A Tall Drink of Water

I've been feeling stupid for a while now ...

2012-01-19T15:38:00.000-08:00

I've been feeling stupid for a while now, but after reading this , I feel just slightly better since apparently its a quite common feeling in graduate school.

At least that's what I'm trying to tell myself.

RIP Mr. Ladue

2012-01-09T14:28:00.000-08:00

Today I learned through a friend that my high school chemistry teacher, Mr. Ladue, passed away. Its been more than 15 years since I had taken high school chemistry. Mr. Ladue's class was considered one of the harder one's on campus, but I managed to get As (I think) in both fall and spring semesters. That year was his last, as he was going to retire. He had taught at Corona since its opening and was quite popular amongst students.

While I've forgotten most of my chemistry, he's one of the most memorable teachers I had in high school. (One thing I do remember was watching films made by noted chemist Roald Hoffmann, whom I met a few years ago when worked at Cornell) While at still liked biology and genetics more than chemistry, his class prepared me well for college chemistry classes. Reading his obituary brought back so many fond memories of his class, my time in high school, and friends and places I hadn't thought of in quite a while, but brought a smile to my face remembering them. RIP, Mr. Ladue.

College athletics - power corrupts

2011-12-31T16:26:00.000-08:00

The college football post season will be culminating in the coming 10 days or so with the BCS National Championship game. The past year has been a tumultuous one with the Penn State scandal, the financial corruption charges surrounding the Fiesta Bowl, and former Ohio State coach, Jim Tressel, resigning under less than ideal circumstances. There is a lot money being made of collegiate athletic programs. For example, CBS signed a 6 billion dollar contract for the broadcast rights to the NCAA basketball tournament. And while a lot people are getting rich off college athletics, there is one group that is not, and that is the athletes themselves.

Joe Nocera published a a column today calling the NCAA a cartel whose main objective is to oversee the collusion of athletic departments whose main goal, lets face it, is making money. He has written a piece in the NYTimes Magazine in which he proposes to pay athletes in football and basketball progams. (At many schools, revenues from these programs helps subsidizes other sports that don't generate a profit). I haven't read the second piece, but at first thought, I think its certainly worth looking into.

I'm not for eliminating collegiate athletic programs, like Steve Salzberg suggests. I think sports programs can raise the profile of college or university and open a door to students who otherwise couldn't attend college. For example, take this recent article on the rise of Ivy League athletics. Its an atypical conference in that university presidents have a lot of control over programs and the football teams don't participate in postseason play.

I would also propose a salary-cap on football and basketball coaches. Urban Meyer was recently hired as the new football coach at Ohio State and signed a contract worth 4 million dollars in base salary and bonues per year. The contract is without its critics. Quoting:

“It’s symbolic of the condition we’re in,” said William C. Friday, the president of the University of North Carolina system from 1956 to 1986. “There’s an unrestrained salary march, where universities are trying to superimpose an entertainment industry on an academic structure. Any salary in that range is excessive.”

If there were a cap, perhaps the line between academic institution and sports entertainment could be less blurry.

And finally, what if schools gave stipends to student athletes as part of their scholarships? Graduate students are given stipends in exchange of the services they offer the university, like being teaching assistants. There are a lot people making money from college sports, except for the athletes. Its time they received some form of compensation too.

=====
Ok, after reading the Nocera NY Times article, he too calls for a salary cap and stipends ... read his piece, its a lot better than mine

A happy Regression to the Mean

2011-12-31T14:18:00.000-08:00

This tweet from Ed Yong made my day. 2012 will be more productive year.

The changing concept of a book

2011-12-25T18:41:00.000-08:00

I was watching a re-run episode of the CBS news magazine, 60 Minutes, today. Thefirst story was a fascinating look into The Vatican's library, founded when Europe was coming out of the dark ages. Its holdings go back 2,000 years and contain works on math, cookbooks, and even love letters from Henry VIII to Ann Boleyn. The library is not accessible to the general public and the only person allowed to check out books is the Pope himself. Many of the books were written by hand of parchment, or treated animal skin.

In stark contrast, today I also read this story regarding the battle between publishers and libraries over e-books. In the ever changing landscape of book publishing, many publishers are finding it not in their best interest in giving libraries unlimited access to e-books based. For example, HarperCollins enacted a policy of after 26 loans of an e-book, libraries must purchase another license to be able to continue to offer the book to patrons. Now, I'm not sure how they came up with that number 26, but its strange rule nonetheless.

But the two stories show how far books have come in serving as a medium to share and expand knowledge. Looking 1000 years in the future, it will be interesting to see if libraries and books will exist only in the electronic sense.

Photographic memories

2011-12-23T21:18:00.000-08:00

Revived my Flickr account today after it was dormant for 2 years. Forgotten I had taken some of those pictures and it was a nice trip down memory lane. A happy reminder to better days gone past and many more to come.

Technlogy and Distraction

2011-12-08T20:32:00.001-08:00

Being at the keyboard means having tons of low hanging fruit to tempt you. Check your email, see your Twitter stream, check your email, etc. Its definitely changed the way I interact. Today I read this interesting post Selective use of technology:

“Technology effects the way you think. The effect is not uniformly better or worse, but it is certainly real.”

I agree with that statement, its definitely changed the way I interact and think. I won't go as so far as dropping email, Twitter, FB. But I've put a block on my browser that disallows me to view any links on those websites during a 10 hour window that correpsonds to regular business hours. I feel its helped me think a bit more clearly without having distractions.

Charles Darwin quote

2011-11-04T10:02:00.000-07:00

Yesterday wasn't a good day for work. I was assigned the menial task of filling in citations and adding bibiliographic entries to an EndNote database for a grant submission because I was told: 'I was the best qualified for the job'. I won't expand my rant about this anymore, but needless to say it was not a feel good day at work.

Later in the evening, after I let out some anger in an epic spinning workout, I remembered this quote I had put at the front of my MS thesis by Charles Darwin:

My industry has been nearly as great as it could have been in the observation and collection of facts. What is far more important, my love of natural science has been steady and ardent.

And deep down, I still feel this way. But some days its hard, but I know I'll soon be out of my current situation and in a better one. And my love for human genetics is going to help get me there.

2011-10-06T05:34:00.000-07:00

Sad to hear about Steve Jobs passing away. As a testament to how much Apple and his vision has changed things, I learned about his passing while viewing my Twitter stream on an iPhone. In a time where the economy in the America is facing a lot of challenges, and increasing competition from overseas, people like Steve Jobs represented the best things about America. May his creativity, perseverance, and courage continue to inspire even after he is gone. RIP, Steve Jobs, and American original.

Quote about R.A. Fisher

2011-10-03T19:19:00.000-07:00

Talked about the Wright-Fisher Model today in class. Here is some R code simulating it. Anyways, on to the subject of this post. Read this clever quote that speaks to R.A. Fisher's influential works in both statistics and population genetics:

Fisher's important contributions to both genetics and statistics are emphasized by the remark of L.J. Savage, "I occasionally meet geneticists who ask me whether it is true that the great geneticist R.A. Fisher was also an important statistician" (Annals of Statistics, 1976). (via Wikipedia)

How to Build a Motivated Research Group

2011-09-25T19:42:00.000-07:00

Some really good points in here in this article on how to build a motivated research group. Feeling connected to the lab is more important than you think. I'm glad I'm not the only one that feels this way.

The Modern Synthesis

2011-09-21T13:53:00.000-07:00

Today in molecular evolution, the prof talked a bit about the Modern Synthesis. This is one of my, if not my favorite topic. I first heard about it when reading E.O. Wilson's autobiography Naturalist when I was a senior in high school. I really wanted to be an evolutionary biology major in college, but ended up declaring as a molecular biology major on my college application. But after I heard about this thing called the Modern Synthesis, I knew I could combine the two. I've wanted be a population geneticists ever since. And 15 years later, I'm still in love with the subject.

Long days

2011-09-20T10:19:00.001-07:00

Its not even a month old, I want to the semester to be over. Ugh.

The Rise and Fall of Fat in India

2011-09-15T13:17:00.000-07:00

Read a thought provoking piece in the NYTimes today, The Rise and Fall of Fat in India. In a story of contrasts both obesity and malnutrition are public health problems in India:

It also may be the realization that obesity is a health problem. Over the past few years, a string of studies have consistently warned of rising obesity rates in India. While the poor continue to be plagued by malnutrition and anemia, the burgeoning middle class is suddenly able to afford a much better lifestyle. They no longer have to walk, cycle, or even take public transport to school, work or the market. They can eat as much as they wish — including Western junk food.

The costs of treating obesity related health problems is not cheap . South Asians are at increased risk for cardiovascular disease, so its good that the government is trying to raise awareness of better nutrition.

Last week was National Nutrition Week in India, where obesity joined malnutrition as a topic of discussion. Next week the United Nations General Assembly is meeting to focus on the obesity epidemic and how it’s fueling other chronic illnesses, like cardiac disease, diabetes and cancer.

Now, if only we can fully make the change in connotation — and completely break the bonds between being fat and being prosperous, between being fat and being beautiful, between being fat and being loved — we could take the necessary steps toward a healthier future.

What kind of country do we want to live in?

2011-09-13T14:00:00.000-07:00

Earlier today I read Ron Paul: Its not the government's job to take care of the uninsured.
Then a few hours later I read Why the HELL Didn’t He KEEP HER IN THE HOSPITAL?

Unity

2011-09-11T19:02:00.000-07:00

Leave it the humor writer Andy Borowitz to have one of the more thought provoking comments on the 9-11 anniversary I read this morning:

The Rising

2011-09-09T08:58:00.000-07:00

This song gets me choked up ...

The $10,000 college education

2011-09-05T18:36:00.000-07:00

Some interesting points of view at the NYTimes on Rick Perry's plan for a $10,000 college education. Reading the first opinion from Anthony P. Carnevale uncovered some facts about the two-tiered college education system currently in place today:

It is tempting to say his proposal is neither feasible nor fair. Even the cheapest online bachelor's degrees, offered by the Western Governors’ Association, currently cost $20,000. And in a world where there are $10,000 degrees at Rick Perry University and $240,000 degrees at Harvard, we know who will go where.
Inevitably, Governor Perry will be accused of "tracking" — putting affluent students on a track for America's elite schools, and poorer students on a track for his less desirable "discount" institutions. In fairness, though, the nation already has such a system. Today, America's selective four-year colleges educate half the students, who are increasingly affluent and white; two-year colleges and the least-selective four-year schools educate the less fortunate, other half -- who are increasingly working class, Hispanic and African American. Elite four-year colleges enroll only 4 percent of students from low-income families, 6 percent of Hispanics, and 5 percent of African Americans.

At the current school I attend for my graduate degree (luckily, the dept pays for my tuition, otherwise I wouldn't even dream of attending here) the undergraduate tuition costs $20,740 dollars per semester. And if the type of car is a fair barometer of a person's income, then at least some of these students come from families that are probably doing pretty well for themselves.

But if America wants to be competitive economically, then there needs to be a way for college to become more affordable. So while I probably won't be voting for Rick Perry, like commentator above, I'm intrigued by his plan.

Finally gave a talk in my department

2011-08-31T17:50:00.000-07:00

One of the stranger things about my dept is there isn't very many opportunities for graduate students to give talks about their research. From working/attending at other schools I've been at, I know its not that uncommon to have a graduate student seminar series. But I finally got a chance to give a talk in front of my dept today at the 2nd annual 'retreat'. (I put it in quotations because the venue is on a different part of campus, but this year they had free beer!)

My talk was a little thin on results because I had just started this project in early August, and as Murphy's Law would have it, I had redo the majority of my data analysis in 24 hours due to some strange errors I was finding. Now my dept has very broad research areas, but its mostly comprised of cell & molecular biologists and not much of the way of human genetics/genomics and bioinformatics. But after doing a practice talk in my lab, I got some good feedback and revamped my slides to make it more exciting for an scientific audience with most members outside my field. More than anything it was really fun to talk about human genetics and my own work in front of a crowd.

Why software is eating the world

2011-08-23T14:41:00.000-07:00

Read a very thought-provoking essay from Marc Andreesen in the Wall Street Journal about how software companies are increasingly driving the growth of the American (and world economies). One noted example he gives is Amazon, the wolrd's the biggest bookseller, which last week signed Timothy Ferris as its first author and will distribute his books via Kindle. In the coming years ahead previous industries that sell and distribute physical goods will increasingly depend on software to do it.

This made me think of the notion of traditional biology, where you need pipettes and and tips to do experiments, increasingly more and more you need to use or write software to analyze data. And while in the fields of genomics and genetics have been early adopters of the the use of software or computation, I forsee other areas of biology not accustomed to computationally analysis will increasingly rely on it more and more. Software is not only driving the economy but driving scientific discovery.

I was a freshman once

2011-08-18T10:20:00.000-07:00

Fifteen years ago this week I started my freshman year at University of Arizona. I still remember the nervous excitement of driving down Interstate 10 to Tucson. For better or for worse I've spend the years since working at or attending other universities, so whenever a new academic year starts, my memory looks back to when I started as a freshman. I will always hold fond memories of UofA. And who knows, when I'm all done with my training maybe I'll end up where it all began. A part of me would really like that ...

Personal Genomics and lifestyle changes for health

2011-08-11T19:25:00.000-07:00

I started reading the The $1,000 Genome: The Revolution in DNA Sequencing and the New Era of Personalized Medicine. While I'm only about ~100 pages into the book, I am finding it an entertaining read. Its also kind of cool that alot the names in the book I've either seen at meetings, or met in passing.

While I think the number of actionable results,from a medical point of view, will grow larger in the coming years from these direct to consumer genetics companies, I think there are cheaper ways to motivate one's self to make lifestyle changes. Take for example this story about Francis Collins who got results from 3 personal genomics companies, all which indicated the had 2x the average risk for type two diabetes. The story goes on to say at the time he was slightly overweight, sedentary, and not really watching what he ate. Since getting his genotyping results two years ago he's lost and kept off 25 pounds. Another striking example is Luke Jostins, genome blogger and geneticist. But in the end if personal genomics leads people to make positive lifestyle changes then that's a good thing for everybody.

There is always next year ...

2011-08-05T11:44:00.000-07:00

Decided to withdraw my abstract for a science meeting this early October. The experimental data wasn't good enough to make any reasonable inference on the hypothesis we were addressing. This was out of my control, but could have found this out a alot sooner than later. I blame this squarely on myself. I was really looking forward to presenting a poster on my own work for the first time in a while. The project isn't dead, but I look forward to this particular meeting every year mostly because I alot of my former labmates/friends attend and its nice to catch up with them. Oh well, there is always next year.

On the flip side, my less sexy project has some reasonable results that I think can land a minimal publication unit. It won't be groundbreaking, but its something.

What the new normal means for Americans

2011-07-12T13:29:00.000-07:00

Found this story What the 'New Normal' Means for Americans disturbing and depressing. I read this story on the heels of this NYTimes piece The Unemployed Somehow became invisible. 14 million Americans are out of work but Congress either doesn't want to do anything about it.

I think the GOP just wants to watch the world burn.

Google+

2011-07-10T20:10:00.000-07:00

Got an invite to Google+, Google's second (or maybe third?) try into social networking. I created a skeleton profile. Not sure how much I'll get into it because I'm not really sure if I should have even signed up for an account in the first place. Between Twitter and FB, I seem to get more useful info out of TWitter. Though I do think they both serve two different niches on the web in my opinion. But if I follow people on Twitter, am I really going to take time to see if they are on G+? Probably not. And I really doubt people are going to drop Twitter for Google+ (and if they do, it will take a bit of time) As for FB, I really think G+ is going to have be a significantly better experience for most people to put in the effort to migrate their networks to G+.

Well, those are my two cents on Google+

My 14th middle author paper

2011-07-06T19:08:00.000-07:00

One of the reasons I wanted to go to go back and get a PhD was the opportunity to do my own project and have the opportunity to write first author papers. I have one first author paper to my name as a result of my M.S. thesis. It was nearly 6 years ago now, which is hard to believe. In the years since I've had the opportunity to be co-authors on nearly a dozen manuscripts. I didn't drive the analysis of the papers nor the writings, but I'm quite proud to has supported and worked with a great group of people in their research. And in a strange juxtaposition of past and present, I got another middle author paper that included my previous PI and current PI. (Science is a small world!)

But I am so anxious to get a first author paper. I remember how proud I was to get my first one and it made me feel like a professional. I just need to be patient knowing full well I my time will come soon enough.

Back in the saddle and the basketball court

2011-07-01T10:14:00.000-07:00

I rode my bike for the first time in 11 months yesterday. I also played my first pickup game of basketball in nearly 3 years this week too. I'm really embarrassed to admit this, but after doing Cayuga Lake Tri last year, the bike literally sat in my desk cubicle in lab. I don't know why I didn't ride it sooner. I have a lot of good memories of rides in Ithaca on that bike, but since moving to Boston, I haven't enjoyed riding it as much. Partly because of the potholes and aggressive drivers, I find it a bit more stress than its worth riding around here. But I finally discovered some nice bike trails along the river that I will explore.

I used to play pick up basketball at Cornell every Saturday morning. It really carried me through the winters there because I had a lot fun playing and made a lot friends outside lab doing it. I finally played again after a labmate asked if I wanted to go shoot some hoops last week. After playing some sloppy games of 1-on-1 21, I played 5-on-5 yesterday. I forgot how fun it was.

I was slowly slipping away from doing activities I really enjoyed doing over the past year, but I've re-committed to swimming and I'm finally climbing back onto the saddle of my bike and shooting some hoops. I needed this more than I realized.

Kindle

2011-06-26T15:57:00.000-07:00

I bought an Amazon Kindle last week on a bit of a whim at Target. Amazon reduced their price for the basic wireless model to $114 from $139. I've seen a lot of other people use ebook readers like Amazon and Apple's iPad and decided to take the plunge. (The iPad I think is way too pricey for being essentially an over-sized iPhone.)

After using my Kindle for a week, I really like it. The display is much more like reading a book rather than content from a computer screen (like the iPad or iPhone) and I think its much easier on the eyes. Content is instantly downloaded from the Kindle store on Amazon to your Kindle device. You can also email content from your computer to your Kindle email address, once you register your device. Its also straightforward to transfer content from your computer to your Kindle via USB. The only slight annoyance for me is you can't transfer PDF files via USB, but KIndle is able to read PDF files if you email them to your Kindle email account.

Another upside to the Kindle is you can get Kindle versions of books anywhere from 10-25% cheaper than hardcopies. And there are also a good number of free ebooks you can get for your Kindle. (They generally are older titles in which copyright has expired. I got a free copy of The Three Musketeers that I started reading) While I still do like books, I can see myself getting used to the idea of reading Ebooks with Kindle.

Stepping outside of your comfort zone

2011-06-21T13:32:00.000-07:00

Sometimes I feel I'm not really living up to my potential professionally. I think alot of it has to do with fear of failure and perceived in ability to step outside my comfort zone. A conversation I had with my advisor a few weeks ago stemmed around the fact I need to learn to develop the skills to develop my own tools/methods. I certainly agree with this assessment and its been a weak point of mine I think for several years. Part of the problem is that I think I'm not capable and that its going to be lead to a dead end. But after reading this column I feel a little better that I'm certainly not the only one who has felt this way. But I finding out part of the growth process in graduate school is going outside your comfort zone. The last part of the essay linked to above sums it up:

Don’t let your comfort zone hold you back from taking risks, reaching your potential, and experiencing success. The more you push through your comfort zone, the larger it will become. Soon it will come much more naturally and easily to do things that move you toward your dreams!

Read some old papers this week

2011-06-18T19:58:00.000-07:00

I really don't know what I would do if I actually had to go to the library and look for back issues of journal papers in the library stacks. I probably wouldn't have mustered the motivation to find these older papers dealing with probability models dealing pedigrees and identity by descent:

Frequencies of genotypes of relatives, as determined by stochastic matrices by C.C. Li and Louis Sacks and A calculus for statistico-genetics by Charles Cotterman. For history of genetics buffs, the second title was published by the first editor of the American Journal of Human Genetics and the American Society of Human Genetics named an award after Cotterman. He never published his PhD thesis, but alot papers still manage to cite it. Thanks to the internet both of these papers were much easier to find. While I like libraries, I hardly step into one physically anymore.

Why I like swimming

2011-06-15T15:38:00.001-07:00

"On my crappiest day, when I'm tired or jetlagged, I jump in that water and just something happens that I can't even put into words. I feel better and stronger, all the soreness goes, and I'm me again, a hundred percent back."

- Michael Phelps

Dealing with "I should be better" syndrome

2011-06-13T11:28:00.000-07:00

Read this article on the tiny buddha website that sums up much of what I've been feeling the past few weeks. For example these thoughts have popped in my head more frequently:

1. I should be more established in my career.

2. I should have started graduate school earlier

I guess most of this stems from most of my age group peers are finishing post-docs, applying to faculty jobs, or starting faculty and/or industry jobs. I know I shouldn't think this way, but sometimes is hard not to. And lately I've been doing more of it, rather than concentrating on things I should be doing. So I need to just snap out of this funk.

Getting to the other shore

2011-05-25T19:33:00.000-07:00

I follow a lot of interests on Twitter and this past week I saw this CNN interview with Diana Nyad through my Twitter feed. Last summer as the age of 60 she was training to swim from Cuba to Florida but government red tape and off conditions forced her to delay the attempt. In the 1978 she tried the same swim, but after 41 hours at sea and off course, she had to give into the ocean. Once again this summer she's attempting it again at the age of 61.

I find her story very inspirational, and on days where I'm not feeling the best about being a graduate student, she reminds me I just gotta do whatever it takes to get to the other shore.

Off the radar

2011-04-27T15:20:00.000-07:00

I decided to mothball my FB account today. It was turning into a low-hanging distraction. While I had x number of friends, the percentage of them I actually have any meaningful contact with was probably 5%. In an anthropological sense, I guess one could trace their personal history through which through your FB friends list. But I think it was giving me a false sense of connection. I used to call a handful of friends every Sunday or so when I lived in the middle of nowhere. It made me feel less isolated. Now I live in a big city, and in some ways feel just as isolated, maybe even more so given that some friends I have live across town and I hardly see them! I guess its just because life/the daily grind gets in the way, but that's still a lame excuse. Maybe I'll re-instate my FB account down the road, but I'll see if by not having it, I make more of an effort to stay connected in a more tangible way.

Poor Jane's Almanac

2011-04-24T19:49:00.000-07:00

A thought provoking editorial piece in today's NYT regarding Benjamin Franklin, his sister, and the Tea Party movement. You can read the piece here.

THE House Budget Committee chairman, Paul D. Ryan, a Republican from Wisconsin, announced his party’s new economic plan this month. It’s called “The Path to Prosperity,” a nod to an essay Benjamin Franklin once wrote, called “The Way to Wealth.”

Franklin, who’s on the $100 bill, was the youngest of 10 sons. Nowhere on any legal tender is his sister Jane, the youngest of seven daughters; she never traveled the way to wealth. He was born in 1706, she in 1712. Their father was a Boston candle-maker, scraping by. Massachusetts’ Poor Law required teaching boys to write; the mandate for girls ended at reading. Benny went to school for just two years; Jenny never went at all.

Their lives tell an 18th-century tale of two Americas. Against poverty and ignorance, Franklin prevailed; his sister did not.

Franklin's sister didn't have an easy life, she was poor, lacked any formal education, but strived to do the best she could with the hand she was dealt. Read the article for yourself, its a bit gut wrenching to some degree. These words struck me the most:

That world was changing. In 1789, Boston for the first time, allowed girls to attend public schools. The fertility rate began declining. The American Revolution made possible a new world, a world of fewer obstacles, a world with a promise of equality. That required — and still requires — sympathy

The Tea Party movement wants to bring back the principles the founding fathers espoused, but perhaps they should try and be a little more sympathetic to those in need.

Its ok to be less talented than someone else, but never ever let yourself be outworked

2011-04-22T21:08:00.000-07:00

I read the title of this post from this article Its something similar a swim coach told me years ago that while some people may be more talented than you and they may not have to work as hard to achieve results, in the long run hard work pays off. I think this advice has a lot of applications whether its your own physical fitness goals or in your work or career and something I needed to be reminded of these past few weeks regarding my research.

The daily grind is not glamourous

2011-04-22T20:55:00.000-07:00

Blog Post: The daily grind is not glamourous | Community | USA Swimming

If there is one thing in this world I wish I could be it is being an Olympic athlete. And of course I would be a swimmer! Though I probably don't appreciate how much of a grind the daily schedule of training really is. Natalie Coughlin, 11-time Olympic medalist, has a nice blog post above that brings some insight into the daily schedule of an Olympic athlete. Part of wishes I could be financially stable enough to devote more time to physical exercise. And a part is happy with my 4-5 times a week routine of swimming/running/weights. But I'm inspired by Natalie's post to continue to test my physical limits. What kind of love brings a pleasure so close to pain?

Limitless

2011-04-10T21:14:00.000-07:00

Saw the movie Limitless this weekend starring Bradley Cooper, who stars as a mediocre writer that is given a drug that allows him to use all the full potential of his intelligence. Pretty good flick. Got me thinking - what if I shut out all distractions while I work - email, internet, music, phones, etc. Would I concentrate better at the task at hand whether it be writing, reading, programming. I think so. There is so much low-hanging fruit in terms of easy distractions. If I could just train my habits to ignore them I think I could accomplish so much more and be so much more productive. The possibilities would be limitless!

I've tried telling myself I'm going to cut down on incessant email checking, Twitter feed checking, and other bad habits. Its getting better, but I think this is the week I am going to make some drastic improvements in concentration.

Cricket World Cup

2011-04-03T09:30:00.000-07:00

Up until last week I never watched a cricket game in my life, nor did I even realize the Cricket World Cup was being played. But in the past week I watched India beat Pakistan to advance to the finals versus Sri Lanka. To an outsider, its hard to grasp just how much cricket means to the India. To get a sense, I read this excellent ESPN article Why you should care about cricket.

So on Saturday, I somehow got up at 4am to go watch the final match between India and Sri Lanka at my friends house who bought a high quality internet stream of the game. I find cricket to be a bit more action packed than baseball. Sri Lanka batted first and put up 274 runs. India batted second. I had never seen Sachin Tenulkar play, so I was excited to seem in action on the biggest stage. The Sri Lankan bowler got him out remarkably soon and the whole stadium became hushed in silence. I at this point was a bit skeptical if India could pull it off. But thanks to the play of Gautam Gambhir and MS Dohni, the team captain, India just became only the second team to win a World Cup batting second. After seeing how exciting the game was, I am definitely a cricket fan now and want to learn how to play!

Aurora boy beats Michael Phelps by a pool length - Beacon News

2011-02-17T13:19:00.000-08:00

I love the Olympics and I love swimming. People say the Olympics are too commercialized, which may be true. But what I like about the Olympic ideal is it brings out the best in people and gives hope to others.
I think this story below is an example of that. Way to go Michael Phelps.

Aurora boy beats Michael Phelps by a pool length - Beacon News

Darwin Day

2011-02-12T12:18:00.000-08:00

Today is Darwin Day, celebrating Charles Darwin's birthday. (And also is Abraham Lincoln's birthday too, for you trivia buffs) In honor of it, I am posting a quote from the autobiography of Charles Darwin, which is one of my favorites that I first read in 1996 in an issue of Discover Magazine.

I have no great quickness of apprehension or wit which is so remarkable in some clever men, for instance, Huxley. I am therefore a poor critic: a paper or book, when first read, generally excites my admiration, and it is only after considerable reflection that I perceive the weak points. My power to follow a long and purely abstract train of thought is very limited; and therefore I could never have succeeded with metaphysics or mathematics. My memory is extensive, yet hazy: it suffices to make me cautious by vaguely telling me that I have observed or read something opposed to the conclusion which I am drawing, or on the other hand in favour of it; and after a time I can generally recollect where to search for my authority. So poor in one sense is my memory, that I have never been able to remember for more than a few days a single date or a line of poetry.

Some of my critics have said, "Oh, he is a good observer, but he has no power of reasoning!" I do not think that this can be true, for the 'Origin of Species' is one long argument from the beginning to the end, and it has convinced not a few able men. No one could have written it without having some power of reasoning. I have a fair share of invention, and of common sense or judgment, such as every fairly successful lawyer or doctor must have, but not, I believe, in any higher degree.

On the favourable side of the balance, I think that I am superior to the common run of men in noticing things which easily escape attention, and in observing them carefully. My industry has been nearly as great as it could have been in the observation and collection of facts. What is far more important, my love of natural science has been steady and ardent.

A Decade with the Human Genome Sequence: Charting a Course for Genomic Medicine

2011-02-11T19:50:00.000-08:00

Didn't get a chance to watch the video stream of this NHGRI symposium, but it will be on the NHGRI YouTube channel next week. I love human genetics and things like these just re-affirms that I made the right career choice. Makes all the frustrating days in grad school worth it, because there is a bigger picture. What a privilege it is to be a geneticist in this day and age.

Genome.gov | A Decade with the Human Genome Sequence: Charting a Course for Genomic Medicine

10 years in genomics.

2011-02-09T20:22:00.000-08:00

Hard to believe its been 10 years since the publication of the first draft sequence of the human genome. Nature this week has several editorials reflecting on the 10 year anniversary, like this one from Eric Lander. I started my first job out of undergrad the week the Science and Nature publications came out as a bioinformatics programmer at Stanford. First of all, I really can't believe its been 10 years since I graduated. Second of all, I can't believe how fast genome technology has progressed. When I started my job, part of my duties were to develop a pipeline for Sanger sequencing of candidate genes involved in Parkinson's disease and heart disease. Today, I analyze whole genome and whole exome (coding regions) of over one thousand people. When I graduated from college, microarrays were the hot new thing, and now they are going out of style . Even two years ago, when I was getting into next-generation sequencing analysis, I thought it would be a while before the next new technology would come to replace it. Single molecule, third-generation technologies are on the horizon . The sheer pace of technology advancement in genomics is mind boggling.

And while I think the promise of genomics has been over sold, I certainly don't think its been a failure! Though 10 years ago, by now I thought I would have had a PhD. But I'm working on one right now, and not having one up till now hasn't prevented me from witnessing and being a part of new biological insights that by sequencing of the human genome would not have been discovered. I hope that armed with my PhD I'll be able to make some novel discoveries myself in the coming decade.

Hearbreak in Tucson

2011-01-15T14:09:00.000-08:00

Nearly 10 years after I graduated from the University of Arizona, the President of the United States, Barack Obama, gave what is probably his best speech as President in the same venue that I received my degree. The circumstances of his presence was sad one. It was a memorial service for victims of a mass shooting that had taken place 4 days before in Tucson that had left Congresswoman Gabrielle Giffords in critical condition from a gunshot wound to the head and 6 others killed, among them a 9 year old girl. Arizona is going through some tough times, and this mass shooting is probably low mark in the state's history that is getting ready to celebrate 100 years of statehood next year. But I hope if there is any good that comes out of this, it will draw people closer together, despite whatever differences they have, and make Arizona a better place for all its citizens.

Visit msnbc.com for breaking news, world news, and news about the economy

Customer service in the age of social networking

2010-12-27T14:39:00.000-08:00

I was supposed to fly to PHX today but an epic blizzard along the East coast changed my plans. Last night I tried to re-schedule my flight on JetBlue.com, but in order to waive re-booking fees you had to call the airline. I was on the hold with JetBlue for nearly an hour with Google Voice. While on hold I decided to tweet JetBlue to see if they could waive the re-scheduling charges via Twitter. In a series of direct messages between JetBlue and I, I was able to get my flight re-booked much quicker than if I had stayed on hold on the telephone.

Some of my friends make fun of me or give me quizzical looks as to why I am on Twitter and what is it good for. In this case, if I hadn't been following JetBlue on Twitter, I would have never had though as resource to communicate with the airline. I've been flying JetBlue pretty regularly for two years and have yet to have a bad experience with them. I wouldn't have expected them to be so responsive via Twitter, but this experience shows what a powerful medium social media can be. Major props to JetBlue and Twitter!

Nobel Laureate Sir Paul Nurse - Succeeding in Science

2010-12-17T19:16:00.000-08:00

A faculty member in my department forwarded this YouTube link of an interview with Sir Paul Nurse, Nobel prize winner, in which he talks about what it takes to succeed in science.

Operating on genomic intervals - basewise subtract

2010-12-08T09:14:00.000-08:00

Interval operations on genomic coordinates is a common task in bioinformatics. Galaxy has a great set of tools for operating on genomic intervals, which under the hood run code from bx-python. I basically wanted to run a basewise complement on the target bed file, in the browser shot below, with the bait bed file to find out what intervals in the target bed file do not overlap with the bait intervals.

The Galaxy webpage has a nice web-interface to do this, but I'm a big fan of the command line, and I eventually needed to incorporate this into a pipeline I run locally. The program bed_intersect_basewise.py and bed_complement.py can be piped together to get the desired output:

bed_complement.py 1.bed <(echo "chr22 1000") | bed_intersect_basewise.py /dev/stdin 2.bed

Basically you complement the bases in 1.bed and then intersect them with the second. I didn't really want to do the pipe, so I glued together parts of bed_intersect_basewise.py and bed_compelment.py into a new program, using the bitset API from bx-python, called bed_subtract_basewise.py, which you see below.

Data Analysis with Open Source Tools - Plotting data

2010-12-03T21:27:00.000-08:00

I recently bought the ebook version of Data Analysis with Open Source Tools by Philipp K. Janert. You can take a look at the Table of Contents on the book website. Its divided into 3 parts: Graphics:Looking at Data, Analytics: Modeling Data, and Computation: Mining Data.

I've read through the first chapter, which starts out simple enough on different ways to plot single variable data: dot & jitter plots, histogram & kernel density estimates, cumulative distribution, QQ-plots, and boxplots to name a few. Taking an example data set of target sizes of exome sequence capture from the 1000G ftp site, I decided to take a look at which type of plot conveys the attributes of the data the best.

First, just taking a simple histogram of the data in R

There are clearly a handful of outliers with large target sizes, in excess of 20 Kbp! Even with the default bin size on this histogram, there is not a lot of detail of the target sizes in the smallest size bin, due to the large difference between the minimum and maximum target size. Since there is a large variation in the target sizes, we can take the log10 transform of the data, and then plot a histogram:

This is much better! Plotting the histogram log10 values of the target size shows a normal distribution, but with somewhat long tails indicating there are some target sizes with extremely small and large target sizes sizes to a couple of base pairs to >10 kb! This plot is a marked improvement over our initial histogram!

How does a kernel density estimate of the log10 values of the target sizes look like. Before I read this book, I vaguely knew of KDEs because my friend showed me the command to how to plot on in R. But as to what they actually were, it was a black box. But chapter 2 of the book shed some light. Basically you place a kernel function, a function that is strongly peaked, at each data point. Then add up the the contributions of each kernel point to make a smooth curve. The area under the kernel should integrate to one. You have to choose the bandwith of the kernel function, which controls its spread. The height of the resulting curve increases or decreases as the bandwith changes, since the area under the curve always has to integrate to one.

The defaults of the density command in R use a gaussian kernel with the bandwith set to "nrd0", as far as I can tell. The R docs are bit hazy as to what the different bandwiths can be, so I need to look at this. But here is the resulting KDE of the log10 target sizes:

Not really sure why the density axis is greater than one, I need to ask my R guru on this. But this is my first stab at understanding how to make KDEs in R.

Another way to plot the data is to look at the cumulative distribution function. These types of plots show what fraction of data points are less than or equal to some value x. The main advantage of CDF plots are they require no binning like histograms, so its difficult to obfuscate data from any strange binning artifacts. Using the ecdf function of R here is the empirical CDF of the log10 target sizes:

Its clear from the CDF there are long tails of very small and very large target sizes. Switching the axes of the CDF, we can make a quantile plot, which I think is even more clear:

I've plotted the y-axis is log-scaled. Its clear from this plot that about ~20% of targets are less than 100bp and maybe less than ~3% of the sizes are >= 1000 bp.

Even with a simple dataset like target sizes, there are many ways to plot the data. I like the quantile plot the best because I can easily figure out that ~70% of the targets are couple hundred bp in length. Which is your favorite?