Phytos and mycos, my 1st independent publication!

The first paper from my own lab is out in PLoS ONE, YAY!

Chen LL, Chung WC, Lin CP, Kuo CH (2012) Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PLoS ONE 7: e34407. DOI: 10.1371/journal.pone.0034407

A lab of my own

I found it hard to believe that almost a year has been passed since I started my current job as a principal investigator. What's even more amazing is the fact that the renovation of my lab space has F.I.N.A.L.L.Y. progressed to a point that we (i.e., two research assistants and I) can say goodbye to our temporary office and temporary lab. For the record, it is not really done yet but at least the space is usable (e.g., there's a window with no glass installed in the wet lab...). Here is what it looks like in my brand new lab, yay!

One of the most critical things, a fancy name plate on the door, is not ready yet. This is our temporary solution:


The wet lab:









The dry lab:





The meeting room:



My office:

Teaching Genetics

If you ask me which course influenced me the most during my college years, the answer would have to be Genetics. After all, I went on to get my MS and PhD in Genetics and my current job classification can be broadly defined as a geneticist. For this reason, I got this funny feeling when I was invited to give two guest lectures in the Genetics course at my old department. Was it a sense of pride? Maybe. Can I give those kids some inspiration as I got before? I certainly hope so!

I finished the first lecture today and felt exhausted afterwards. Lecturing for three hours on genome mapping and sequencing certainly is not something that one does for fun on a daily basis. I just hope that at least some kids got something useful out of it. Guess I will know in a couple of weeks after the mid-term...

On a side note, I found students with their laptops a bit distracting as an instructor. Are they so happy because I gave a good lecture? Or they found something funny on Youtube? I don't really know.

When in doubt, ask wife

One thing that bothered me a lot after moving back to Taiwan is not having a bike to ride. When we lived in Tucson, I used to ride my bike to work everyday. While the bike commute can turn into a painful experience from time to time (e.g., riding in 100+ degree Fahrenheit with 20+ mph head wind), having the chance to spend about 2 hours everyday on my bike is quite a luxury. Unfortunately, with so many things going on at home and at work, I fell into the common trap of "if I cut out exercise, I'll have more time for X". Half a year later, this unhealthy and unwise decision started to take its toll and I decided I must get back on my bike.

I figured that there are two possible ways which I can squeeze out some time to ride from my busy schedule: one is to ride to work just like before and the other is to go out for evening rides after the kids go to bed. However, this creates a dilemma for choosing a new bike (my old bike was sold before our big move). For commuting, I will need a folding bike so I can keep it in my office and not have to worry about thieves. However, if I can stick to the plan of evening rides, a road bike will make it much more fun (and probably give me better results from the work out). As usual, I got caught in the details and couldn't make up my mind about which way to go. Days passed after my resolution to ride and I grew restless about all the missed riding opportunities. I finally talked with Ann about my dilemma and she suggested an easy solution: why not get two bike?

And that, is how I ended up with four more wheels. In case anyone is wondering, yes, the one and only reason for me to write this is to brag. :)

I am a free man

Resigned from my postdoc position today and currently living without any formal affiliation. I will remain a free man for the next 2 weeks or so. It actually feels kind of weird this way, perhaps I have spent too much time at work.

It is official!

The contract for my new job finally arrived, so I guess it is safe to say this out loud now: I will join the Institute of Plant and Microbial Biology at Academia Sinica in Taiwan this summer as an Assistant Research Fellow (a tenure-track position that's equivalent to an Assistant Professor in the universities).

We are all very excited about moving back to Taiwan, however, how we are going to handle the upcoming move remains as an unsolved mystery...

No cure for a busy mind

Things have been quite intense and stressful at work during the past few months. Fortunately, the situation is more under control now and I somehow retained my sanity through all that craziness. After being told to relax repeatedly by several people, I decided to do something that always works for me: shopping for a new fountain pen!

However, this turned out to be anything but relaxing. After failing to find anything that meets my expectation, I started the process of ordering a custom-made pen. With so many decisions to make, it actually requires no less work than designing a research project or writing a proposal. Well, at least these are the "good" kind of problems to have on hand. :)

The secret handshake

Finally my boss approved that I am worthy material and granted me the privilege of reading his treasured copy of "Academic Gamesmanship: How to Make a Ph.D. Pay" by Pierre van den Berghe (ISBN: 0200717154). The author's cynical view on the inner working of academic world was hilarious, which makes the reading experience some sort of a guilty pleasure. The level of sarcasm is truly astonishing; Bill Bryson's work reads like children's literature in comparison. Too bad the book is out-of-print now (1st edition was in 1970) and the price of a used copy is simply outrageous (ranging from $35 to $468 on Amazon), otherwise I'd want one just for the fun of it.

hPDA rocks

As a part of my recent experiment with GTD, I started using a hPDA to organize things in my life. Incidentally, I had to make yet another intense week-long business trip to Taiwan earlier this month, which provided a good opportunity to test out this new system.

I am happy to say that the ingenious hPDA works great for me, particularly when things are getting crazy with an international trip that was filled with dozens of important meetings in a week. The flexible formatting of hPDA worked much better than any app that I can find for my iPod Touch. Furthermore, the portability/robustness/responsiveness of a hPDA is way better than any electronic alternative. Although backup and syncing remains as an issue with hPDA, I think I am hooked.

What was I thinking?

I was going through my old files this afternoon to get rid of things that I don't need any more. A mid-term report from the Evolutionary Genetics course that I took during the first year of grad school caught my eye with the following paragraph:

"Godzilla godzillus is a large reptile species endemic to the Hollywood Desert in southern California (Emmerich 1990). Due to its popularity on pet market, human collection caused extinction of several natural populations during the past decade. Of the five remaining natural populations, three of them have very small population size (N<=60, Figure 1). To preserve the species, a captive breeding program was initiated at the Hollywood Fantasy Zoo (Emmerich 1998). However, the founding individuals used in this breeding program were all collected from one population (A1). This raises the concern that future restoration efforts will greatly change the genetic composition of the species. To access the level of genetic variation and pattern of genetic structure in remaining populations, this study collected samples from all five remaining populations in the Hollywood Desert."

I honestly don't remember doing such silly things. Good thing that they didn't kick me out of the grad program.

Another trip to Taiwan

Back from my second trip to Taiwan in two months, very tired but nevertheless quite happy. It is interesting to see how my body adjust to these frequent international travel and jet lag. Last time I slept quite well from day one, but lost my appetite almost completely and couldn't taste the food at all. This time I had trouble sleeping for the entire trip, but thoroughly enjoyed all the delicious food that Taiwan has to offer.

Work aside, I got to see my mom and my brother's family again, and of course, my nephew's excellent performance of making faces:


I also visited my in-law's new house



and saw a bunch of orchids and roses that have been keeping my father-in-law busy:




Luckily, my travel schedule allowed me to stay for my father-in-law's birthday, so I prepared a Think Tigre FP for him


and also a Lamy Pico for my mother-in-law as a very late b-day gift. What I didn't expected was that I'd come away with some really awesome party favors, including a Delta Napoli limited edition FP/RB set (FPH-exclusive)




and a yellow Aurora Ipsilon.


Now while I deal with the jet-lag (yet again), I will have some great time playing with these new toys.

A short trip back to Taiwan

Still recovering from my trip back to Taiwan. It was a great trip, but in the same time totally exhausting.

During the trip, I took a chance to visit my alma mater, National Taiwan University, and had a lunch to catch up with some old friends from college.

It is stunning to acknowledge the fact that we all graduated from college more than 10 years ago. When we talk about all the amusing memories, they all seemed to have happened in last month or so. It is also very funny to see how almost everyone is pretty much the same as they do back in college.

Outside of the campus, I saw some interesting sights in Taipei. Here is a restaurant called Tamago Ya (literal translation: Egg House):

I wonder what they sell inside.

Right next to the campus, I am surprised to see that Taipei is running out of the space for everything, including bicycle parking:


The main point of taking this trip was work-related, so as rare as this sort of things happen, I need to be in suit and tie:


The evening before my return flight, I met with my mom and my brother's family. Here is my only nephew who was trying to have some fun making a mess for his mom to clean up:


Anyway, really need to get some sleep now, which is very hard to do. Will see how well that melatonin pill works.

Home sweet home

Finally get back from my week-long trip to Taiwan and settle back to my normal life. It is amazing how much stress/anxiety/excitement can do. Sleep deprivation? Not a problem! Jet lag? Doesn't feel a thing!

The only problem is that when the payback time comes (and it did), it sure is punishing.

On being a good son-in-law

Because of my boss has joint appointment in different departments, and also because UA is doing some departmental reorganization to deal with the budget crisis, my appointment here gets transferred around quite a bit for accounting reasons. Within a year, I have been associated with three different departments. Fortunately, my boss told me to stick with the first one on my CV, so I don't appear to be job hopping like crazy.

My latest appointment, starting from this month, is in the Department of Chemistry and Biochemistry. When I found out about this today, I thought it is quite funny. Everyone in Ann's family, with the exception of Ann, is a chemist. By being a postdoc in a chemistry department, I am truly becoming a part of her family, maybe even more so than she does. Ann got so excited and instantly called her parents when I told her about this, and they just couldn't stop laughing.

I wonder how many people out there has this kind of strange experience.

A powerful recruitment tool

A while ago Alyssa made a drawing of me and Howard sitting together at a table and has the words "best friends" and lots of colorful hearts on it. I thought it was pretty funny, as this is how she imagines what we are doing in the office all day, so I pinned it on the wall next to my desk in the office.



When Nancy saw the drawing today, she told Howard that he should use it to recruit new people, because "It is a proof of how good you are treating people in the lab. See all those hearts floating around in the air? If Chih-Horng is cursing at you all the time at home, his daughter wouldn't have drawn something like this.". I thought that this is a very interesting way to interpret the drawing, and even more so when I see Howard seems to be embarrassed by the praise.

The most embrassing event of the year

THE GOOD: got the page proof, made corrections, and sent it back on the same day.

THE BAD: I misspelled my boss's name, twice, in the references.

THE UGLY: I didn't catch the mistake, my boss did.

Out of one writing, back into another

The most recent writing frenzy at work has finally come to an end. Feeling somewhat relieved, the thought of blogging seems to be flowing again.

Looking back, no wonder I was sort of stressed out. Over the past month, I finished a manuscript from scratch and submitted it, got another revised and formally accepted, attended the SMBE meeting and gave a short talk there, and most importantly, sent out the first batch of job applications.

Time to get back to play with perl some more, while waiting for some good news.

DokuWiki is awesome!

After poking around a bit, I settled on DokuWiki to set up a small experimental site. All the good things that I heard about it seems to be true. Setting up is totally painless and fast, it took less than 10 minutes from downloading the source code to having the first page up. The syntax is pretty straight forward, although I'd prefer the default rule for header levels to be reversed (without installing plug-ins). Customizing the appearance, either by tweaking the templates myself or installing custom themes, is also easy enough, but because I like the default ones, I don't plan to change that yet.

Guess now the really challenge is to put enough useful things there. Right now I only have some random notes on the site, serving as memos for myself. Hopefully I'll have the time to organize my major bioinfo protocols there soon.

Time to tidy up

Just discovered a wonderful tool to tidy up my perl codes, Perltidy.

I don't think my codes were bad, but seeing them got "prettified" by this nice tool is kind of cool. Somehow they got this nice sterile, straight-out-of-textbook feel to them after the reformatting. Reading old codes is almost a fun thing to do after this, so I went crazy and reformatted my whole library.

It's not fair

The girls had their last day of school today. We are all very happy that the school year is finally over and almost everyone can enjoy the summer vacation. But, here is what the girls have to say: "It's not fair! Why daddy has to go to work and not staying at home with us?"

Yeah, right. Why? Hmmm... may be I should throw a tantrum at work tomorrow?