Where does biomedical informatics belong within an academic center?

A question posed by Prof Miller during class today.

Options:
A) Within many different individual bioscience and clinical departments?
B) In its own department
C) In a computing support unit?

What do you guys think?

Although this question seemed more for hospitals and perhaps academic institutions, it occurred to me it can apply to a more general research setting - research institutes, even other drug/pharmaceutical companies too. And it happens that it seemed to be able to be applied to my ex-job at Genome Institute of Singapore (GIS). If you think about it, RCG is like a biomedical informatics group, with people doing a myriad of different biomedical informatics - sequencing, population genetics, maintaining and creating applicational tools and database management for biologists and webpage and software mediation for the institute as a whole. It IS a support unit, on the institute's point of view, but yet functions as an individual department. And, if you think about my friend Ri in Mark's lab (I will want to believe he has a team of bioinfo guys now haha, but then he might still be outsourcing hehe, which isn't exactly a bad thing) previously or the bioinformatics specialists recruited to the different labs, you can also imagine a one-person support unit within the bioscience department or group.

The answer to the question will have to depend on the needs of the center. A center that is organized into labs, and heavily relies on computational technologies would necessarily require bioinformatics personnel in their own departments, in which themselves will have their own needs. And if the center is large enough, a new department can be established, to act as a home-base for additional personnel and it can serve both as an autonomous entity, with its own managerial and administrative arrangements and/or a consultancy firm of sorts, and also a common resource pool that everybody in the center can tap into. Such could relieve budgets on the individual departments and consolidate manpower, and allow development of the individuals that join the biomedical informatics department. So, suddenly, I am in awe of GIS (or maybe just Ed's or Guilliame's) foresight in putting together such a department in the first place =)

I do not think it should be a computing support unit, but rather a biocomputing support unit. If it just involves simply building IT infrastructure with no biological or clinical relevance, then this ought to be a separate group altogether. But then again, if the center is not that big enough, they could be integrated too.

Outside the academic center, however, biomedical informatics organization would probably act as a consultancy and/or educational firm or quite a buzz thing in Singapore now - contract-based. Much like CROs (contract research organizations such as Quintiles or Kendle) or just intermediaries that other organizations/research institutes/academic centers can outsource their work to (like Beijing Genomics Institute for very large scale sequencing and bioinformatics analyses).

You can also look at these options in order of their importance. I would deem the role of biomedical informatics as (A) be most important, followed by (B) and (C). So a center can acquire these resources in this order as they grow.

So, if you are getting the drift, basically, relevance is the key to deciding which is more beneficial to the center's organization of resources. Choices are relative to the needs and demands of the institution.

I think I articulated really badly that day... Kind of convoluted... But I will improve on that! =)

Maiden trip to the U.S.!

Hallo ALL!! Greetings from New Haven once again (for those of you who didn't catch the first one on Facebook)!!

And if you haven't noticed already, whether it's on Facebook or my blog title, yup, I am currently at Yale in the US, pursuing my phD at Graduate School of Arts and Sciences (GSAS). And if you are interested, my major is Computational Biology and Bioinformatics (CBB) under the Biological and Biomedical Sciences Department (BBS) and am in a relatively new program Integrated Graduate Program in Physical and Engineering Biology (IGPPEB). Quite a mouthful, isn't it? Pardon me for the excessive use of acronyms and jargons (LOLX!). If you can't catch entirely, and they (do) appear in my entries hereafter, just know that they are just affiliations that I might be associated with for the next 5 years or so... Just a brief introduction, and since I have not started school yet, there isn't much of what I am doing that is pertaining to my graduate studies per se, so those would come later, in due time.

What I was excited about as well, was my maiden trip to the US. Yes, my first EVER setting-foot on American grounds! But well, there's always a first time for anything, isn't it? Took China Eastern Airlines (because that's the cheapest one-way ticket I could find on cheapoair) at Changi Airport T3, transited at Shanghai Pu Dong International Airport after 5 hours from Singapore (same time zone), then the last leg of 13 hours flight from Shanghai to John F. Kennedy International Airport at New York City! Yeah, the ever infamous Big Apple, which I unfortunately could only catch a glimpse of, be sure I will be back to soak it all in LOLX!

I wanna thank CS, J and Owl for insisting to send me off despite you guys needing to work the next day, R, my best buddy, and K, despite R having to go endure post-operation trauma (hope you are feeling much better) for sending me off!! I am really happy to see you guys there before I fly off. Thank god though, I manage to "shake off" those of you who had wanted to come, haha. No hard feelings, just thought that it was really an unearthly timing to make a trip to the eastern tip of Singapore on a midweek night. But I do appreciate the thought nonetheless =) And all those that called and messaged =) To all the weddings and housewarmings I would miss, just know that I would be giving you guys my wellwishes all the way from US!! hehe. To my family, XL and her family (who came in the end despite having dinnered only the day before), I have only gratitude and more gratitude. Gonna miss you all. I will take care of myself and call as often as I can =)

China Eastern Airlines flight experience was pretty much so-so, for me. Without any individual flight entertainment systems (except the sound system), it has got most of the other things above average - meals, services, minimal delays. I got bumped up to Business class from Singapore to Shanghai - no significant difference though from the economy class. So if you are into cheap tickets but do not mind the absence of in-flight entertainment systems, then this is fine. But the 13+5+waiting+5 (transit)+4(shuttle to new haven)=29-hour travelling was horrendous!! I mean, seriously, I should start thinking about teleportation as my new form of transport, or else just KILL me LOLX. On the hindsight, it wasn't that much of a thing after I touched down, but I think I wouldn't want to do that again in the very near future...

Pu Dong Airport was a little disappointing, despite all the Expo 2010 hype. I found it messy, despite knowing the language and all. They had put up counters solely for the purpose of the Expo and ended up confusing most of the travellers, because they were mostly closed already. Very sparse shopping district, with the shops having very minimal international outlook. The flight from Pu Dong saw a very different demographics of passengers - a lot of American-born Chinese kids (ABC) returning to US from vacation in China, with their very Chinese parents and some in-betweens (like myself), and some US citizens. So the whole plane was filled with a hodgepodge of English and Mandarin accents, kids with American accent but zilch Mandarin, parents with Chinese English accents but local Mandarin accents, visiting Chinese zero/minimal English but full of local dialects (Shanghainese, Cantonese etc.), total Americans - just pure acoustic disaster... The entire flight was filled with babies crying, little ABCs screaming to English pop songs, kids jumping around, mums scolding the kids, mums scolding each other, dads laughing and standing up and blocking everybody's view of the TV (I had to get some to sit down)... As if sleeping on a badly-positioned economy class seat wasn't bad enough... And you could see the somewhat belligerence (albeit stifled) of the Chinese at the Airport and on-flight. And note to self, bring a converter on the carry-on luggage... BTW, though, the plane has a power socket for charging!!

Arriving at JFK did not evoke the mirth that I was expecting (of myself), but more of a sigh of relief (haha). It made me miss the comfort, convenience and efficiency of Changi Airport (well it has been consistently the best airport in the world ya know) even more. Surprisingly, I encountered little extraordinary hiccups; the queue was just plain long and slow, with people crowding at a few counters (and blatantly jumping queue, though I think this experience has something to do with the demographics of the flight than anything else) and with many other counters not opened until much later.

I was happy I managed to make two new acquaintances even through this flight: J and A. J's from IMCB haha, if yy is reading this, he's from your lab!! He's going to Columbia University to pursue phD in neuroscience. All the best, I will try to find you on Facebook. And A's a Turkish and a second-year student from Bioengineering from Yale. He was so helpful and taking the extra miles with explanations and trying to give me recommendations for admin matters (since he is also an international student) and even gave me his email and phone number!! Grateful eternally, and will probably catch you for lunch soon =) And I am glad the taxi driver was nice too, knowing this is my first time to US and Yale for that matter; he stayed and made sure I was safe before driving off. And boy, am I overjoyed when I saw C haha!! And so, the story starts now...

Last Day @ GIS

2nd August 2010 was my last day at GIS. Took me a while to finally settle down to writing this. Well, my dearest got sick and I was caught up in a series of administrative stuff, so... Here's an entry nonetheless.

I didn't think my last day at the institute was going to be anything heartbreaking. Well, for one, the turnover rate there is so high (defiintely not because of the "gruelling" working environment LOLX, but that's another story for another day I guess) that it seems quite like a norm for people to be leaving anyway. As it turned out, while it wasn't downright emotional with sobbing goodbyes and heartwrenching farewells, it still felt kind of nostalgic.

CS was especially earnest in helping me keep memories of my last moments at GIS, helping me take photos. We went for my last gym session at the NTU Alumni Club, where I had spent weekly more socialising with colleagues and friends than actual fitness training LOLX. Thanks CS!! =) And, there was my last RCG weekly meeting. It was CS turn that day and after that, CS and I went to have a tea break at the Rockymaster. J would have joined, if he wasn't on course. Hope you are enjoying yourself there haha.

We met E on the way there!! Speaking of coincidence =) He joined us for a while. We really had a great time reminiscing and chilling and of course, somehow it always comes back to genomics research - the one thing that bound us in the first place. Incidentally as well, M and T wanted to return money to CS for my farewell lunch last week and I was glad I get to meet my Thai friends for the last time before I fly off. We go a long way back manz, back when we were just interns... Send my regards to K in Thailand ya =) I am sure with T and K's diligence, your phDs will be simply splendid. Take care!!
Just 10 minutes before I was due to leave for HR department to return my security pass, I decided to say my last parting farewells to people I know... That's when I realised, I had to start combing from Level 4, 7, 8 and then finally back to Level 3. I had wanted to meet alot more people... But alas, there wasn't really enough time. So I left a farewell email to everybody at GIS. At this juncture, I really want to make a full version of "thank you"s (that I wasn't able to on the blanket email) of all the people at GIS that have made my 2 years there extremely exciting, memorable, fruitful and rewarding:
1) Andr, Pad, Kelv, Ch Tin and Alv, for always expediting my IT requests, alot of times as personal favors and on top of their already heavy schedule. Extremely thankful though I am sure you guys would say those are tremendously trivial tasks, still, thank you. To Gare, don't run too much ya... addiction (of any kind) is seldom a good thing =) Keep up the camaraderie and trips to the gym though! Thumbs up for healthy lifestyle haha!

2) Ch Wei, H'en, for your occasional chats
3) Ken and JiaN, for your ready approachability when I asked for advice.
4) my RCG team mates! Like I mentioned in my farewell speech, I love how the group, despite having different portfolios, would patiently help each other with no reservations. Take care people! To Atif, thanks for granting me almost total freedom in my work, and all your care and concern, really appreciate that. To KS, sorry you have to handle the full brunt of all the sh** that is coming now. JIAYOU! To CS, Owl, 小Paul, J - my best lunch and gym buddies - hope you guys like the parting gifts I made. Keep in touch on FB or MSN ya and may the force with you =) I am going to miss all the jive and chaff and mirth. To J, in particular, thanks for being my friend right from the very beginnning and stuck by me despite my whinings and complaints and what-nots, dishing out your insights and advice to a naive me that just started out in the working world as a fresh grad =) We will all keep in touch!
5) Vik, Mark, JJ and YY for your advice, help, guidance and have always felt I owe much of my current achievements todate to you guys. And also, Ed, despite not having met you in person, thank you for your emails.

6) XueL, R, E and A, all the best for your phDs and work!! We might meet in US one day (definitely FB though) =) It's always entertaining, a great pleasure and learning experience to work or have lazy chats with you guys at the pantry, or online.

7) Rec Club, for making my first DnD a blast in the first year (haha!)
8) Cynt, for giving me ample opportunites and your advice and help!! Thank you!!
9) Chang H, it's always entertaining talking to you haha. Get married soon!!
10) Soni, Yang, KK, Eil for all the help in my projects. Congrats on your promotion too, Soni!

11) Mich, Shar for giving me a great impression of HR!! LOLX
12) HuiQ, Astr, for all our chats online and good luck!
13) Dev, for simply being such a great friend!!
14) 大Paul, better late than never =)

Ok, that was quite a feat, trying to remember people... lolx

GIS was a place of serendipity for me. It started off with a serendipitous interview, followed by (odd) fatalistic forces that propelled me into the realm of research (although my job scope does not entail "research" per se) and subsequently graduate school. Somehow, retrospectively now, it feels like I have just alighted from a roller coaster ride. You went in not knowing how the ride would be, then you get to experience an adrenaline rush and a high that leaves you wanting more. Touching down from the mad ride thereafter, gives you a discombobulated sense of simultaneous surreality and satisfaction - it's like you have just crawled out of the rabbit hole after slaying an evil fire-breathing dragon called Jabberwocky. You grew confident of what you want now, at the same time, you grew jitters of what the future holds for you. But you take that step forward all the same.

Thank you GIS, for creating such a genial environment, and all my friends and colleagues at GIS, for allowing me to laugh and whine, to err and grow. It is you guys that made the difference =) A final thank you. Take care all and keep smiling!! And because the world is round (*laughs stupidly*), we might meet again somehow, someday, somewhere, sometime in some future. So keep in touch!! (the power of technology indeed). =)

Tennis at NUS

Tennis is really a sport I haven't got a chance to really explore. Well it seems I might just have a chance to play it every week now that my colleagues are pretty into it! Today tennis is at NUS, but 1 hour's a little too short.

Shit, I forgot to take picture... NVM next time i will try to take... Gotta know lots of my colleague's AD's friends. They seemed a pretty closely knitted bunch of friends, maybe cos they are from the same church. In any case, it was pretty fun time hanging out with them and playing tennis with J and PT.

After our short tennis matches, with me the most clownish of them all, we even went for a 2.4km run!! Ok more than 2.4km cos we ran the outer rounds; damn it was good!! The power of having people to run with you is amazing!! Being no longer in Redhill, means I lost YC as my running partner; not that we run regularly together anyway, in fact it was only once, but nonetheless... And the 3 of them can really run - JJ, HJ, AD!

After which we went to an Indian restaurant to eat Indian food.. duh... Got introduced to Naan, smaller and supposedly healthier version of prata, and Dhal, the soup and some other wholemeal pratas (?!?) Couldn't rem the names haha! It was really cool chilling out there, where I listened to them talk about their past, their current jobs and current situations etc...

I, as a fresh graduate, realised I am in league with (other than married men and women) experienced people who are willing to share their working experiences and life and I am glad I am so blessed once again to be meeting such nice people. Reminded me of lunch today where guy colleagues, think almost 12 of us, sat in a coffee shop and talk rubbish and lunch at the same time. Though they are much older, I was having so much fun listening to them talk. They are VERY entertaining indeed. And realised CB's a running fanatic, jio-ed me to run Standard Chartered *faint*.. Let me consider... HAH! Anybody else wanna join?

AD's planning to get married, stepping into the Hall of Fame for married men at our level 3, HAHA! Seriously, everybody's either married or married with kids, even J whom I thought looked so young (but much older) actually has a 2-yr-old daughter!! Gosh!
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Last day in Hoi An brought us to the late kings' mausoleums, 2 of them only actually, the supposedly more representative ones. Forgot the names, think they were Tu Duc (cos I think the Vietnamese pronounced it very intriguingly nice haha) and the other one dunno father or son of Tu Duc. One representing the romantism, the other forgot wat LOLX. But both are pretty nice la just that they probably have become worn out after years of war and rampage and disuse, and of course nobody actually uses them.. But it took us half the day to actually finish visiting the places, with the guide giving a lecture on both. SERIOUS! A LECTURE! Well ok nvm. HA!

YT with El's work of art haha!!

Our lunch!! nice hoh..

Seriously 古色古香, an obvious influence by the Chinese

tour guide said this was a true replica of a man then - a bit vertically challenged hoh..

another statue

Subsequently we embarked on our final destination in Vietnam - HANOI! Where we will meet Ph!! And of course her fiance, who is her legal husband now as we speak. Woohoo! Overnight train was the same arrangement... Somebody commented I got a tummy... I never knew I had one HAHA! Ok well, at least given the amount of exercise I do, I hope I would never get one... So I showed her my waist pouch under my shirt... zzzz... but it's quite funny cos nobody has commented that on me before. Something to think about.. HA!

train station
Wonder what's the ice for? Anybody can answer me?

My Office Desk

I got my desk at work today as well!! With my own phone and desktop to boot... Though I haven't gotten my desktop, I heard I gonna get a 19" (or was it 22") screen, and a dual core desktop CPU!! Ok big screen... haha...

Well but I am on probation... Hopefully I get past this stage to be officially employed... My boss looks like a no-nonsense guy with high standards... So I think I will have to work harder.... Things are still shaky at the moment definitely, as in nothing's festgelegt; room's not ready, work's not totally taken over, everything's a mess. But oh well, quite trivial actually everything haha; alright i am just complaining... And I got my second upper so who cares? Oops, did I mention I got my second upper? LOLX.. Thanks to my FYP distinction LOLX and I have this sentence to thank: "I have full confidence in you." Think it contains "alot" of meanings in there HA! O well, now I AM officially in the working world.

I am truly grateful though, to my upper, Adrian, for painstakingly taking time off to teach me the complicated ropes and he even offered to teach me via MSN after last week!! Think I can't find a better teacher than this.. And also to Chee Seng, for making me feel at home and always lending me a hand... Well, in the house of married men, I can only say I have lots to learn haha...

And TC's getting married!!! Congrats!! Haven't seen the lucky girl =P I am sure they make a good couple. I better mark that day on my calendar and that makes 2 married frens liaoz... *edit* TC's going MIT to study phD, and his wife-to-be is following him there. All the best!!
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Second day at Vietnam was off to the Mekong River!! One of the longest river in the world, flowing through more than 5 countries!! I like water - rivers, seas, lakes etc... I think I have a certain affinity with water, though I dun exactly love swimming, I love diving. Anyway the trip to the river was really cool... Went to visit this Kampong-like place where we tasted coconut beer, sweets, delicious cart food, play with a python, play amongst bees and honey, sat on a donkey-driven cart and ate delicious fruits which are head-sized big!! Amazing!! Pictures speak a thousand words~~~





Our lunch was filled with fish... Hahha, the big round thing is actually fish cake!! It's empty inside but a bit sweet and crispy when you bite. The whole table is full of seafood lo!! Check out the fish in Kang Min's hands! Think it's a piranha!!

After the day out at the river, we head out to the train station for an overnight train ride to Da Nang and Hoi An, a world heritage town. Overnight train ride was another big experience. We divided up 4 girls and 3 guys. Things that guys do and girls do when they r bored are so different.... HAHA! Well for us, we just fish out a laptop for a versus fighting game!! And check out the thing that I and Elvin bought for breakfast - eggs with the embryonic veins popping out, meaning the chick embryo is in formation... Looked so dodgy and to me it looks a bit irksome.... Well, we disposed of it, cos creepy just by looking at them.... ie we went without breakfast... *edit* Apparently this thingy, according to Tipin, is a delicacy from the Philippines, called Balut... The Wiki images give me the creeps...

I am hot!

DEFINITELY NOT in the physical sense HAHA!

I din believe XH that bioinformatics specialist is a hot position until I received another principal investigator's (PI) email from GIS asking me to go down for interview.

Well, I can't be in GIS and then going for another GIS interview right? Totally duh... Or am I missing something here? Xh care to explain...

Nonetheless greatly appreciate the fact that most probably my resume looks good, haha. Thanks to my referees (I super kiasu got 5 referees, and I actually used all of them by discretion) and internships I guess. Really must thank Bob, Leonard and Prof Chen for writing my referral letters (though the last one is more of I draft out one); Bob, I have seen his testimonial, thanks for writing such a superbly nice one for me :P Felt that all the hard work then was well worth it. HAHA! Well, if you r reading this, from the bottom of my heart, you are a thoroughly likeable boss too. Just couldn't thank you enough.

Din feel very good from correspondence with a particular prospective employer, but well, she thought I was a snob. Maybe like what YC said maybe I said something confusing. Though I thought what I asked were really prim and proper. O well, let's just leave it behind.

Now it's back to my FYP presentation prep, stats project and stats exam, which I SERIOUSLY hope I dun fail.