Tuesday, December 20, 2011

Christmas Gift Wrapping - How to tie a gift bow on a Christmas present

For my Xmas this year, I learnt how to tie a bow on a Christmas present from Youtube!! 

A new handicraft skill I think I will forget soon, so I definitely need to document it somewhere with the videos with some annotations:

1) Take a free end, form a loop, then twist!
2) Twisting is the key, hence this tests your finger dexterity, since you need to be making multiple loops.
3) Lastly, make a final twist, then estimate how long of a free end you gonna need to bundle up the loop in a knot.

I do like this one, because she makes present wrapping look so posh, with velvety/glittery ribbons and wrappings:

And this one uses streamer-like ribbons (as I would like to call them). So it's slightly different from the one above, but just as neat.

I am having fun trying out different gift wrapping techniques, color combinations and gift choices/making.

Enjoy the holiday season people!

Monday, December 12, 2011

Failures to success

The idea of failures en route to success has been supported, discussed, widely disseminated to bits that I don't think I should put more to it... Well, just one more article maybe.

An extension to this idea is the introduction of this concept in education. I truly think children and adolescents should learn how to handle failures when they are growing up... Even to the extent of spiking those naive worlds with some 'white failures'. Of course, the counterargument might be the palpability of these 'failures' and how they might (adversely) impact the later lives of the young ones. And that extra-curricular activities contribute enormously to this aspect of education already.

I guess my point is that education is also about imparting life skills. And I am not talking about teaching it in the theoretical sense, but something dynamic, practical and leaves a deep impression, so that they can learn in an applied manner rather than the didactic, often intangible form.

While perhaps passively letting nature take its course might be an option, I think there is still room for such introductory life lessons.


"A lively culture is nebulous, indefinable, ever-changing. Try to package it in a formal mission statement and you just may suffocate it."

"When you make a mistake, you're forced to look back and find out exactly where you went wrong, and formulate a new plan for your next attempt. By contrast, when you succeed, you don't always know exactly what you did right that made you successful (often, it's luck)." 

Outlook 2007: Minimize Outlook to Systray instead of Taskbar

First off, some terminologies so we are on the same page:

  • taskbar = the bar that has your windows and icons at the bottom of your screen  
  • systray = the small menu of icons you can pull up when you click on the arrow icon beside the clock on the far right of the taskbar.

1 simple step to minimize Outlook 2007 to the systray to save space on your taskbar.
1) By default, Outlook minimizes to your taskbar. So to save space, right click on the Outlook icon in systray, choose "Hide when minimized".

Voila! It should work now!

Note that earlier versions might require some tinkering with the registry or additional options in the Outlook options, if this doesn't work.

Sunday, December 11, 2011

Failures: when it becomes more than just yours

I wrote an entry about failures a while back.

Incidentally, the most recent TEDxYYC by David Damberger talks about failures. But at a grander scale. I am exceptionally touched by the candidness of the speaker and his openness in talking about his own failures and sincerity in admitting it.

There IS a general aversion in talking about failures. But when that failure becomes more than just you, the 'self' becomes insignificant. There is much more at stake. Admission to failure and possibly documenting it is then not your first step in realizing and coming to terms with that mistake, but it's the community's first step to do that. Only then, can improvement be made as a collective.

Failures suck. Big time. Individually, you can try to make sure you don't repeat it. But how do you make sure other people don't?

Thursday, December 8, 2011

States of my brain

Clear, lucid state
-I have clear focus.
-Bent on finishing tasks.

Semi-lucid state (more-than-half lucidity)
-Partial focus.
-Found that music actually keeps the messed-up portion of the brain busy while the lucid portion can be focused on tasks.

Semi-lucid state (less-than-half lucidity)
-Partial focus.
-Music doesn't help. It actually adds on to confusion.

Totally chaotic state
-Almost-nil focus.
-Good for automatic tasks like keying in numbers.
-Everything is happening in my head all at once: grabbing ideas, task(s) at hand, mundane issues etc...

Comatose state
-No focus
-I am basically a walking zombie.

Sometimes I find music helps. Surprisingly, going through Facebook sometimes help too.

Ongoing discussions of relevant issues definitely help.

But if I need a reboot, I try
1) play computer games
2) play squash
3) go to the gym
4) take a nap

Tuesday, December 6, 2011


Failures suck. But I guess that's how they are supposed to feel.

I think I am starting to deal with them though. Appropriately.

Re-learning life skills that I should have decades ago. Singapore should learn to let her citizens go take risks sometimes. It's really good for them.

Sheltering does produce crops of homogeneously fine quality though. Just that the world out there, is always never the same. And that's why even Nature promotes heterogeneity and variations. It's interesting when you look at bottlenecks and natural selection. Sorry, I digress. Somehow, I have this impression that the strategy Singapore was adopting is starting to change. It might lead to catastrophic consequences. But I guess, change is constant.

Oh well, the ambivalence of life.

C'est la vie. And a new phrase I picked up: La vita e bella. It's amazing just to be alive

Saturday, December 3, 2011

Ubuntu installation in VirtualBox and set up Shared folder with host

Helping LA has made me realize that I need to document this procedure for archival purposes. I will try to make this as detailed as possible. Hopefully, I don't miss any steps. If I do, anybody can send an email to me.

Host OS: Windows 7 Home Premium  64-bit (HP laptop), CPU-i7 quad core @  2GHz, 8GB RAM
VM: Oracle's Virtualbox (VB)
Guest OS: Ubuntu

Installation of Ubuntu:
1) Download ubuntu .iso file. I downloaded the 64-bit (amd64).
2) Download VirtualBox. After installation, got through the wizard to install Virtualbox. En route, you will see these prompts:
a) OS Type: OS=Linux, Version=Ubuntu
b) Memory: Depending on how extensive you are going to use VB, I put about a quarter of my RAM. You can adjust it later anyway, so don't dawdle here.
c)  Create new hard disk -> with Dynamically expanding storage -> give it a name and half size for me (~4GB).

3) These should bring you to the end of the installation. Now, you need to additionally customize your VM environment. Open VB, right-click on your Ubuntu, click 'Settings'.
a) System > Processor: 1 CPU for now. We will increase it later. KIV.
b) System > Acceleration: ensure that Hardware virtualization options are checked in both 'Enable VT-x/AMD-V' and 'Nested Paging'.
c) Storage > Storage Controller > Empty > Right panel: click 'browse' and find the Ubuntu ISO you downloaded in (1).

4) Double click on ISO to initiate VM. Install Ubuntu (not 'try'). Follow wizard.

**Watch this video on Jane Talks Tech for a more visual and detailed demonstration of a 32-bit Ubuntu installation.

Everything else should be kept default. Until this point, this is the normal procedure for all installations (32- and 64-bit).


1) You need to restart the computer and enter the BIOS. To enter BIOS, reboot the computer, press 'Delete' button.

2) After you enter the BIOS, find Advanced BIOS settings > Virtualization > Enabled. Remember to 'Save and exit'. Most new processors should be capable of this function, make use of it.

3) After you log into host, restart VB. Go Settings > System > Processor. I set to 4 out of my 16 CPUs.


Set this up to allow access of host files from the guest system.
1) Create a folder, name of your choice. For illustration purpose, the path of my folder is "C:\Shared".
2) Open VB, go Settings > Shared Folders. Click on the 'Add folder' icon, key in the path, and the folder name. Checking 'read-only' means you will not be able to change anything from the guest machine - guest can only 'download'. A good picture, refer to this website: http://ipggi.files.wordpress.com/2010/03/11-03-2010-10-08-06.png

3) Open a terminal. Type in command:
sudo apt-get install build-essential linux-headers-'uname -r'
This installs some software not installed by default.

4) Start VM and login. Select Devices > CD/DVD Devices > VBoxGuestAdditions.iso
This ISO contains an image of a DVD that contains essential files. Mount this image (something like putting in a virtual CD/DVD into a virtual drive). Run the image using:
sudo /cdrom/VBoxLinnuxAddition-amd64.run
5) You might need to restart the VM.
6) Finally, mount the Shared folder. Open a terminal, type command:
sudo mount -t vboxsf Shared ~/my-shared-foldername-on-guest-OS

7) Check that you have that on your home directory. Put something in that folder on the host and see if you can transfer it to your guest.

8) IMPT: Do not close the terminal. FYI, the above has to be mounted every time you log into Ubuntu, much like an external harddrive. To do this automatically, open this file:
sudo vi /etc/init.d/rc.local
Edit this by adding the "sudo ..." line to the second last line, just before "exit 0;".
Then save and exit (:wq).

9) Close and reopen the terminal. You should see the folder still there.

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: http://www.pearltrees.com/#/N-p=24598257&N-u=1_199189&N-fa=2133196&N-s=1_3262934&N-f=1_3262934

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 conscription...men 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: http://soundingboard.plantronics.com/t5/Mobile-Bluetooth-Headsets/backbeat-903-no-power/td-p/4451/page/2

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." ----- http://www.nature.com/news/2010/101215/full/468880a.html

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.

Monday, October 31, 2011

How to add Official Sharing Buttons to Blogger

Found Blogger actually has official sharing buttons!! LOLX


Go Design > Page Elements. Click on 'Edit' under 'Blog Posts'.

How to add the official Twitter's Tweet button to Blogger

Learnt to add the Tweet button to blog. Haha, gotta keep up with the generation man. Was contemplating whether to add a counter beside the Tweet button. Might be too embarrassing to see them lower than 10. But then again, might be interesting to see what entries actually get tweet-ed the most. Haha. So I will let the numbers stay there for a while.

Step 1:
Go to this page: http://twitter.com/goodies/tweetbutton
to create your code to embed the button.

Step 2:
Copy that code

Step 3:
Go back to Blogger > Design > Edit HTML. Check the box "Expand Widgets Template".
Search the code for this:

Paste the code AFTER this line. If you paste it before, the button appears in between the entries.

Find a suitable position on your HTML code by experimenting: cut and paste the code into certain segments of the HTML code, like after "Post Labels", "Author" etc. to obtain an optimal position for your tweet button.

Apparently you can also customize messages. Got the know-how from this page:

Sunday, October 30, 2011

Nerd Love

The Personal Genome Project


Interesting videos on the PGP and 23andMe cofounders.

“The potential to discover what contributes to red hair, freckles, pudginess, or a love of chocolate—-let alone quantifying one’s genetic risk for cancer, asthma or diabetes—-is both exhilarating and terrifying. It comes not only with great promise for improving health through personalized medicine and understanding our individuality but also with risks for discrimination and loss of privacy.”, Science, Vol. 318, 21 December 2007, p1842.

Steven Pinker's article to the NY times on sequencing his genome:

Types of Bulbs

blue IKEA desk lamp
I was looking for a bulb size that fits my IKEA cheap lamp. I had a previous purchase before, it was an incandescent light bulb, which is very energy-inefficient, and too bright for my liking. I am worried about my eyes, which I just did my LASIK on. It turns out, there are SO many kinds of bulbs. So I had wanted to get a fluorescent bulb. But a warning sign says that this lamp takes only Type R bulbs 25W 120V, which only are available as incandescent bulbs.
Incandescent bulb types. Life-size type R and PAR20 (circled) are shown below. 
Why is that so? I did a search on the very informative website (above), and noticed that incandescent light bulbs are typically the conventional bulbs we see, and fluorescent ones are usually the longer kind. I reckon it's due to limitations imposed by the way fluorescence works. There are also fluorescent compact versions which I used for the bulbs in the living room (see last image below). 

This website provides an extremely good overview of bulbs. I bought also a variety of bulbs just to try them out, so that I know which to get in the future (or try more bulbs LOLX they all fit into the living room lamp anyway). Easily available from Amazon

BTW, the above figure for incandescent bulbs is not drawn to scale. For comparison, see image below:
Type R (left) and Type PAR20 (right)

Type R (right) and compact fluorescent spiral
(hidden within)

Type PAR20 (left) and compact fluorescent spiral

Saturday, October 29, 2011

The World's Ugliest Music

Turns out that this piece of TEDx video provided some extra trivia for me:
1) SONAR: if the sound reflects back to you at high frequency, the object is moving towards you, low frequency away.

2) Piano has 88 notes.

3) Beautiful music has repeated motifs.

The last point - I wonder if this is a recurring motif in itself in the universe, that the desirables are often conserved and reiterated. Then maybe not: rarities are considered gems.

Life Length: The Teleological design of Telomeres


Always a pleasure to learn about the exciting research and/or work Nobel Laureates are STILL doing. It does legitimize the prize that they receive, doesn't it?

Ada Yonath
Roger Tsien
Sidney Altman
Steven Chu

I have heard them speak about their current research - simply awesome...

It just makes me remember why I am here in the first place.


Personal Genomics

The raving about personal genomics has been ongoing for a while now that sequencing has become increasingly common. I have been thinking about different applications of personal genomics. It seems the most direct impact is clinical.

1) For the first time, science is being directly in touch with the masses, through companies such as 23andMe, Genetic Alliance are reaching out to the public at a large scale. People are getting in touch with microarrays, DNA, SNPs, genomic mutations - technical jargons - thought to be associated solely with just scientists. At this interface, the interplay between scientific ethics, communication, education and journalism is gaining importance. A great summary of the "Personal Genomes" conference at Cold Spring Harbor 2011 at Finchtalk gives a good summary of an outlook of this.

2) Pharmacogenetics is translational. Elucidating individual genomes means a more customized healthcare at the population and individual level. But medical informatics at the hospitals has not caught up to this. The deluge of data with just selected sequences is giving the clinicians and informaticians at the hospitals a hard time, let alone integration of full sequence data. While basic and translational research might have caught up, we would have to wait before medicine can fully utilize these information. A recent excursion to the Yale-New Haven Hospital jolted me to the fact that this is more than a technological affair, especially when healthcare becomes an enterprise.

3) Genome information is the first level of the central dogma. The primary sequence and the most fundamental, and the first to be done at high throughput. The next milestone, should be the full integration of this first level of information into healthcare. At least variability of drug dosing must be incorporated.

4) I have never thought I would be surprised by adamant resistance to knowing about your genetic material until I come here. I realize things are getting tricky with religion and insurance companies. At the other end of the spectrum, there are the apathetic people, who did their profiling and do not really care. It's scary because this nonchalance, if persists, kills the interest of the general public in the long run. When that happens, the use of such a fantastic clinical tool seems like a farce of the educated.

5) Is there anything about personal genomics that might be important beyond just being clinically relevant? The ability to distinguish maternal and paternal parts of a genome at high resolution allows a different scientific perspective of variability in the genome. But can we glean anything further? Interplay with the different other omes: transcriptome and proteome and metabolome?

M has an entry of the summary of the NIH Proteome Meeting that he spoke at: http://blog.gerstein.info/2011/10/summary-of-data-integration-session-at.html. That should be the next frontier that science is going to in clinical research - where CSI's instant mass spectrometry comes alive. Or perhaps science fiction might be gaining the most out of this.

EDIT: new science blog entry on CSHL conference on PG

Monday, October 24, 2011

Miranda on BBC

Type "Miranda" in Google and you will come up with lots of hits. Miranda Cosgrove just got involved in an accident (don't know who she is actually; but she is born in 1993, so young!), Miranda Lambert (singer) and Dr Miranda Bailey (from Grey's Anatomy, one of favorite characters). Wonder why Miranda is such a popular name.

But I am going to just zoom in on Miranda of the BBC sitcom - wait for it ---- Miranda... It's really about the life of a 6 feet tall, slightly overweight British lady who frequently gets mistaken for a man and her funny and clumsy behavior, especially in front of handsome men. She has feelings for her college crush, Gary Preston, played by Tom Ellis - undeniably charming and has feelings for Miranda too! He JUST happened to be the chef in the restaurant round the corner of her joke shop. Yes, joke shop that sells chocolate willies (seriously).

That's just a very rough synopsis. It is not giving justice to the amount of humor (even if a lot of them are British) that is packed in those episodes. They kept me laughing and rocking about the chair the whole time. "Such fun" indeed!! Really entertaining! Most importantly, it's only half an hour per episode - I can watch during mealtimes. They are onto season 2 but season 3 is expected to be out only in 2012. Highly recommended! One of the funniest shows I have watched.

Saturday, October 22, 2011

What is a SNP

iPhone iOS5: Contacts Wiped and Viber does not work...

Recently upgraded my iPhone OS to iOS5. Took quite a bit of time.

A few changes on the design of the interface. The messaging is definitely much better, in the sense that now it doesn't slam the entire message right across the screen and pause what I am doing. The messages and texts are now placed somewhat less conspicuously at the top and stack up as more come in.

Another great feature is the camera and the music activation at LOCK screen when you DOUBLE-CLICK the home button. There is a pictorial explanation here if you do not know what I am talking about:

I find the Newsstand quite useless though and you can't really get it out of the way by grouping or deleting the icon.

iMessage works like a Whatsapp now. I would still use Whatsapp for international anyway.

I do realize though my contacts were supposedly wiped. And Viber doesnt work either.

1) I edited one of the entries in the Contacts, save it - all the contacts came back. Then I changed back that edit I made in the first place. This website here gives you FIVE ways to recover your contacts:

2) I reinstalled Viber. It works again. But I realize if the person you are calling doesn't have an updated version of Viber, you can't call him either.

Friday, October 21, 2011

My alcohol flush

Some people would know that I never had an alcohol reaction until I went for an exchange in Germany a couple of years ago (after that huge dose of alcohol from my birthday party LOLX). That rash breakout lasted two weeks...

Since then, I have been trying to find out why am I getting an alcohol reaction now?! It's really kind of weird. Because red wine's fine, most white wine is ok. Radler is the only beer-mix that I can withstand for beer, before breaking out the next day. And the rashes (thankfully) is only limited to my torso that is hidden usually behind clothes. So, it's probably not the alcohol per se, perhaps the LEVEL of alcohol, or some other substance.

Just something somewhat related. Recently did 23andme. I was told rs671 gives rise to a variation of ALDH2 - ALDH2*2 - which is a mutation of G>A that results in an alcohol flush reaction. Each copy of A is an ALDH2*2. I have a genotype of GG.. This is expected since I do not have past history of having a flush in any way.... Not even now, since the reaction I described above occurs only A DAY after I drink... An actual flush reaction (see image below) occurs typically almost immediately. I have friends who turn red like lobsters.

"In the body, alcohol is first converted into acetaldehyde, a potentially cancer-causing toxin, and then into a harmless substance called acetate.  An enzyme called ALDH2 is responsible for the crucial detoxifying step.  But a genetic variation known as ALDH2*2, most commonly found in people with Asian ancestry, can render the enzyme unable to convert acetaldehyde into acetate." 

What's wrong with your hand (rhetoric)

I need to put up my hand - ask MORE questions or make MORE comments on the spot.

It's this hardwired mechanism in the twenty years of my SG education that is costing me dearly: fear of failing, fear of asking questions that make you seem stupid, basically fear of being "wrong".

But what's wrong with being "wrong"? It just shows that you are thinking... even though it might be in the wrong direction.

Ok, I am going to start kicking the habit. It's part of my own resolution and definitely part of my own training.

I would rather look stupid now, than later. Hack. It doesn't actually matter, does it?

ripping this image off XL's page:


Favorite season

I am falling in love with fall after 2 yrs of New England autumn :)

Cooling yet sun-filled and always the correct combination of hues. A pity that it's always so short. But perhaps that's how the heart grows fonder .

Thursday, October 20, 2011

Ginger supremacist?!

What the hell is a Ginger supremacist?!? lolx...


But the new episode of Glee is really much better than the other episodes so far in the season.

Windows 7 VS Vista

Stumped when M asked me what is the difference between Windows 7 and Vista, when you look at it?!

Speed is definitely the main difference I felt, between the two. W7 is MUCH faster to start up - less than a minute - Vista takes AGES. Same applies for Microsoft Apps as well, especially EXCEL. But then again, it could be that it's on 64-bit. Also, speed can be relative thing, even though for a gizmo-insensitive guy like myself, the change in speed from 7 to Vista was quite palpable.

It was 12 midnight in the office, so I rambled something about the gadget bar in Vista not being customizable, until I found a site that taught me how to modify the registry to get rid of it. Talking about trivial lolx

Anyway found this more thorough comparison:

Wednesday, October 19, 2011

Biologically Useful Numbers


This is an extremely useful site!

I am always forgetting numbers like the diffusion limit of enzyme reaction rate in a cell especially (10^8 - 10^9 per M per sec). I had to stick something on my desktop to remember. LOLX...

Cite this pretty recent paper: Milo et al. Nucl. Acids Res. (2010) 38 (suppl 1): D750-D753.

The Gerstein Lab @ Yale also has a good compilation of Genome Statistics:

Proteins compilation: