Saturday, November 26, 2011

Conception to Birth - Alexander Tsiaras

I gotta post this TED talk... Now we are able to visualize the formative process of the fetus of conception to birth. Isn't this just amazing? Just how much complexity is infused into our growth to make us the way we are, and mostly without much glitches along way so that we can come into this world, bearing resemblance to everybody else but not totally the same.

The educational implication of this video to the general public is immense. When before, people thought the babies popping out of a mother's womb is something bizarre, arcane and inexplicable, now there is at least a glimpse of the macro-processes that are taking place.

Science is advancing. Sometimes, it's so fast and fascinating, it frightens me...

Tuesday, November 22, 2011

Create HTML with Google Spreadsheet: Python Google Docs API

Recently, I helped set up the Gerstein lab's Alumni page. All the information of the current lab people and alumni are situated in a Google Spreadsheet: name, past affiliations, date joined etc. Google Docs API allows the creation of webpages directly based on these information. They recommend the use of the Python scripts. A predecessor did all the work. I merely modified his script to do what I wanted it to do.

M named it BLIS - Bioinformatics Lab Information System, which is quite true in the sense that the entire process is streamlined to minimize fuss and making consolidation of dynamic human resource data a "blissful" procedure for the general administrator. However, it can be a pain for the system administrator trying to put these together, as Mi can testify. So BLIS comprised of a couple of lab resources - people, papers, lectures and images - based heavily on Google spreadsheets. A sanitized code and somewhat abstract walkthrough (pardon me, because I could only better express this by SHOWING how it is done) can be found here. This resource is made free and public for all. Nothing very fancy but it works for the lab and it does make a lot of things easier once you get it to work.

Eventually, M wants to centralize all resources by the use of the Google Spreadsheet, grabbing information off each column. I can however, foresee that the spreadsheet will get outrageously big/messy/both at some point, making the new person looking at it a headache. Now, it is still rather manageable.

Now, Mi is trying to interface Googlegroups with the spreadsheet, to manage mailing lists in this "central repository". M wants me to help him, given my relative success with the People's page. Mi is pretty stuck now since he can't find a way around connecting Googlegroups with GoogleDocs. Any Google team or experts out there who can help?

Here on, I am going try documenting what I did for the People's page:
1) Found in the lab server, is a Python script, some sort of a wrapper, that
a) creates a HTML file for the People webpage (the people's page points to this file)
b) grabs information off GoogleSpreadsheet (refer to mini-walkthrough)
- This is essentially your workhorse.

2) Every time you update the Google Spreadsheet, you need to update the web page too. This can be done by running this file each time you update. A quick and dirty way that can be done is to circumvent the problem of accessing the file in the background is to create a link run the script manually.

I would say 95% of the credit that this works goes out to Mi and the predecessor working on this (I don't know the name). I am merely a modifier that builds on the established success.

Found a pretty neat page that talks more in detail:

Google Spreadsheet gadgets targeted at data visualization mostly:

Saturday, November 19, 2011

Quidditch in our world HA!

Inspired by Yale Band's Harry Potter skit (in an attempt to slam Harvard) at Yale-Harvard Game today, I stumbled upon the game of quidditch played in real life without magic. And believe it or not, it seems to be here to stay!!  I read about it last winter, and my jaw dropped... LOLX

2011 marked the fifth edition of the IQA (International Quidditch Association) World Cup. According to IQA:
"Quidditch was adapted from the Harry Potter novels in 2005, at Middlebury College in Vermont, by Xander Manshel, a freshman looking to change up his dorm’s tradition of Sunday bocce. That first group wore towels for capes and came with an assortment of broom-like implements, including a Swiffer mop and even a lamp. One kid wore his graduation robes. The game was an immediate hit on campus and was played on an intramural level until 2007, when Alex Benepe founded the Intercollegiate Quidditch Association after the first intercollegiate match between Middlebury and Vassar College. Since then the sport has really taken off (figuratively if not literally): students from more than 1,000 colleges and high schools from a dozen countries have contacted the IQA looking to start their own teams, and over 300 are actively playing in the United States, Canada, Australia, New Zealand, France, Britain, and Brazil...The game has been described as a cross between rugby, dodge ball, and tag, which is a good approximation."
I am amazed haha. Probably should catch one of these games in action! You can get the rule book for free here, complete with chasers, beaters, keeper, seeker and the snitch!

Check out a write up on Wikipedia for Muggle Quidditch!

And a cool documentary:

Wednesday, November 16, 2011

I am waiting for Christmas!

This year's Xmas and countdown we will be spending it together again. The last time we had it on foreign shores, it was a blast =)


Can't wait... =)

In the meantime, I will transferring all my luck to you for Friday! 加油!!!!

Is Redstar Worldwear a scam?!

I got the RedStar Worldwear event card from the Stratton Faxon New Haven Road Race this year. I got pretty excited about the prospects of having cheap but good sunglasses.

But first I wanted to see if this is a hoax. So I scoured the web and found some websites stating that people do receive their products, even though there were dissatisfaction at some point. I decided to give it a shot.

I bought 5 pairs of sunglasses and 1 free watch for 72 dollars - average ~14 USD per pair of shades. My conclusion is that it isn't a scam. But it's not an Amazon either. Let me try to break it down:

1) Service
- Took more than 3 weeks to reach my place. Registering my order itself took a week. It makes you wonder how efficient the people are.
- phone customer service was not professional. They were generally nice, but they do not know what happened to my order when I called them.

2) Website
- mediocre interface. Their business heavily relies on this but fails to give a convenient interface. Order is not updated. I initially ordered 7 sunglasses and 3 watches. 2 shades and 2 watches were out of stock, but I only knew this when I received the products. How late is that! Gives a sloppy and unprofessional impression.
- hard to navigate.
- hard to keep track of products on order list by product ID. Pain in the neck because you have to remember which ID corresponds to which sunglasses or watch.

3) Product
- I bought an aviator which I always wanted to try. I would say it feels durable, since it feels heavier. Looks not too bad. But I think the design does not seem to be what I expect from the photo online. It's not different, but the online image glorified the sunglasses many times I would say.
- I tried it outdoors, and I still prefer my own pair of shades in terms of shielding; I still have to squint my eyes when the sun is strong where I did not have to for my own pair.
- It doesn't have a good fit.
- can't try, can't return.

So all in all, I would say, for the price, it's good value for money. IF you have the patience and time, and some extra $15 bucks to spare, just get one of these to try out. Seems durable and aesthetic enough. I don't think it's a scam just because I got my products as promised and in very good condition.

REMEMBER THOUGH: there is a check box when you check out on the website that states that you want to receive shades every time they push out new models. UNCHECK THAT! Because they will charge you for every sunglasses/watch they send. JUST KEEP A LOOK OUT FOR THIS.

I unchecked it and haven't got any calls nor sunglasses nor undesirable deductions from them yet.

Sunday, November 13, 2011

Big 3 in DTC products

23andme, Navigenics and deCodeme.

With the bankruptcy of deCodeme, we are down to 2.

What are their fates?

Anyway, why is deCodeme website still on?!?

Conscription or compulsory military service


I thought Germany has compulsory military service too! But apparently they stopped this year.
"Germany had conscription (Wehrpflicht) for male citizens between 1956 and 2011. On 22 November 2010, the German Minister of Defence proposed to the government to put conscription into abeyance on 1 July 2011.[1] The constitution, however, retains provisions that would legalize the potential reintroduction of were obliged to serve six months either in the military, which they could refuse, and do alternative civilian service, or honorary service (like any volunteer) for at least six months in a civil protection organisation."

Open Science

TED@Waterloo talk today is by Dr Michael Nielsen:

Funny, couldn't find the embed button.

Essentially, he talks about the power of crowdsourcing, but slightly different from the ones I have been talking about. Starting from positive examples from the Bermuda Principles of genomics (everything open-source for sharing) and the Polymath Project (free collaboration ending in publications), he provided insights into tapping the potential of massive collaborations in scientific discoveries and creating a third revolution in science sharing. I have blogged about the prowess of crowdsourcing with the masses. But crowdsourcing within the scientific community is a tad more complex because of conflicting interests, the lack of incentives, constraints imposed by history and mostly, IMO largely also due to inertia.

He didn't provide much concrete actions, but I am looking forward to this revolution. It might take years or decades. But with the Internet and the Semantic Web as the catalyst and the workhorse, this duality in role might expedite the entire process. It just needs the right spark, to create that wildfire...

I will read his blog here:
"There are already many well-known but still striking instances of this change in parts of culture outside of science [1]. For example, in 1991 an unknown Finnish student named Linus Torvalds posted a short note in an online forum, asking for help extending a toy operating system he’d programmed in his spare time; a volunteer army responded by assembling Linux, one of the most complex engineering artifacts ever constructed. In 2001 another young unknown named Larry Sanger posted a short note asking for help building an online Encyclopedia; a volunteer army responded by assembling the world’s most comprehensive Encyclopedia. In 1999, Garry Kasparov, the greatest chessplayer of all time, played and eventually won a game of chess against a “World Team” which decided its moves by the votes of thousands of chessplayers, many rank amateurs; instead of the easy victory he expected, he got the most challenging game of his career, a game he called “the greatest game in the history of chess”."

Friday, November 11, 2011

WCUB 2011 (What can you be with your PhD)

This is a 2-day career convention at NYU Langone Medical Center. I must say this is the most informative career convention I have been to. The panel of speakers were engaging, cordial and candid and the participants asked really pertinent questions.

I went for the seminars in resume writing, mentoring, grant and fellowship application writing and careers in the pharmaceutical industry. I think there are some tips covered in this convention that people looking for jobs in general can use, like resume writing. I have some notes if anybody is interested. You can drop me a line.

This also serves as a short getaway from the work that is being piled up. Chelsea Market is just awesome! Thanks G and P and O for suggesting it!!

Where we cut our hair - 196 Centre Street NYC.
New Haircut - not too bad for 27 bucks?

Primate sequencing

The first primate to be sequenced was the human3 in 2001, followed by the chimpanzee4 in 2005, the Indian rhesus macaque5 (Macaca mulatta mulatta) in 2007 and the orangutan6earlier this year.

Not surprisingly, genome sequencing projects for nonhuman primates have multiplied, with projects on gibbons, baboons, bonobos, gorillas, African green monkeys, squirrel monkeys, galagos (bushbabies), pigtailed macaques, aye-aye (lemur), sooty mangabeys and other species underway or planned


Almost all the primates are endangered species, mostly because of humans encroaching and destroying their habitats. Now, we are sequencing them and using them in our science experiments, so we do want to save them. Someday, when this loop-sided tug-of-war finishes, I wonder who will be the last ape standing.


Point in time: the ability to create a sense of inertia in its product users...

Some ethnic propensities for genetic diseases

Ethnic GroupGenetic Defect
African AmericansSickle Cell Anemia
Central or Eastern JewsTay - Sachs disease
Italian, Greek, Middle Eastern   Thalassemia

Ashkenazi Jews have also a higher propensity for Cystic Fibrosis



It's the Happy Singles' Day in China but a more solemn Veterans' Day in the US.

Do they really have to go that far in disparity?

Anyway, a very interesting article on 111111 =)

Wednesday, November 9, 2011

Single-gene diseases

Huntington's disease - HTT gene (chr4) - dominant and penetrant
Alzheimer's disease - APOE gene (chr19) - strictly not single-gene disease but 1 epsilon allele copy x3 chance, 2 copies x15 chance
Cystic fibrosis - CFTR gene (chr7) - autosomal recessive - mainly Caucasians
Tay-Sach's disease - HEXA gene (chr15) - autosomal recessive - almost exclusive to Ashkenazi Jews
Hemophilia - X-linked recessive (hence more males than females)


Tuesday, November 8, 2011

Plantronics 903 and 903+ headphones do not charge/no power

Previously my headphone from Plantronics SUDDENLY played dead and wouldn't turn on. It was irritating because it happened just right a few days BEFORE I was about to leave for Singapore.

So I scoured the Web for any resolution. It turned out there were a slew of complaints and yelling and profanities on this problem but the gem of a solution only turned up after my persistent search on page 2 of this forum and in the middle:

For archiving purpose and for those of you lucky enough to find my page or the forum above:

I found a solution you connect the device to the charger and keep the on/off button pressed like 5 seconds, at the same time you unplug the AC charger and reconected so the blue light truns on
iIT worked for me and I had the same problem they just died when I listened to music no sweat no nothing 
---- Dna

TIP 1: This works for 903+ as well!!

TIP 2: this doesn't always work the first time. The first time this happened to me, it worked like a charm (happy). The second time I have to try a couple of times relentlessly (DON'T give up) before it came back to life.

I like the sleek design of the bluetooth device. Hopefully I get to use it a year or 2 more.

Let me thank "Dna" again. Whoever you are. You sure made a lot of people happy with that simple post.

Monday, November 7, 2011

Personality tests

Eating dinner while doing a personality test helps concentrate the mind on some other things. Tried the Jung and Briggs Myers Test again.

The first time I tried some years ago I had INFJ - articles 1 | 2 | 3 | 4 - they call this type "the protector, or "the confidant".

This time round I have INTJ - articles 1 | 2 | 3 | 4 - "the mastermind", "the scientist" or "the strategist".

With heavy percentages on the Intuitiveness and Judgement categories.

So I guess it's a straddle between both personalities. Wow, both belong to a mere 1-2% of the human population. I am a rare species. =) People belonging to these categories even band together: INFJ Dolphin Cove and INTJ Central. I am very surprised people actually find the effort to put these things together.

I find personality tests very entertaining to do and sometimes very interesting. And most of the time, overrated. Oh, also they have really fancy names for the personality types.

The power of crowdsourcing

I am sure alot of people do not realize that scientists are slowly tapping into the power of the masses. I have known the use of online computer games in helping to solve protein structures by David Baker's Lab at University of Washington, and protein folding problems at Stanford. Ed Yong of "Not exactly Rocket Science" has an extremely good post on one of the latest developments at Foldit. Recently, I have come to know personal genomics projects that extended from the minds of the public too.

You submit your genomic information to them and get it analysed FOC and/but also get it publicized online. People might be concerned about privacy issues but more often, the submitters know about the risks and are not unduly concerned. Notably, the Dodecad Ancestry Project and Eurogenes Genetic Ancestry Project have garnered a substantial number of volunteers in their analyses (order of 1000s). This is a good number for a peer-reviewed publication!

In a way, it sounds ironic that the general population pays taxes to fund these genomic projects, pay scientists/clinicians etc to do the jobs they do, and end up having a part of the useful results being generated from the public themselves.

Closer to heart, it brings up two concerns:
1) Informal bioinformatics is on the rise. With the advent of Web 2.0 and the Semantic Web, it is here to stay. Probes the question: What becomes the value of bioinformaticians?

Healthy competition breeds higher-quality academic/industry bioinformaticians; you basically have to prove you are better than the layman or just the technical-savvy people out there. Set ourselves apart by depth and breadth.

i.e. They are here to stay. Deal with it...

2) Church argues that better access to high-quality data could help this kind of informal bioinformatics to flourish, enabling computer-savvy people to make important contributions to genomics, just as they have with online businesses such as Facebook. "It didn't take that much training to become a social-networking entrepreneur. You just had to be a good coder," he says. With bioinformatics, "I think we're in a similar position." -----

I am particularly concerned about George Church's comment. I am a fan of his work. This might be misconstrued but a great scientist of our times making comment on your profession on being "just a good coder" (AKA with little sense of biology) hit a raw nerve. The acceptance of the scientific community on bioinformaticians has been ambivalent. With this public encroachment into our ambit, this is simply unnerving: What am I doing in grad school doing all these?

EDIT 11/8/11: Kaggle pays you to crunch numbers! An article describes this.

Sunday, November 6, 2011

9000 tumors for personalized cancer treatment

"The £5.5 ($8.7) million Stratified Medicine Programme, led by the charity Cancer Research UK in partnership with the National Health Service and London-based AstraZeneca and New York-based Pfizer, aims to develop a standardized national genetic screening service to help tailor oncology treatments for patients. "

"Genetic stratification allows clinicians to determine which individuals will respond to which treatment, for instance, KRAS testing in bowel cancer to see if Amgen's Vectibix (panitumumab) and Imclone's Erbitux (cetuximab) is indicated."
------ Aldrige, Nature Biotechnology 29, 854 (2011)

Indeed, Pharma firms are moving away from the conventional "one drug fits all" doctrine. It is exciting to see how personalized medicine will pan out. Especially with each individual's data currently in seemingly fragmented states: Person X can do genetic testing on 23andMe on an array, exome sequencing and cancer profiling but she/he will never find them consolidated all under her electronic health record.

Friday, November 4, 2011

Cannot open Office 2007 docx document!!

I haven't had sleep for more than 30 hours now.. We are trying to rush this manuscript out for M to vet before he goes off on vacation. Been a hell of a week.

Anyway, Ja sent me her Word docx and I couldn't open it in Windows Office 2007. Got this error:
Tried all the ways on this error warning but to no avail. But I really need it to work. So I sent emails out to Ja and A, they re-sent me the original files >_<. A said he got it to work by converting to PDF format (right-click) for Mac. That is a good solution for Mac (if you guys are Mac users), except that it's not editable now and that doesn't work for me because Windows needs to still open the file for conversion; they use Mac, so maybe that was a good workaround but truth be told, I have no idea about Mac .

An epiphany suddenly occurred to me. Without even thinking twice, I changed the extension "docx" to "doc" and voila! Open sesame indeed! Then I just re-saved it as a "docx" Office 2007 format file.

Speculation what has gone wrong:
1) Maybe the saving process by Ja was somehow interrupted on her Mac.
2) Somehow encoding got scrambled.
3) Just bad luck.

Just wanted to share a quick and dirty way to get around this problem.

Tuesday, November 1, 2011

Friendster to convert and Mark Zuckerberg's profile

I was astounded to see this page when I tried to access Friendster's website:

Apparently, it has revamped to a social music and gaming site, relinquishing the share of social networking to Facebook totally. Old news but I just came to know of this:

They had called for old users to "export" their data out by June 2011. I am 5 months behind. Oh well, it did provide me with fun and amusement back then. Like everything else, "nothing really lasts forever".

Mark Zuckerberg might need to think about this adage and reinvent himself if he desires his legacy to persist. Anyway, here is an article about his Friendster profile. Just an entertaining gossipy read on a celebrity.

And on the other face of the coin, you have Jonathan Abrams, touted often as the pioneer in social networking, the original founder of Friendster and also the cause of a biotech company management failure. But. there isn't even a Wikipedia page on him. Perhaps not so down and out, he currently has his hands full with a pub (Slide) and a site that does what seems like social networks based on socializing events (Socializr). A very ambivalent interview with him can be found here:

His story from this article sounds uncannily familiar, akin to a certain Steve Jobs in many ways.