Today I used grep to quickly extract chromosome-specific info from a gigantic dataset and put them into separate files.
AND I found that grep -w will get me chr1 info without giving me chr10, chr11 etc.
Computer languages.... who would have thought I could find it so much fun? Or addictive?
I am also en route to learning Perl and Python.
Soon-to-be-computer-language-polyglot signing off...
Thursday, May 30, 2013
Friday, May 17, 2013
Varsha Shridhar is...
... learning Unix!! OMG!
....Taking a giant leap into the dark side!
Actually, this stuff is a lot more exciting than I'd envisioned.
Might I direct similarly clueless, yet interested, folks to this page: http://korflab.ucdavis.edu/Unix_and_Perl/
Hoping to be able to write my own Perl scripts to quickly extract large amounts of relevant genomic data!
....Taking a giant leap into the dark side!
Actually, this stuff is a lot more exciting than I'd envisioned.
Might I direct similarly clueless, yet interested, folks to this page: http://korflab.ucdavis.edu/Unix_and_Perl/
Hoping to be able to write my own Perl scripts to quickly extract large amounts of relevant genomic data!
Wednesday, May 8, 2013
Ani and Durga
Durga is 8 weeks old today. She smiles, follows me with her incredibly beautiful eyes, and lets out indignant hollers if she's not carried around while awake.
Ani is 3 years old and is in preschool. He says, "Only babies go to daycare, mummy! Big boys like me go to preschool", conveniently forgetting that less than 10 days ago, he was still in daycare himself.
Ani is fascinated by Durga- for now. He gets highly tickled if she pees or poops, he says "Bless you!" when she sneezes, he thinks her flailing limbs are toys to be tinkered with, and he likes to put his nose into her mouth when she opens and closes it while hungry. He also sings to her when she cries, wipes her nose free of snot that arises from the various nasal infections that he bestows upon her, but gets upset with anyone holding her when he is hungry or sleepy.
Durga, in her turn, seems to know when Ani is happy; she is quiet then. And when she hears him bawling, she starts crying too.
Life with two kids. It is hard. But it is also getting to be quite a lot of fun.
Ani is 3 years old and is in preschool. He says, "Only babies go to daycare, mummy! Big boys like me go to preschool", conveniently forgetting that less than 10 days ago, he was still in daycare himself.
Ani is fascinated by Durga- for now. He gets highly tickled if she pees or poops, he says "Bless you!" when she sneezes, he thinks her flailing limbs are toys to be tinkered with, and he likes to put his nose into her mouth when she opens and closes it while hungry. He also sings to her when she cries, wipes her nose free of snot that arises from the various nasal infections that he bestows upon her, but gets upset with anyone holding her when he is hungry or sleepy.
Durga, in her turn, seems to know when Ani is happy; she is quiet then. And when she hears him bawling, she starts crying too.
Life with two kids. It is hard. But it is also getting to be quite a lot of fun.
Friday, March 29, 2013
At Long Last....A Couple of Great Books
Have been using much of maternity leave devouring the online books available at CLP. For the past few months, I haven't been able to read anything too upsetting- my mind goes into overdrive and I get visions of those horrible things that I've just read about happening to my kids and I spend the next week broody and depressed.
This happened after reading the first half of J.K.Rowling's "A Casual Vacancy". That book upset me no end. Sure, the writing is beautiful and there are some sentences that are masterful in their understated irony. But the story itself? Drugged mothers, abusive fathers, rape, looting, despair,drugs. I hated the story. I kept wondering if Ani and Durga would end up like some of the kids in the book, if we would ever have a cordial relationship and how in the world I was to become a good parent.
Anyway, that's why I stopped reading the book halfway. Couldn't take the sheer nastiness anymore.
The safest feel-good books are romances, but God, spare me those implausible plots and the saccharine dialogues. I still read romances, of course, but it's getting harder to find truly good books. My safe options- Eloisa James, Lisa Kleypas and Loretta Chase- are not bringing out books fast enough for me.
Since time is on my side, I have been scouring the pages of CLP's "eBooks Available Now" looking for something decent. What do I mean by "something decent"? The book should have good writing and a plot that engrosses me. It shouldn't be vulgar. And it should have something in it, some deeper meaning or nuance that I can ponder on long after I read the book. The gold standard here is something like "Atonement"- a book that sweeps one away, a book that is filled with compassion, horror and humanity that it is instantly recognizable and yet quite unforgettable.
Here are my picks so far:
a) The Descendents by Kaui Hart Hemmings. Exquisite. Poignant. I am curious about how they made the movie, because so much of the story lies in what is not expressed.
b) More down to earth, but quite entertaining: A Duty to the Dead by Charles Todd. Mystery novels set in the time of WWI with the protagonist as a nurse serving with the Brits (who else? Why can't somebody write a novel with a German or French protagonist in the times of WWI or WWII? Oh wait, I suppose you could say that 'Allo 'Allo is a work with French protagonists... though it was actually created by the British. As for the Germans, I can think of one.... a novel by Chris Bohjalian... though not in this genre)
*****Update****
On much more reflection, I don't think The Descendents is worthy of my gushing praise above. It's too black-and-white.
Charles Todd's Bess Crawford books are far nicer to read than the Ian Rutledge series. But where's the romance? There needs to be at least a hint of it, for me to continue the series!
This happened after reading the first half of J.K.Rowling's "A Casual Vacancy". That book upset me no end. Sure, the writing is beautiful and there are some sentences that are masterful in their understated irony. But the story itself? Drugged mothers, abusive fathers, rape, looting, despair,drugs. I hated the story. I kept wondering if Ani and Durga would end up like some of the kids in the book, if we would ever have a cordial relationship and how in the world I was to become a good parent.
Anyway, that's why I stopped reading the book halfway. Couldn't take the sheer nastiness anymore.
The safest feel-good books are romances, but God, spare me those implausible plots and the saccharine dialogues. I still read romances, of course, but it's getting harder to find truly good books. My safe options- Eloisa James, Lisa Kleypas and Loretta Chase- are not bringing out books fast enough for me.
Since time is on my side, I have been scouring the pages of CLP's "eBooks Available Now" looking for something decent. What do I mean by "something decent"? The book should have good writing and a plot that engrosses me. It shouldn't be vulgar. And it should have something in it, some deeper meaning or nuance that I can ponder on long after I read the book. The gold standard here is something like "Atonement"- a book that sweeps one away, a book that is filled with compassion, horror and humanity that it is instantly recognizable and yet quite unforgettable.
Here are my picks so far:
a) The Descendents by Kaui Hart Hemmings. Exquisite. Poignant. I am curious about how they made the movie, because so much of the story lies in what is not expressed.
b) More down to earth, but quite entertaining: A Duty to the Dead by Charles Todd. Mystery novels set in the time of WWI with the protagonist as a nurse serving with the Brits (who else? Why can't somebody write a novel with a German or French protagonist in the times of WWI or WWII? Oh wait, I suppose you could say that 'Allo 'Allo is a work with French protagonists... though it was actually created by the British. As for the Germans, I can think of one.... a novel by Chris Bohjalian... though not in this genre)
*****Update****
On much more reflection, I don't think The Descendents is worthy of my gushing praise above. It's too black-and-white.
Charles Todd's Bess Crawford books are far nicer to read than the Ian Rutledge series. But where's the romance? There needs to be at least a hint of it, for me to continue the series!
Wednesday, January 2, 2013
The Name Game
What's in a name, after all?
Everything, I think. Or at the very least, a lot. A name can be, and is, more than just a label. A name embodies traits and meanings and can serve as a beacon to its holder.
And that's why choosing a name for one's child can be so fraught with stress. It needs to be perfect!
The process of choosing a name is just as important as the name itself. In my parents' and grandparents' generations, the process of choosing a baby's name was very different than it is in mine. In their generations, the name was likely to be chosen and bestowed, not by the parents, but by the family elder, or a priest or a scholar, in a process completely entwined with family politics and dynamics.
In my household (if not generation), Ram and I are democratic and exclusive in equal parts. We are adamant that the choice should be ours, while being receptive to the ideas of close family members. And we follow a democratic process between ourselves: we discuss possible sources of names and shortlist some, go through the sources, pick a list of names and discuss those. This process has worked really well so far.
However, I'm finding that choosing a name for a daughter is harder than choosing a name for a son.
When I was pregnant with Ani, Ram and I had a sure-shot method of finding a name. We got hold of a copy of the Vishnu Sahasranamam (a convenient repository of 1000 names of Vishnu), parked ourselves down on the floor and chanted out the text. And sure enough, within a few pages, we found the name that we both liked, which not only sounded good, but was rich in the meaning that we wanted our son's name to have: Aniruddha means unstoppable, someone who recognizes no barriers. This, we felt, was a good trait for a son to have. It would inspire him to great heights and help him overcome difficulties on his way. Plus, it was also the name of a grandson of Krishna, a God who is much loved by both Ram and me.
Now, there are tons of girls' names that sound incredibly pretty. The names that leap to my mind are variations of 'happy' (Shambhavi, for example) or 'playful' (Lalitha, a favorite of mine), or 'beautiful' (too many to list).
But what do I want my daughter to be? Sure, she should be happy and playful and no doubt, she will be beautiful. But I want her to be so much more! I would like my daughter to be strong, resilient, fierce, truthful, and optimistic. I also want her to be ethical, just, and loyal. So she needs a name that reminds her of all this. She needs a name that will lift her out of darkness and show her the light.
So the hunt for the perfect name is still on.
Everything, I think. Or at the very least, a lot. A name can be, and is, more than just a label. A name embodies traits and meanings and can serve as a beacon to its holder.
And that's why choosing a name for one's child can be so fraught with stress. It needs to be perfect!
The process of choosing a name is just as important as the name itself. In my parents' and grandparents' generations, the process of choosing a baby's name was very different than it is in mine. In their generations, the name was likely to be chosen and bestowed, not by the parents, but by the family elder, or a priest or a scholar, in a process completely entwined with family politics and dynamics.
In my household (if not generation), Ram and I are democratic and exclusive in equal parts. We are adamant that the choice should be ours, while being receptive to the ideas of close family members. And we follow a democratic process between ourselves: we discuss possible sources of names and shortlist some, go through the sources, pick a list of names and discuss those. This process has worked really well so far.
However, I'm finding that choosing a name for a daughter is harder than choosing a name for a son.
When I was pregnant with Ani, Ram and I had a sure-shot method of finding a name. We got hold of a copy of the Vishnu Sahasranamam (a convenient repository of 1000 names of Vishnu), parked ourselves down on the floor and chanted out the text. And sure enough, within a few pages, we found the name that we both liked, which not only sounded good, but was rich in the meaning that we wanted our son's name to have: Aniruddha means unstoppable, someone who recognizes no barriers. This, we felt, was a good trait for a son to have. It would inspire him to great heights and help him overcome difficulties on his way. Plus, it was also the name of a grandson of Krishna, a God who is much loved by both Ram and me.
Now, there are tons of girls' names that sound incredibly pretty. The names that leap to my mind are variations of 'happy' (Shambhavi, for example) or 'playful' (Lalitha, a favorite of mine), or 'beautiful' (too many to list).
But what do I want my daughter to be? Sure, she should be happy and playful and no doubt, she will be beautiful. But I want her to be so much more! I would like my daughter to be strong, resilient, fierce, truthful, and optimistic. I also want her to be ethical, just, and loyal. So she needs a name that reminds her of all this. She needs a name that will lift her out of darkness and show her the light.
So the hunt for the perfect name is still on.
Wednesday, December 19, 2012
Kids and Pregnancies and Men
I am trying to imagine all the men in my world as being pregnant. How might RK, for example, be?
He would get in his complaints, I think, but try to do so while pretending that he actually was not. He would talk about it like it was some kind of a scientific question, but pepper the statement with all his aches and pains.
"Oh, yeah, I think my deep throbbing knee pain is really due to the fact that my ..ahem.. lateral patellar retinaculum is being stretched. I wonder if there have been any studies done on how inflamed this muscle can get in pregnancies. I mean, I'm sure...ha ha... that I'm not the only pregnant man in the world to be in such great agony"
"You laugh, Varsha, but you don't know the stress! It's very stressful to not be in control of your own body! I don't know just how I manage it, but I must say, I have some incredibly good coping mechanisms. Hmm... you might do well to try some of them"
Or my dad:
"My motto in life is to grin and bear it.
Bloody hell! Where the h$##$$# is my $%##$$ towel? Who in bloody #$### moved the TV remote? Arrrggghhhh... if that truck doesn't move out of the street already, I'm going to PUNCH the damn ##$### wall!"
PG (thesis adviser, for those of you who don't know him):
"You know. It's interesting. They have all this technology, but they just cannot take a LITTLE vial of blood without clotting up your whole arm. I must tell Wishwa and ask him what kind of education these doctors get these days. Of course, these days, doctors don't do any kind of procedures. They only want to get more and more specialized"
LOL
This is fun. Now every time I meet a guy, I'm going to imagine him pregnant.
Not too many guys at MWRI, but quite a few at IDM- imagine the great Don Burke, or better yet, the skeletal Paolo. Snap! Just like that, they are all pregnant, at least 2 trimesters along, waddling down the corridors.
Friday, December 14, 2012
A hard week
I have wept a bit this week. I attribute part of the reason to hormones. Apparently, hormones rage during the 2nd trimester. I'd like to know, when do hormones not rage? Teenagers, menstruating women, menopausal women, pregnant women, lactating women- everyone appears to have hormones that rage. Why don't hormones just do their thing quietly and leave?
And really, why haven't more hormonal studies been done in men? I'll bet my bottom dollar that men in their 30's, men in their 40's, men with 2 kids, men with no kids, men who are bald, men with big bottoms and men with sweaty handshakes are also afflicted with indiscreetly fuming hormones.
Other possible reasons for my general state of weepiness:
a) Lack of support from that esteemed spouse of mine in the specific area of housework: really, my man, could you PLEASE, for crying out loud, move that ass away from that computer and help me a bit? Or at least, spend some time while I am doing housework so I don't feel alone?
b) Incredible support from my lovely little son: the more Ani spends time with me and tries to help with whatever I am doing, the more weepy I get, because really, what a big heart on such a small kid!
c) Lack of sleep: thanks to those indiscriminate hormones, I suppose. Am too big to sleep on my tummy, too nasally-obstructed to breathe easily, and too prone to vivid dreams in which I have to eat the frogs that come out of Ani's nose.
What I need is an escape from my real life. Romance novels don't cut it anymore. I'm like the druggie who needs coke, and not marijuana, for a real fix. What I really need is...
....a Hindi movie, luridly romantic, incredibly silly, laugh-out-aloud funny, with a heart-stoppingly handsome hero and a stunningly beautiful heroine.
There's a scene at the end of the song "Bol Na Halke" where Preity Zinta (who satisfies my criterion for a beautiful heroine) and Abhishek Bachchan (Yuck. Double yuck.) walk in front of the Taj Mahal with their grown-up kids. The sun is setting behind them, everyone is dressed simply but oh so elegantly, and you can't see Bachchan's face (thankfully), but his physique is perfectly hero-material. The music is splendid, the evening is indescribably beautiful and the scene is perfect. Zinta and Bachchan have done their jobs of bringing up their kids and now can spend time gazing at the Taj Mahal without a care in the world.
Wow.
They probably have a couple of maidservants to take care of the house and a cook for their meals.
That is where I want to be.
And really, why haven't more hormonal studies been done in men? I'll bet my bottom dollar that men in their 30's, men in their 40's, men with 2 kids, men with no kids, men who are bald, men with big bottoms and men with sweaty handshakes are also afflicted with indiscreetly fuming hormones.
Other possible reasons for my general state of weepiness:
a) Lack of support from that esteemed spouse of mine in the specific area of housework: really, my man, could you PLEASE, for crying out loud, move that ass away from that computer and help me a bit? Or at least, spend some time while I am doing housework so I don't feel alone?
b) Incredible support from my lovely little son: the more Ani spends time with me and tries to help with whatever I am doing, the more weepy I get, because really, what a big heart on such a small kid!
c) Lack of sleep: thanks to those indiscriminate hormones, I suppose. Am too big to sleep on my tummy, too nasally-obstructed to breathe easily, and too prone to vivid dreams in which I have to eat the frogs that come out of Ani's nose.
What I need is an escape from my real life. Romance novels don't cut it anymore. I'm like the druggie who needs coke, and not marijuana, for a real fix. What I really need is...
....a Hindi movie, luridly romantic, incredibly silly, laugh-out-aloud funny, with a heart-stoppingly handsome hero and a stunningly beautiful heroine.
There's a scene at the end of the song "Bol Na Halke" where Preity Zinta (who satisfies my criterion for a beautiful heroine) and Abhishek Bachchan (Yuck. Double yuck.) walk in front of the Taj Mahal with their grown-up kids. The sun is setting behind them, everyone is dressed simply but oh so elegantly, and you can't see Bachchan's face (thankfully), but his physique is perfectly hero-material. The music is splendid, the evening is indescribably beautiful and the scene is perfect. Zinta and Bachchan have done their jobs of bringing up their kids and now can spend time gazing at the Taj Mahal without a care in the world.
Wow.
They probably have a couple of maidservants to take care of the house and a cook for their meals.
That is where I want to be.
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