sleepless night

Now  the time is 4.00 am  at  Calcutta, feeling hard to sleep and tossing myself in my bed and closing my eyes tightly and trying to sleep, but couldn't , the reason may be am going to be away from my lab after one year, usually my routine is from morning 10.30 to night 9 or 10 Pm i stay in my lab though my PI is also not strict or forcing me to stay in lab , since mine is computational biology, i can work from anywhere, for that also i have a full permission from my mentor still i feel full-fledged to complete my given task at my lab @computational biology and Genomics lab ,IICB . for the past one year  i didn't take any leave i work in all the days even during the most famous durga pooja , being attentive at IICB learnt many things , now i have completed my coursework  part in my Phd i feel that am half way through, some times i feel iritating about the asignments, and boring classes and hard part is exams still i took it in a sportive way and the good thing about the coursework is i came to know many colleague who work in different areas and got so many friends in my facebook list also, my masters and bachelor was purely bioinformatics i knew very few things in biology , during coursework i learnt so many new-things it was really a basic knowledge but it was very useful and essential for me, firstly i learnt the principles of many apparatus how it works such as gel electrophoresis, SDS, confocal microscopy, staining techniques, western blot and it made me to think , the very basic and common methods we use in research i learnt from there, such as statistics, etc .... then successfully completed my 1st sem of my coursework , once i entered into my 2nd sem i learnt little higher things such as signaling pathways how it can be blocked and approaches, genome sequencing , genomics etc ... i also have some of the favorite teachers who thought me, i really enjoyed my 2nd semester since it has less number of subjects, there i learnt how to become a good scientific learner,  given many assignments and submitted within the given time, also managed to work in lab within my deadline , gave many seminars though some of them really went good, and many of them were unsatisfied , In structural biology and bioinformatics we have journal club also i really came forward to organize many of my lab-mates felt as a headache still i went forward so that i can manage to do multitasking, i keep myself busy in doing my stuff,  and i did some household things in my lab such as taking care of purchases, cleaning, defrosting  the fridge and maintaining the cleanliness, and taking care of one of the prestigious server we have that is corona with 48TB RAM and 4 compute nodes with 16 processors in each node , fortunately whenever we had a power-shutdown or any problem with the server i was there to maintain , and i really care for my server since all our data's are there and tats like our gold mine, i really dontwant to talk about other labs here, i want to comment about my lab is all my lab members patiently bared with me and they full-fill all my wishes eating pizza, giving me chai party, helping me in programming and troubleshooting my problems, professionally we all are healthy friends no ego's  and simple life living researchers , moreover my lab is like my home i have all my belongings over there , i make maggi and green tea whenever am tired and hungry and shops are closed, though am away from my home i celebrated rakshabandan, friendship day, independence day, ganesh pooja, saraswati pooja with my labmates and got so many cadbury's also and i shared with all. am really very far from my home though no home-sicks managed myself and my family is also very co-operative and really they helped in all my times, Now its time to spend my time with my family am going for my vacation once i think that i will be away from my lab, first thing comes in my mind is all my work will get postponed and i miss my second home that is my lab @IICB though i will be at home still planning to work for at-least 2 hours per day so that i can complete atleast some part of my work and save time, though many people will think that its not right, but i believe in hard-work its the best time for learning and achieving, i believe in the quotes that Today's hard-work is tomorrow's fruit , and would like to mention here that i had to apply for my passport as my Duty i did, police verification also done at my place where i live now and the police shamelessly got bribe and went, i have paid since he is demanding, still the passport office have hold my passport i was not aware about this once i checked my status came to know then i went regional passport office and enquired i was thinking that since i was not in my permanent place during verification so dint get passport but at my place they are so loyal they dint ask for bribe and they mentioned in the paper that candidate was residing here and now studying at calcutta, but the kolkata police took a bribe also and i have shown all my proofs he is unable to understand english i guess he dint fill the clearence form and gave empty one to regional passport office and the officers showed me i have seen by myself i feel like blasting at him i told them am going home i will not be here for month explained my case they considered and undstood my situation and they said no need of verification at permanent they have cleared and asked me to meet them once i come back from home since i can again start the verification when i come back , the good people also there very nice to know this and  i have many things to share since dontwant to make very long essay i will stop with this.... and will be missing my lab days and IICB very MuCh.... i thank my Mentor for giving me  this opportunity.....

The uncertainty principle and challenging d impossible!!

I was reading this book “A brief history of time” by Stephen Hawking; a person I am quite fond of. While reading, I came across this chapter “The Uncertainty Principle”. This chapter gives a crisp description on the uncertainty principle and its implications. Most of us know what uncertainty principle is but just in case we forgot, it states that at a particular time, its impossible to accurately calculate both the position and velocity of a particle; the details can be found in the book I just mentioned.

During 19^th century, in the wake of Newton’s laws, the famous French scientist Marquis de Laplace suggested that the future of the universe and also human behaviour could be completely predicted if we could calculate its present state. This implied that the future events could be determined by us humans and hence it challenged the intervention by God! Unfortunately (or maybe fortunately!), Heisenberg came up with his uncertainty principle which proved to be a setback to Laplace’s dream of a deterministic universe because if one is unable to exactly measure the present position and velocity of an entity, how can one determine its future state?

The uncertainty principle together with Quantum mechanics led to the sad death of Laplace’s deterministic theory and gave way to the probabilistic universe which states that a future event could not be fully predicted but what could be predicted is a number of possible outcomes. (Einstein was not quite convinced with this theory and he also got God involved in all this which was evident in his emotional statement “God does not play dice”!)

What happy thing I could visualize from this is that this theory favours probability and thus there is no certainty or even impossibility for any event to take place; though some events are favoured more than others but this does not kill the chance for a seemingly impossible event to take place. So, if we want something and the present situation makes it seem impossible, we shouldn’t give up because with the uncertainty principle prevailing, nothing seems certain and also nothing impossible!

Bit of odd...

I think the way people in west look at us could be little odd. I have forgotten all about that forcibly. However, a very recent encounter with a very old professor reminded me all of that and I wanted to muse about it here. There is this poster number 100 something and near that sits a old professor. I will not name him. That place was very empty, so I decided to ask few questions on the poster.

Then while talking the professor asks me where am I from,I said India. Then he says I know that but where exactly in India. Then I said Kolkata. To that he says I travelled to Kolkata once via a train through Howrah.I knew what he was going to tell next - and that is what exactly he said. He fell sick with the contaminated water. The place was very dirty and he felt very sorry for the people who stay there etc. etc. He also made statement that those who come to USA are atleast saved from the bad life people have in India. This got me into thinking why do we make ourselves look like that to the external world? Are we so pitiable. People generally judge from the outward look of everything,be it road, people or dirt. Hope someday we will appear and behave cleaner so that people look at us with respect.

This is not the end of it.He even went on to ask if my name was a brahmin name?I said names are not brahmin, sometimes surnames are! To that he surprised me to say that Tripathy is a brahmin name. That got in to me and I did not want to stand there and talk. Basically he was trying to point out all the evil we have. From dirt, to poverty to anarchy to caste system. So, I feel it is time for us to behave differently portray ourselves differently and change the system. Only  by voting right we can do it.... 

Visiting Cold Spring Harbour for a meeting? Here is what you should know

In my over a decade stay in the USA, I have not visited the Cold Spring Harbour Laboratories. Although there were a lot of very interesting meetings took place there, the registration cost was a big deterrent. I decided to attend the fall Genome Informatics Symposium starting 30^th October 2013 this year. Although the whole journey was rather unpleasant I will not discuss that here. I will talk about my experiences of staying in affordable places and travelling to long island from there and the science.

Internal Transportation:

I booked a place in Bronx through the trusted AIRBNB web site. I have had pleasant experiences before using their services. I stayed very close to the Botanical Garden Bronx. Getting to the hosts place from JFK was not an issue, only taxi fare was a bit higher. So, try avoiding taxis and travel light is the first lesson. After I reached there first day I just slept, did not know when I was sleeping and when getting up. Then one of friends picked me up the next day to her house in Brooklyn. The best way to travel is take a metro card for a week (If you are travelling a short term) . This friend was staying in Avenue H and daily it was a train from Avenue H to 34^th Herald Square before taking another transit to Long Island Rail Roads.

How to go to Cold Spring Harbor:

From anywhere in the city; the best way to go to cold spring harbor is to take the Long Island Rail Road (LRR) to Syosset (Not cold spring harbor). The final destination for this train is Huntington. This train starts from Penn station, and goes via Jamaica. So whichever place is close to you just take. Suppose I am coming from Brooklyn, then I will either get down at Atlantic or 34^th Herald Square. From Herald square I have to walk one block towards 33^rd street and 7^th avenue (Herald square is at34th and 6^th avenue). There is Penn station. Upon exit from Herald square you will find several boards telling which way is the penn station exit. Upon coming out also there will be boards and direction to Penn station (This is opposite to Hotel Pennsylvania). Then for going to cold spring harbor you have to take Long Island Railway services. Your Metro card will not work.

Word of caution for buying weekly LRR weekly pass:

 Here one thing to take care is if you are starting on Saturday then take a pass, otherwise travel as a daily passenger. For instance I took a weekly pass that is around 88 USD on Tuesday, but its validity was between saturday through Friday. So, in other words, I paid for the travel I have not made. This is something you have to be careful about since it is not written anywhere. If you take a train from Penn station, it takes easily one hour to reach Syosset (Remember you are suppose to go to Syosset – don’t go to the cold spring harbor station). Just get down the stairs on the opposite end. This is where the cold spring harbor shuttle stops and ferries people through the station and institute. It stops right at the Grace auditorium where most of the meetings take place. I was attending the EBI workshop that preceded the genome informatics meeting. It was taking place at Blackford hall which is at the right hand side of the grace auditorium and easy to find.

Going for EBI workshop what to expect?

If you are going to attend the EBI/Ensembl workshop, they will ask you to install the virtual machine which is a typical linux box created on any operating system. A word of caution is to bring in an OK sort of laptop. With my small laptop, I had terrible time doing anything. I am going to write on how to create a virtual machine shortly (watch out my blog site). 

The Meeting:

The meeting is itself very tiring. It starts at 9 AM and ends at 9.30 PM. And they have these poster sessions in between. So, it may be better to stay very close by. Even I was told that all other meetings are also arranged that way.

The Science:

This meeting is all about algorithms and software for genomics, so it is very appropriate for people who are in this field. Lots of tools and algorithms are discussed here before they get into publication, so students watch out for this. Met Allpaths assembler creators, ENCODE people and many other familiar faces. Overall pretty good!

By the way I am live tweeting talks #genomeInformatics 

WE ARE ALL MOTIVATED- either positively or negatively

I heard a story of two brothers and wanted to share with u all.
One was a drug addict and drunk who frequently beat up his family. The other was a very successful businessman who was respected in society and had a wonderful family. How could two brothers raised by the same parents, brought up in the same environment be so different??????The first brother was asked, "What makes U do what U do? U r a drug addict, a drunk and u beat your family. What motivates U?" He answered, " My father. My father was a drug addict, a drunk and he beat his family. What do U expect me to be? That is what I am."The second brother was asked, " How come U are doing everything right? What is your source of motivation?" And guess what he said?????"My father. When I was a little boy, I used to see my dad drunk and doing all the wrong things. I made up my mind that that is not what I wanted to be."

MESSAGE

Both brothers derived their motivation from the same source, but one was using it positively and the other negatively. Negative motivation brings the desire to take the easier way which ends up being the tougher way.
Thanks!!!!

Fly above the cloud when it rains...

I have posted this on my lab door to motivate my students and myself. This is what I tell to myself time and again when there is a crisis situation - although technically there should be no-crisis-like situation.

I have joined IICB during a time when all the Networking projects were decided, 12th 5 year plan was laid. So, there was very little scope for me to get into any of these lucrative fund giving projects. Fortunately or unfortunately I have been included in one of the networking projects but I am still clueless about the fund part. I only see occasionally some mention of the fund, its reduction and so on, but never saw anything for my lab as yet... Anyways leaving the complaint part aside, how do I run my lab? Director is generous enough to have granted me some money for my sequencing programs and servers which I thought was adequate, but balancing sides such as purchase, vendors, payments have been a herculean task for me.

I will give an example here. I want to do some genome sequencing with a third party. I call them, negotiate a price (With promise to give them more business later). They take few days finally before making an offer. Now I look for money, get it sanctioned and raise an indent. But unfortunately there sits a man who has the power to reject it for no apparent reason. The reason - he does not understand what it is. Fine, no one is suppose to understand everything, but will it not be nice to come back and ask? Then you go back and ask, and then  he agrees to reverse it. By then the buggy software makes the account zero. You then go and talk with the same man he holds the power to change that zero status to previous status, will make you wait for 30 minutes and may be finally do that. You raise the indent again, then he sits on it before you really go and ask about the status. Then comes a committee formation and finally giving an order. When you get the order you send your samples to the company and the company does the job and sequences the samples and gives you the bill. The lousy department sets some date cutoffs (twice a year). If your bill reaches later than the cutoff date, your money disappears and truly disappears and you are responsible for paying the bills. Just imagine the life of a scientist is suppose to be much more skewed towards research rather than these mundane activities, but it is unfortunately so here.

All these money giving, money disappearing act happens when the money is given by the institute. Now, the only way around is to get your own fund. So, I am rather more determined to get the money from outside rather than from inside. With lot of deadlines hovering on my head for grant submission let this be a motivation rather than having negativity towards the people that create impossible situation. So finally I can say amidst my work trips,  my carrier trips (Carrying DNA samples, getting the bill in hand), my personal trips, I have survived, meeting deadlines and submitting 3 grant proposals back to back to DBT. Hope atleast one of them gets funded. So, this is what I would say running above the cloud when it rains....

A million heroes!

Aamir Khan, Madhuri Dixit, Amitabh Bachchan, and ofcourse not to forget the bollywood baadshah Shahrukh Khan; they are all heroic figures to atleast a million people! Few of us even worship them, celebrate their birthdays, and go mad to get a glimpse of these sitaare zameen par! Like all others, I also admire these actors but not to a point that makes me go crazy. I admire them because I like their acting skills. But, unlike a crazy teenage fan, now reason for my admiration has changed from looking them as stars to looking them as workers doing their job!

Once I got to listen to an Art of Living preacher; the words which stayed in my mind were “everyone and everyone’s job is equally important in this world; noone or no job can be put above the other”; if sweepers are considered quite low in society then just imagine what difficult situation can arise if all the sweepers in this world goes on a week’s strike; it could lead to some pandemic kind of situation! I know that still we would talk about the superiority of professionals like doctors or for some of us the priests, both of which are worshipped, atleast in India! But are we not aware of the greedy doctors involved in organ thefts or the so called great preacher cum rapist Asaram Bapu!

I guess one shouldn’t be assessed by what profession one belongs to but by how good one does in his/her respective field. In every profession, there are some people who excel, some mediocres and some who bring bad names! In this context, for me every single person is a hero if (s)he does good in his/her respective field; be it a scientist, a sweeper, a driver or a doctor!