often caused a backache from leaning forward and the  hands ached from holding the hard stick. They later learnt that tying a rope to the stick and pulling at the rope made it more easy. No one cared why, it simply worked better.

Serendipity sometimes gallantly steps in to help create an innovation which  can herald a new era.

Take the era of biotechnology, for instance.

An article in Nature journal described the birth of biotechnology, which apparently was born during a meeting at a Hawaiian delicatessen in 1972.

Stanford medical professor Stanley Cohen had earlier on reported the ability to introduce plasmid DNA (circle-shaped DNA) into a bacterium (E coli), which allowed researchers to propagate and clone the plasmids in the bug. In this manner, one can get many, many copies of the same DNA threads.

At about the same time, Herbert Boyer, from the University of California, San Francisco, had reported on his work with a novel protein that can cut a plasmid (bacterial DNA) at precise positions, generating ‘sticky ends’ in the process.

Cohen met Boyer at the meeting in Hawaii, and, over tea, they put two and two together. What if one could introduce alien DNA in between these sticky ends of the plasmid, and shoot it into bacterial cells, where it would multiply in leaps and bounds? A gene for insulin, a growth hormone gene- cut the gene and stitch it into a plasmid and voila! That heralded the birth of genetic engineering.

Scientist Kary Mullis was once struck by the 'I' factor while he was driving from Berkeley to Mendocino one evening. That heralded the birth of PCR (or Polymerase Chain Reaction) technology, which revolutionized genetic engineering. Beginning with a single molecule of the genetic material DNA, the PCR can generate 100 billion similar molecules in an afternoon.

The DNA may come from a hospital tissue specimen, from a single human hair, from a drop of dried blood at the scene of a crime, from the tissues of a mummified brain or from a 40,000-year-old wooly mammoth frozen in a glacier.

In 1993, Mullis got his Nobel Prize, and later on, we got Jurassic Park

So it's clear that you control not only the Information Age. You actually control the I- Age.

Which is why you're now able to float on blogospheric clouds. You can now blame almost everything on your designer genes. Thanks to those wondrous chefs, you can bite into Lasagna-Pizza, (or should it be 'lasizza'). You now have do-it-yourself yoga kits, and exotic teas that promise eternal youth.

So take heart, we can safely march ahead into FY07 with a song on our lips.  Like someone once said 'What me worry?'

Happy New Year!

 A.E Neuman - High on the I factor

Posted at 12:42AM Dec 28, 2006 by Manju in Sun  |  Comments[0]

Porta/pardon?

With the launch of Porta-person, another Sun-ovation docks into cyberland.

It doesn't really need a hard core degree in neuroanatomy to prove that a picture is worth a thousand words. Now, with virtual teams being separated by the oceans and mountains, it is hard to reach out or energize one another through a simple phone call.

Porta-Person,  straight out of Sun Labs, enables people participating remotely in teleconferences to make their dignified (virtual) presence to conference rooms. All they need is a white paperboard box, a tablet PC as a screen, and stereo microphones and speakers affixed to its sides. The screen would display a live video of their faces.  But if they wanted to keep their faces private, they could present themselves as line diagrams. (Wonder if they even get 'greyed out' when they log out of the call?).

 

Earlier on, academic groups and companies from Microsoft to IBM have been developing prototypes and selling teleconferencing systems. High-end corporate systems broadcast images from one conference room to another, for display in each other's offices. Simple webcam systems, such as iChat, can communicate with others via desktop computers or laptops. So can netmeetings. But  they are often either too unaffordable or come with a limited number of features and functionalities.

 I recall having participated in a netmeeting some time back. The soundbytes came faster than the visual, so we had to use the phone to synchronize with the picture. The picture by itself often grew hazy. Sometimes the camera must have tilted precariously on the remote team's end. So we'd tilt our heads appropriately, just to see 'em straight. We must have presented a funny sight to those passers-by.

When the brand new videooconferencing equipment arrived at our office, the support engineer would fiddle around with the equipment for days on end, like his life depended on it. The very nature of preparation seemed too high maintenance, so we hardly used it.

But Porta-person, the new technology from Sun has received rave reviews.  And for good reason too. Just look at the rich functionality that Porta-person provides.

Like most conferencing solutions, you can definitely see who is on your call. But not just who is virtually present through a Web or phone connection but also who is present in any of the conference rooms that are tied into the call. You can also connect with people seated in more than two rooms.

Porta-Person also comes equipped with private audio chat facility. With private audio chat, two or more participants talk privately and the system automatically dims the audio of whoever is speaking at the larger group. Cool, huh?

More often than not, we often not exposed to the person who is actually doing the talking. Porta-Person automatically figures out where the audio is coming from and in the list of participants, gives you indication of which person on the list is doing the talking.

The list of goodies just goes on. 

There is a need for human expression in communication and this is so often lost with other media such as email, phone, and chat.

Full gaze awareness, defined as knowing what someone is looking at, might be expected to be a powerful communicative resource when the conversation concerns some object of common interest in the environment.

So for the next remote meeting, let's bring out those vanity cases.

Or better still, just fax the ol' heart to send out a smile...

Posted at 08:41PM Dec 22, 2006 by Manju in Sun  |  Comments[0]

On personalized medicine and Information technology contd..

Around the world, health care software is moving from hospital-centered departmental systems, to patient-centered medical records that are distributed across networks. These patient-centered medical records are slowly including not merely physiological data (such as a patient's blood pressure, temperature, etc) but also the patient's own genetic and genomic data. Genetic data is obtained by conducting laboratory tests using the patient's blood and serum. Blood samples are generally stored in a Blood bank and retrieved upon demand from hospitals and Health centers, to conduct diagnostic tests. This generates a large amount of data which needs to be stored, analyzed and also conform to HIPAA norms.

Information technology (IT) is an important element in maximizing the role genetic, genomic and proteomic technologies play in personalized medicine. IT can reduce the costs and improve the quality and efficiency of research and clinical operations. IT can also ensure that the clinical test results are fully integrated into electronic medical record (EMR) systems where they can be targeted by clinical decision support algorithms. Finally, IT plays a critical role in ensuring data integrity in complex modern information flows.

The HPCGG (Harvard Partners Center for Genetics and Genomics), situated in the prestigious MIT campus in Boston, is a unique collaboration between Harvard Medical School and Partners Healthcare, with the aim of contributing to the cause of personalized medicine. The center has several state-of-the-art laboratories which include genetics lab, microarray lab, laboratory for molecular medicine, proteomics lab, bioinformatics division, just to name a few.Using state-of-the-art diagnostic techniques and modern instrumentation techniques, the HPCGG has developed genetic tests which can help predict the onset of several diseases such as cancer, Noonan's syndrome, cardiomyopathy, Cystic fibrosis, hearing loss, lung cancer and several other diseases.

The Information technology (IT) team at HPCGG team was formed as a collaboration between the HPCGG and the Partners HealthCare Information Systems department (Partners IS). Hewlett Packard provides substantial hardware and services to the center, which includes a globally distributed software development team that assists the center in information systems development. The HPCGG IT team constructs infrastructure that supports research and clinical operations within the laboratories of the center.

The team also focuses on constructing data rich interfaces to Partners EMR and research infrastructure. The HPCGG IT team, headed by Samuel (Sandy) Aronson, developed a one of a kind application called GIGPAD (Gateway for Integrated Genomic and Proteomic Applications and Data). GIGPAD brings together, on a single platform, patient data obtained from several laboratories at the center. Being a secure clinical and research information management system, it supports personalized medicine which relies on quickly bringing research data and clinical data onto a single platform, enabling rapid diagnosis, and possible cure. GIGPAD is capable of managing workflows that involve not only multiple laboratories but also integrates with 3rd party Laboratory Information Management Systems (LIMS). The application is rapidly evolving to include interfaces to many other laboratories and also external applications. It has both a clinical interface and a research interface, supporting multiple user profiles.

GIGPAD leverages J2EE, Struts, Oracle, and XDoclet. Users access the database through Entity Beans and system architects construct security at this layer. It also allows the generation of data transfer objects, Oracle tables, and security configurations based on tags in the class files, which speeds development.

The GIGPAD application won several awards such as the Bio-IT award and the J BOSS award.

The healthcare market is uniquely poised to leverage such robust applications, which cater to build a knowledge base for personalized medicine.

The growing need for electronic health records will naturally see a rapid rise in the need for IT support. In all this, how will the open source philosophy cater to the healthcare market? Both of these are community driven, so how will they work synergistically for a generous cause? Perhaps it's a good thought to close on...

Posted at 09:58PM Dec 10, 2006 by Manju in Sun  |  Comments[0]