Yes or No?

Sometimes, I wish life was one long series of true or false questions, there must have been no need to turn back, or even look back, cos there's only one way - the right way to do things...

Well, the reason I'm writing this is - I have a mid term + a presentation coming up soon ( a big deal for someone as lazy as me ;-) ), but there is a whole lot to do as part of my RA.

So is it nice that I am being paid to study, or is it not nice that I have to keep that as my top priority, come what may, since that is paying for me to study?

Yeh Dil Maange More??

Its only human to want more - more money, better grades, better looks, better clothes, a better shelter, better food, and what not.
I received a forward today, one of the typical 'starved african children' forward. Not having done anything towards promoting their well being, it would definitely be hypocritical if I were to criticize everyone about being as selfish as me.
Well, the first step would definitely be not to waste anything - food, clothes,money.


A story for the inevitable doubt :
There were innumerable starfish lying/slowly dying along the beach of some ocean. A man was systematically picking up them using a hovel and throwing them back to where they belonged - the ocean . A cynic asked - "How in the name of anything are you going to save all of them?? Its just a waste of time!! " .
This person said nothing, just picked up yet another one, made sure it landed in the ocean, and then says - "Made a difference to that one" .

:-)

Of Fountains and Moonbeans

Moonbeans is your equivalent of the ubiquitous "College Canteen" - the most flamboyant part about it being its location - forming a modest third of the triangle between the Green Library, the fountain hoop and itself .
The coffee haven for people 'studying' (well, some actually do!! ) in meyer/green, or the more unfortunate people breaking their head over some code in sweet hall, it fully lives up to its name.
It's a fine afternoon, and you decide you've had enough of acads, and you just want to grab a cup of coffee, watch life zoom by (or rather, bike past you) ; you invariably end up getting slightly shocked when you perceive the serpentine queue waiting for their own potion/poison. Still, never mind, you wait patiently for tea/coffee, or sometimes samosa (yeah!! they have that too!!) .
The guy behind the counter is a really warm person, and he sometimes asks for your name, tries pronouncing it, usually with a good measure of success, and if the crowd is not too bad, will also say - "Kaise ho" (Apparently, he does know a smattering of several languages! ) .
You smile, conveniently forget politeness, and wait for your coffee.
With the cup of life in hand, you then head to the fountain, the steady drone of water drowning away any directed noise, so the only thing you hear is a steady gush of H2O. Another ideal location to go over that paper which doesn't seem to make sense even though you think you've read it enough.
Things now move speedily towards a happy ending, and that paper is no longer greek and latin.
Peace is restored, and you head back home to search for something else to break your head on.

Looking forward to many more fountains and moonbeans!! :)

Stopping by the woods on a snowy evening

Robert Frost

Whose woods these are I think I know,
His house is in the village though,
He will not see me stopping here,
To watch his woods fill up with snow.

My little horse must think it queer
To stop without a farmhouse near
Between the woods and frozen lake
The darkest evening of the year.

He gives his harness bells a shake
To ask if there is some mistake.
The only other sound's a sweep
Of easy wind and downy flake.

The woods are lovely, dark and deep.
But I have promises to keep,
And miles to go before I sleep,
And miles to go before I sleep.

lovely poem :-)
My take?
I think sometimes its okay to stop by the woods because life is about the journey, and not just the destination....

I was coming back from my lab, and happened to notice several sets of people across
Serra Street, apparently it was a reunion, so 'students' from the batch of 1951-61-....1981-1991 (I think) came over..
Coming back to your Alma mater, meeting, catching up with long lost friends/acquaintances, must be pretty exciting!!

I cant wait for my 'reunion' !!
See you in 2017 !!!

cooool!!!!!!!!!!!

There was this Matlab Program which was (apparently) consuming huge amounts of memory, and wasn't executing right,

my suggestion?? Restart the computer, and guess what?? It worked!!!

What Next

15 Sep 1984 - 1987 - Ignorance
1987 - 1989 - Kindergarten
1989 - 2001 - KV Bolarum
2001 - 2005 - SNIST
2005 - 2007 - Stanford
2007 - ____ What next?

Went to the career fair today, told everyone how awesome I was, and why I should be considered for the best position in the world!

Lets see what comes up!!

RNA Secondary Structure Prediction

Paper Reference
Björn Voß (Voss), Structural analysis of aligned RNAs . Nucleic Acids Research (Oxford Journals). October 2006.

Abstract
In this paper, the author describes the need for structural analysis of different classes of RNAs and discusses RNAlishapes, a tool/algorithm which facilitates the prediction of a consensus structure of a class of RNA sequences. The algorithm uses extensions of several techniques from single sequence RNA structure prediction.
The input here is a set of aligned RNA sequences, to which a shape abstraction technique is applied first. The biggest utility of the shape abstraction technique as a first step is that it retains only the nesting and adjacency pattern of helical and unpaired regions, so any exponential growth of the number of sub-optimal regions is curtailed.
Structure prediction (based on an adaptive technique using a grammar describing the search space) is then performed, which accepts user defined inputs too, providing the ability to assign confidence levels to different structures. The grammar used in RNAlishapes describes RNA secondary structures without isolated base pairs and handles dangling bases differently. This branching into grammar and algebras facilitates the application of already existing grammars on individual sequences and then averaging it over the entire alignment sequence.
Unpaired bases and gaps that arise due to alignment of different RNA strands are taken into account by considering the thermodynamic energies of various scenarios. Ultimately the consensus structure predicted has the minimum mean free energy (MmFE).

Discussion:
The author has come up with an algorithm that forms a consensual prediction of the given aligned RNA sequences, which is a significant step ahead of the prediction of the structure of a single RNA sequence that was discussed in class. Different (classes of) non-coding RNAs are characterized not by their sequence similarities, but by their structural properties, and under this light, this study could definitely lead to a more generic algorithm.
In my opinion, one of the best aspects of the algorithm was having shape abstraction as the first approach, and then opting for more specific filtering/prediction schemes. This must have been the prime reason for the asymptotic complexity to be significantly less (O(pN,N3,M) for an alignment of length N holding M sequences, where p depends on the shape abstraction chosen).
Typically, genetic algorithms that work best have a mix of learning/stochastic and deterministic techniques, with a carefully selected feature vectors (for the training sets/learning algorithms). In the “Structure Prediction” section for instance, the author illustrates a base-pairing parameter, where there is a threshold level which would be user defined. ‘Hardwiring’ the threshold is not considered good practice. Also, in calculating the free energy, the parameters selected to determine the MmFE alignment sequence may/may not be functionally complete.
RNAlishapes builds upon existing algorithms for consensual prediction of aligned sequences and manages to keep the asymptotic complexity within bound. It would however be useful to check if self learning schemes could be incorporated into Structure Prediction.

Home

I sit here, contemplating, of all things about you
Reflecting on every aspect of life, that revolved around you,
Your blissful presence was a presupposed fact,
You were there for me, every scene, every act,
shielding me from the unforgiving sun,
protecting me from rain and hurricane,
being indulgent and letting me have all the fun,
remaining irrevocably benign, while I was raising cain.

Your thoughts come unbidden now,
The dewed mornings when it appeared
as if you were fresh from the laundry,
The mild days when the wind lapped up the waves
playing them softly against your feet,
The delicious evenings, when you stuck out like a pearl
amongst plastic :-)

And yet, when future beckoned,
You let me go with open arms, and an open invite
Isn’t that love at its best, not seeking a return?
I grew wings, flew out of sight,
With the tiniest sliver of doubt,
If you shed tears at the loss, but was I contrite?

And now, when I come back to wintry evenings,
When your care and concern is a thing of the distant past,
My thoughts suddenly fly to you,
and everything about you becomes rosy once again,
So loveable, so pristine in its affection
and so unattainable….

I can’t wait to see you again,
I keep crossing out dates
So I can speed them up and see you sooner,
Aah! If only I was all mighty,
None of these days would intervene,
But that is not meant to be, time takes its time,
And then one day,
I will be with you, and make you the happiest in the world!!
A lesson learnt from the school of life,
never to be forgotten.

And yet, something nags me at the back of my mind,
what is it that I miss the most,
Home, or the idea of one?





:-)
Courtesy: A gtalk chat with "d" :-)

Welcome :)

Well,

I dont really want to write too much of an intro, I am sure its going to be deja vu :) .
I've always been really interested in creative writing (or the idea of it :p) , and now that I've become reasonably good at managing my time, I've decided to get back to it, and unleash it to the world!

so, welcome to my blogspace :-)