Archive: ‘Grad School’ Category

Health Journal #12

Friday, July 16th, 2010
July 7
  • Breakfast: frosted mini-wheats
  • Lunch: italian sub, oatmeal raisin cookie
  • Snack: ice cream!
  • Dinner: broccoli, avocado, ham, cheese and ranch dressing
July 8
  • Breakfast: frosted mini-wheats, tea
  • Lunch: brie and ham, maybe some eggs? can’t remember
  • Dinner: chicken vegetable soup
  • Snack: ice cream, multiple rounds
July 9
  • Breakfast: frosted mini-wheats
  • Lunch: chicken sausage ravioli with tomato sauce
  • Dinner: leftover chicken sausage ravioli with tomato sauce
  • Snack: ice cream, multiple rounds
July 10
  • Breakfast: frosted mini-wheats, sunny side-ups (2)
  • Lunch: spinach salad with grapefruit, avocado, prosciutto and ranch dressing. Possibly the best salad ever.
  • Dinner: steak.
  • Snack: ice cream, multiple rounds
July 11
  • Breakfast: frosted mini-wheats
  • Lunch: spinach salad with grapefruit, avocado, steak and ranch dressing
  • Dinner: steak
  • Exercise: 3 mile run/walk. the cubital tunnel syndrome is getting better!
  • Snack: ice cream, multiple rounds
July 12
  • Weight: 118 lbs. Must be the running. I don’t feel dehydrated, so maybe i normally carry around a couple extra pounds of water?
  • Breakfast: spinach and cheese omelet, plus an orange. Power breakfast for my qualifier oral exam!
  • Lunch: sushi, wonton noodle soup, a blueberry donut. Lots of food to celebrate passing the exam!
  • Dinner: More celebrating! Spaghetti al adriatico (or something like that) at La Viola. Only the Ouest side was open since it’s Monday. There are two La Viola’s across the street from each other; the Bistro is a little more casual than the Ouest side, but they basically have the same menu I think….honestly don’t know what the difference is!
July 13
  • Breakfast: frosted mini-wheats
  • Lunch: ravioli and tomato sauce
  • Dinner: sunny side ups (2)
July 14
  • Breakfast: frosted mini-wheats
  • Lunch: spinach, crab and cheese omelet
  • Dinner: chicken sausage ravioli with a homemade sauce of sun-dried tomatoes and porcini mushrooms – soooo good =)
  • Snack: ice cream!
July 15
  • Breakfast: frosted mini-wheats
  • Lunch: the leftover chicken sausage ravioli plus sauce
  • Dinner: post-workout strawberry smoothie, a mini-bag of kettle corn, and 2 sunny side-ups
  • Exercise: 10 mins on the elliptical to warm up, then focused on weight training since i haven’t done that for a while. 36 Lat pull-downs, 36 rowing, 36 overhead triceps, 30 back extensions, 80-ish incline sit-ups, 20 pushups.

World Cup vs. PhD

Tuesday, July 6th, 2010

World Cup fever is high now that we’re into the semifinals with the Dutch and the Uruguayans facing off today. I’ve managed to catch a good bit of the tournament despite having this qual hanging over my head. With both of these entities demanding my attention, I LMAO’d at this head-to-head comparison in PhD Comics, spotted by Ingrid:

Why Hurricane Harbor is terrible, and Health Journal #10

Friday, July 2nd, 2010

Yesterday we to Hurricane Harbor, a water park at Six Flags in NJ. Online, it looked promising, but wow, by the end of the day I realized why they invested in decorating the place. The rides were totally understaffed, so even though the park wasn’t very crowded or busy, the lines took forever. The lazy-river type thing, in which you can cruise along the gentle current around the park, and a staple attraction at just about every water park , didn’t have enough rafts and tubes so people were hoarding them for their friends. And then, in the process of training their lifeguards, they repeatedly kicked everyone out of the wave pool. Maybe I’ve been spoiled by Florida water parks, but the ratio of fun to waiting was too low.

Yes, the place looks really nice, but I’d rather spare the decor and have a good time doing stuff instead of waiting. Even my little hometown local water park, the Rapids, is better than this. So I guess it’s not surprising that the parent company Six Flags filed for bankruptcy last year. Once they have your ticket money and get you in the park, they don’t seem to prioritize running the park in a way that optimizes your time there – sure, you can wait while two staffers manage six different slides! At the Rapids, every slide had a staff member to make sure rides ran efficiently and smoothly. Oh, but Hurricane Harbor does have plenty of overpriced food items and ads plastered all over the park – I don’t think I had ever seen a Starburst billboard before. And they definitely keep plenty of staff at the food stands – after all, every overpriced piece of pizza they sell means extra profit. Contrast that with the profit gained from every extra slide ride – hmmmmm.

Speaking of food, here’s the next health journal:

July 1
  • Breakfast: two sunny side-ups and toast.
  • An Italian shorti from Wawa, which I ate at Hurricane Harbor!…and which was probably the best part of my time there.
  • Dinner: round bottom roast.
  • Snack: Yogorino fro-yo with chocolate shavings and kiwi. I <3 Yogorino.
July 2
  • Breakfast/lunch: arugula salad with broccoli, feta, avocado and ranch dressing, with tilapia on the side. Also some neapolitan ice cream.
  • Dinner: Manhattan clam chowder.

QE paper done, resuming life with Health Journal #9

Tuesday, June 29th, 2010

Done with 11 minutes to spare! Done with the written part, that is. For Bioengineering at Penn, our qualifying exam consists of a mini research grant proposal and then an oral defense of that proposal. We have two weeks to prepare for each part. The first part was definitely harder for me; coming up with experiments is not my strength, nor is discussing topics that are relatively unfamiliar to me. I find it weird that the spirit of the assignment is to become an expert in some sphere of research within two weeks…but this seems to be a common theme in grad school.

Needless to say, I was a frazzled mess last week, madly reading and writing, in between watching the ridiculous ref’ing at the World Cup(!). Seriously, check out the merits of instant replay, FIFA, or at least goal line sensing technology. Between WC watching and QE writing, my diet and exercise routine fell apart – when I don’t hold myself accountable, boy do I go to town. Oh well. Ice cream is brain food, I say. But the important thing is to get back on track, so here we go:

June 28
  • Breakfast: frosted mini-wheats
  • Lunch: arugula salad with broccoli and ranch dressing, plus tilapia for protein. Salad could have used more embellishment, maybe some cheese or fruit.
  • Snack: ice cream!
  • Dinner: bottom round roast and a bowlful of cherries. I guess I wasn’t very hungry because I ate a pound of steak yesterday. Oops.
  • Exercise: went to zumba, but I was so mentally and physically tired that I didn’t get much out of it.
  • Weight: 123 lbs. Could be that pound of steak.
June 29
  • Breakfast: frosted mini-wheats
  • Lunch: we shall see. Currently watching Paraguay-Japan in OT. WTF IS UP WITH THIS REF?!?!!! Okay, lunch: arugula salad with broccoli, cheese and prosciutto.
  • Dinner: bottom round roast, mint chocolate chip ice cream.
June 30
  • Breakfast: scrambled eggs, large caramel macchiato.
  • Lunch: needle noodles from Sang Kee Noodle House. Like Starbucks, this place is highly suspect of receiving way too much of my income. Needle noodle is a thick tapioca noodle (i think), one of my favorites!
  • Dinner: some appetizers from MidAtlantic in West Philly with Karla! We had the pig wings, cheese dumplings, and crab-crusted scrapple. Interesting food, a little too rich and heavy but glad we tried the place. It’s super-duper close to lab, so I probably will be back.

Pendergrass Dinner!

Saturday, June 12th, 2010

By chance, the grad students in the Interfaces imaging program had the opportunity to go the Radiology Department’s swanky annual Pendergrass dinner, a semi-formal event. I am ALWAYS up for fancy dinner =D It was held at The Four Seasons. The appetizers were awesome, except for the piece of salmon that fell down my (non-existent) cleavage while we were talking to my PI, Jim Gee, at which point Jim quipped “Nice catch” as I retrieved it and ate it. Chris approved of the steak – that’s all the approval I need, the boy knows meat. Here are some pictures! More in the photos section here.

It was great to see everyone all dressed up, and even better to see people get down on the dance floor =) At one point I started tipping my school mates out of their chairs so they would come dance too. Doing theatre certainly has made me less inhibited about bopping around, although I think my year at Disney really fixed that. (Once you dance in costume, you learn to go all out and not care about anything but having fun.) Plus, a total stranger lady told me I had the best dress of the night! It’s all about penguin-style =)

Play Google PacMan!

Tuesday, May 25th, 2010

Another way to procrastinate: apparently almost 5000000 work hours have been lost due to people playing PacMan on Google’s homepage (here’s the game).

To play, click “Insert Coin.” Evidently a two-player keyboard scheme is also functioning.

BBC News – Google Pac-Man eats up work time.

MacPorts “build.cmd” error fixed with Xcode

Saturday, May 22nd, 2010

While I’m reporting on my computer mishaps (go here if you want to know how to install ITK), here’s another headslapper. (BTW, this applies to Snow Leopard/OS X 10.6.3.)

MacPorts is a command line tool for installing software, and I was trying it out for the end goal of getting ImageMagick on my computer. Installing MacPorts itself went smoothly. Then, as its documentation suggested, I tried to update by running sudo port -v selfupdate. “Tried” is the operative word, as I kept getting this:

Error: Unable to execute port: can't read "build.cmd": Failed to locate 'make' in
path: '/opt/local/bin:/opt/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin' or at its
MacPorts configuration time location, did you move it?

No, you twit, I did not move it.

Sarcastic frustration being ineffective for compelling my computer to cooperate (whew alliteration of c-p sounds), I turned to Google and found that a few other people also experienced this problem. At least two arrived at resolution by (re)installing Xcode with Unix Development Support. I installed Xcode from my OS X install disc, and after that MacPorts updated properly. I’m not sure if the version of Xcode available online for download will also work.

How to install ITK on a Mac: CMake >> MacPorts

Saturday, May 22nd, 2010

Installing Insight Toolkit (ITK) shouldn’t be that hard to do, but I wasted a lot of time trying to figure this out, so I’ll share what I’ve learned. If you’re in a hurry, here’s the gist: go with CMake, it took about half an hour on my 2-gb, 2.13-ghz MacBook Air.

Since I have a Mac, specifically OS X 10.6 (Snow Leopard), I reduced my installation options to two routes: CMake and MacPorts. Both are free and run from the command line; CMake also has a GUI. Initially I tried MacPorts, since it seemed the easier of the two with a one-liner:

sudo port -d install InsightToolkit

For reference, here’s the wiki guide on ITK with MacPorts.

However, the process seemed to stall after several minutes, attempting to download something at ever decreasing speeds. I let it run all night and it still didn’t finish. The longer it went, the more the download rate slowed, like an annoying instance of Zeno’s paradox. So finally I ^C’ed outta there. I did try initiating the build again and it seemed to bypass the steps it had already taken but again stalled at a similar downloading step.

After that failure, I set about learning some of this CMake compiling business. I should have known to start there from the beginning, since CMake is from Kitware, the open-source software group responsible for ITK as well. Here’s what would have made my life easier if it had been spelled out for me:

  1. Download and install CMake using the familiar and friendly .dmg format meant for simple folks like me.
  2. Download ITK and unarchive the compressed file. This folder is the ITK source folder, which CMake will need.
  3. CMake can be run from the command line or from a GUI. Since I’m feeling particularly noob, I went with the GUI. It looks something like this, once it is running (note the output in the bottom window):
    CMake GUI
    Set your Source (the ITK source folder that you downloaded) and the Build folder, which should be an empty new folder where you will build ITK. I called mine “ITK_bin.”
  4. Click “Configure.” A window will pop up, asking you to “specify the generator for this project.” I went with the defaults on this and it worked. After you click “Done,” CMake will write files to the build directory. At some point it should have a red screen and ask you to choose from a set of options such as the one below:

    I unchecked “Build Examples” and “Build Testing” since I don’t need them. When you have set the options as you like, click “Configure” again. Repeat this until no new options are available, at which point the screen is no longer red.
  5. At this point, you will need the command line, but this last step is very easy. Go to your ITK build directory and enter “make.” E.g., if I am in the parent folder of my ITK build directory,
    $ cd ITK_bin
    $ make

    ITK should start building, with progress displayed as [4%], [11%], and so forth.

Yay done with classes!!

Saturday, May 8th, 2010

As of 11:31pm last night, I finished my coursework for the semester. Unless, of course, the profs are unable to download my report. But let’s assume my server hasn’t failed them. And I already celebrated end of classes anyway; Chris took me out for dinner at FridaySaturdaySunday on Thursday. We had outdoor seating on a beautiful evening, and we even had Henry along! The waitstaff were great, keeping his water dish full and giving him treats. He was pretty well-behaved, considering how difficult it is for a 90-pound golden retriever to sit still when so much food and so many delectable aromas are around. You MUST try the goat cheese-honey-walnut salad. The softshell crabs were satisfying, too; I forgot that I’m not that big a fan of red bell pepper which was in the sauce, but the crabs themselves were great.

To recap since Pirates: since I had to take a whole week off from school for daytime rehearsals plus some extra mornings for shows, I had to catch up on work and basically did nothing but lab and class, with a little soccer thrown in. For the computer science class, we had presentations on our semester projects instead of final exams. As I listened to my classmates describe their work, I realized two things:

  1. My project was a heckuva lot easier than everyone else’s because it didn’t involve any novel programming challenges, just implementing stuff that had already been developed.
  2. I felt very acutely for the first time in a while that this class was about computer science, and I was not a computer scientist. And evidently a flow chart of your algorithms is a key component of your presentation if you are a computer science person, but I, not being one of them, was ignorant and had no such chart. Who knew?

Fortunately, I got good feedback from some of the postdocs in my lab who had come to the presentations, so I guess it’ll be okay.

So, I can relax somewhat for the next month, sort of. I have qualifying exams (QE’s) this summer, so that will be stressful. My buddy Ingrid suggested I try to get my committee members to argue with each other during the oral exam, as she did, so that they’ll be distracted from actually grading me :p

Oh, and being the well-intentioned but myopic do-gooder I am, I accidentally volunteered to work on a poster on our lab software for a Penn research retreat next Thursday. This is the trouble with being accustomed to busy as my normal pace – I keep finding more work for myself. I think my friend Anne has lost her faith in me to grow out of this habit. Not that she should talk; she’s starting general surgery residency next month. We had dinner at Supper last night. Amazing multigrain bread, and the duck and waffles was worth the plunge. Yes, that’s right, duck and waffles. My adventurous epicurean appetite can rest easy for a while.

Yay, my first professional theater gig! At WST, no less!

Wednesday, March 17th, 2010

I’ve been doing community theater for a few years now, mostly musicals and a scattering of other random performances. I once did a brief internet commercial thingy for $50, but that’s the extent of any compensated work I’ve done. Well, I can now proudly say that I’ve landed my first professional gig, a small one but important nonetheless. One small step for penguins, one giant leap for penguins in theater. From March 26 to April 10, I will be an extra – a water person, more specifically, although I’m still not totally clear on what that means beyond being interactive scenery – in “How I Became a Pirate,” a children’s musical playing on the mainstage at the Walnut Street Theatre! I believe the Walnut is the oldest theater in the country, and it’s certainly the largest and most prestigious in this region.

One of the complexities of trying to get more serious in theater (while you’re trying to live your other life) is that professional theaters rehearse during the day, when you would otherwise be at work or school. I’m extremely fortunate to be in graduate school with a professor (Paul Yushkevich, who teaches Image Analysis, which is possibly the most awesome and most useful class I’ve taken since college) and mentors (Anjan Chatterjee and Jim Gee) who are supportive of my creative pursuits. So next week, I will experience for the first time the workings of a professional production. I can’t wait!!!

I bet all the engineering for the technical stuff will be waaaayyyy cool. I vaguely remember all the coordination that went into putting on Fantasmic! at the Studios, involving dancing water effects, pyrotechnics, you name it. Although I don’t think this show will involve quite as much, I will see its preparation with a much different perspective and appreciation for the end goal of not just having cool stuff to wow the audience, but to communicate our story and invite them into our world onstage.