April 2007

RECOMB, aka my 1 year UCSD reunion!

Graduate school has some weird things, which I'm sure I have mentioned a few times. Retreats are strange enough, basically a few days where you leave, during the work-week, and do nothing but talk about science, meet more scientists, and miss work and class with people in your departments. Conferences are the same thing, except on an international scale!! People miss work from all over the world, in order to talk science, show results, and network.

RECOMB was my first time at the conference, although I had a paper in it last year with Eleazar Eskin about the history of the conference, neither one of us was able to attend the event in VENICE, ITALY!! (That was a major loss)!!! This year I was not presenting anything, but I was expected to go, and it was in Oakland, so really, how could I not?! I carpooled with Tom, Konrad (the visiting scholar), Marc and Andreas.

There were TONS of people there from UCSD. Ben Raphael, my undergraduate postdoc adviser, Pavel Pevzner and Vineet Bafna as well as a ton of students, including Erik Corona, who will be joining our program next year (yeay) was there to present! It was a great talk! Also other people from Eleazar's lab. It did feel a bit like a reunion. Also, Ali Bashir was there, one of the most inspirational TAs I've had! He is a Berkeley graduate, so he has to hate Stanford, and even made a comment about how I said something like someone from Stanford! I resent that!!! He had some pointer about grad school, how it is full of ups and downs, and the first year vacillates significantly more than other years. I like that, it's a positive comment.

Eleazar has moved to UCLA, which is pretty cool! He has such a great lab and such great work, I emailed my former summer program, SoCalBSI about him being a potential adviser. Unfortunately he will not be able to coordinate a talk this summer, but I definitely think he is just the perfect example of a professor who needs to be involved in this program! Assuming he has time! He mentioned I should come talk to his group!! I'm so honored, but also extremely nervous. I am down there a lot, so we'll see what I can work out (once I have more results and work). Nuno Bandeira, from UCSD as well, spoke to the program last summer, so this seems ideal!

There were some great keynotes as well. My favorite by far was Jenny Graves from Australia! George and I were laughing throughout the talk, getting strange looks. But the last slide (shown left) was proof that everyone else simply had no sense of humor, and we caught on sooner! She is really great. She showed how Y-chromosomes are shrinking, and that eventually the human Y will disappear, and pointed out that males in her audience are usually quite offended by this (and laughing said she doesn't understand why). She also had interesting theories on speciation, how these changes make the males unable to mate with certain females, so two species develop!!! It was AMAZING!

There were also a couple poster sessions. I have to give out my awards.

Second place goes to the following poster. I know it's hard to see, not so much because George is reading it, but mostly, because it's a small picture of it (in all fairness, it was also redirecting us to its new location).

The winner, with no real excuse, except maybe a lost poster, is the following:

In all fairness, this were both amazing posters, particularly the winner which I think attracted more people because it looked like that, and the author had to explain it! I was very impressed overall! You really do learn a huge amount at these conferences. I told Marina, I think if Russ had a choice of sending us to a conference, or having is sit in class, hands down the conferences win. I learned way more cutting-edge science at this conference than in any class!!

On Wednesday night, we went up to LBL and got the most amazing view of the bay, while munching on dinner! There were some fun toys we got to play around with! Later we went to a pub back around Oakland with students. Sean O'Rourke and Erik from Eleazar's lab joined us, they were both celebrating successful presentations. I also met new people, Barrett Abel from UC Davis, and I even bumped into a student from USC I met during interviews (she is a student there)! It's pretty crazy!!!

Ryan also buzzed his head, after much coaxing! I had him buzz it when we first got together, I think it looks really great! He let it grow long again, and he does have amazing hair, but he is not necessarily willing to put the full effort into keeping it long. I even got him an appointment once with my stylist Guy. It looks amazing...as always!

What do you think?!

Stanford AI Lab Retreat (wow, nerdy!)

Yeay! Retreat number two! Retreats are so fun, for those of you who have not gone to one. They are full of presentation, ways to get to know your classmates, labmates and professors on a more personal level. Of course you also get to hear about all the crazy and amazing research you didn't even know was going on!

The last few weeks have been fairly exciting! I had a chance to redesign my project for the Batzoglou lab, and I am really starting to feel more at home in the group. We went to the Stanford Artificial Intelligence Lab retreat, where I got a chance to bond with the new group! It was quite nice!

My dad was in town over the weekend, before the retreat. We had a good time going to the city, and walking around in the fisherman’s wharf. We also moseyed over to Ghirardelli square where I bought a bracelet, and Ryan bought a couple of amazing pictures from a photographer. They are great pictures from around the San Francisco area. Our moving company that brought our San Diego storage unit up to the bay area has been withholding our framed pictures that we had around our apartment in San Diego! It’s pretty upsetting because our walls are pretty bare because we do not have these pictures, and there are so many amazing places for them! I hope we get them soon, some of them were gorgeous creations like the one on the right that Ryan has taken! He’s a great photographer!

On Monday I dropped my father off at the airport, and went to San Francisco to have lunch with Beth. She goes to San Francisco State University, in the MBA program. It is quite insane! I was impressed when Stanford had a shopping mall, but SFSU’s MBA program where Beth attends classes is actually IN a mall. The Westfield shopping mall in Union Square has a huge Bloomingdales, a 6-story Nordstrom, a Furla store, and, oh yes, a whole floor of classrooms and computer labs for SFSU MBA students! It is absolutely insane. I have noticed some fundamental differences between southern California and the bay area. Movie theatres are sparse, and when they do exist they have a crazy amount of concessions (including pastries, food, and ice cream), which is NOT common in SoCal. There are very few chicken restaurants, such as California Chicken Cafe and KookooRoo and no Pinkberry ice cream stores (which I must say is a very recent addiction for me). I was hoping to open one of these, but it seems that with a 4 month waitlist to even receive information about a franchise, there must already be one in the works in the bay area. And finally, major universities must have shopping malls to prove true prowess!

On Wednesday I had lunch with Alex, Andreas and George (the latter are from the Batzoglou lab). I realize that I have become close enough with Alex, David and Noah to be able to talk about just about anything, however I need to learn how to ease my way in with other people. I think I am far too forward for some people, so hopefully we can find a good middle ground! I headed out to Monterey that evening, for the SAIL retreat. It is in a hotel RIGHT on the beach (see picture of Marina and Eugen), and although it was rainy and not great weather, I could hear the ocean when not in my room! We headed out to a bar at the Cannery, which is a historic region in the area. It was not a particularly classy place, which made it hilarious, and a prime target for the next evening.

During the talks at the retreat I heard some really fascinating stuff! I have not had much exposure to AI, so it was really interesting to me. Talks ranged from autonomous cars to linguistics, and some amazing robotics. Am I in the wrong field? At nights we went out to this bar in downtown Monterey (in the old Cannery). It was interesting to say the least. I've never been to a bar where bartenders drink more than their customers (Cory on the left shared his pitcher, don't worry)! They were taking shot after shot and eventually whipped out this blow up doll, and did some highly inappropriate stuff with it, after flashing their assets to the crowd. Isn't Monterey supposed to be super classy?

This guy is passed out, sitting up, holding a pen... There was also a guy who had his hand up against a dartboard while his friend threw darts at the wall.

We also had a planned entertainment portion of the evening! It was great! Tom (from Serafim's lab) did some amazing yoyo tricks, and there was a game similar to the newlywed game, except it was a student-advisor situation. The best part was that Serafim and Sam won! The runners up were Andrew Ng and his student Rion Snow, for whatever reason people were rooting against them, even though Rion had some great answers. They both agreed that if Rion were a vegetable, he would be a coffee bean! We also had a keynote, Jorge Cham (below), who is the creator of the PhDComics strip. It inspired the following comic strip...notice the little caption in the corner!

Later that evening we headed back to the bar with a much larger group of people. I think we pretty much filled up the whole bar! There were a few other people there, but it was Thursday night. We played a game called hands, the same one as at the retreat, but later we played this ridiculously weird game where you go around a circle counting off to 15. Every time you arrive at 15, the last person gets to change a number to any word, for example, the number 5 was changed to obecron pur C I 8 (or something along those lines, it's from Futurama). Although no one could remember that word, and eventually we started making up our own. One guy started saying "Oh my god, CIA!" With a really freaked out look on his face, it was hilarious. Abe Bassan, from Gill's lab, could not get one number right, and somehow he always had to say it! At one point he would just crack up instead of trying!

All in all it was GREAT retreat! It was in an amazing location with a GREAT view! The keynote was unforgettable. He went over many of his comic strips, which we all thoroughly enjoyed. The science is completely amazing, and I'm so glad to have gained more exposure in the AI field, I have really had none up until this point. I even got excited about it! The food wasn't half bad (notice the HUGE sandwich Andreas made)! Unfortunately since it has been something like 20 years since the last retreat, I'm not sure I can rely on it happening in the future. The Genetics Department seems to have the ultimate retreat, maybe I can get on the guest list somehow? Or just join Gavin Sherlock's lab. He has some amazing ideas!

On Saturday, after I got back, Noah had his annual Beer Olympics, followed by slip-n-slide activities as seen on the left. I was dead tired from my 3 day retreat (that seems counter-intuitive) and needed some rest, so Ryan and I slept most of the morning, and showed up late. It was also raining, which was completely unfortunate.

I watched the events, but missed the best one! We used to have a similar event at UCSD, minus the beer of course. It involves two (or more) teams, who are lined up on one side of the field, with a broomstick on the other end. You run across, pick up the broomstick, spin around like 10 times, and then run back across. Of course, the back across part is the tricky part. Now, in the Beer Olympics you are suffering from impaired balance in the first place (since this is not the first event). Noah had some great videos of people running into the house. At least it wasn't the street.

This was the one event I did get to see.

Most people were soaking wet, but it did not stop the festivities. At one point a Fire Engine drove by, and they honked and waved. A lot of people seemed interested. (What is Noah doing?!)

I think they need more beer!

Ryan and I went out to Rudy's with them later that night, a local, pretty sketchy bar, that is not necessarily my favorite. Saiqa had never been, but we decided to have a drink, and they were so ridiculously strong. We decided it was in order to impair our judgment so we wouldn't be so aware of our surroundings. Noah's roommate's girlfriend, Claire, told people she was getting married, a ploy to get free drinks. From the sounds of it, it worked pretty well. His friend Mark had also bought her a balloon animal with a flashing light in it...It was pretty strange. But apparently this kid that makes it is trying to make money to go to college! I guess he's been on the news.

So tomorrow I start RECOMB! I'm excited to see all these UCSD folks again!!!!

A bike named Penelope Cruiser

I am feeling EONS better since last week! On Saturday I had a chance to go to the bike store as well to finally get a bike helmet. While I was there I also wanted a basket to carry my bag and laptop, and then I realized...the bike I was riding was DEFINITELY too small (my knees hit the handlebars when I ride it)! It's a hand-me-down from Vincy, and she is TINY! Even the seat feels too small!

I tried out this bike that is sort of like a cruiser, without the bent handlebars. Ryan said it wasn't a good idea, and the sales person said that she thought they are hard to ride quickly, but they had a 21 speed one, and it was so comfy, that I got it! I called it Penelope (Penelope Cruiser). I wanted to ride it so badly, but Ryan said it was too dark out! I thought I looked a little stupid on it after buying it (it felt like an impulse by), but a guy complimented my bike, and the girl he was with said I looked good on it. The bike completely reminds me of the night we spent in Rimini over summer (a small town on the Western coast of Italy) which is easily one of the best days of my life! We road around on these cruiser bikes (picture left) that the hotel provides. There were no working brakes so we just had to ring the bell constantly.

On Sunday we rode our bikes to Castro to get some food, and then we rode it to and from school. The ride is soooo pretty. Larry Fagan gave me a map with the route, and I saw the Donkeys he had mentioned (below). I was really happy and excited about being able to ride in and out of school for the next few weeks. The only problem is that the campus and areas around are INFESTED with Caterpillars! As we were riding there are all of these low-hanging trees and these pretty tunnel-like tree areas (like in the pictures) and I noticed there was a spider-like web on one of them that I ran right into. We rode by this high school, and all these people along the path, and I had to get off at one point, and I look down and I see A GIANT CATERPILLAR on my leg!!!! I froze, and just stood there freaking out until Ryan came and got it off for me!!!!

We rode in, and had a bite to eat at Tressider and a drink. When I went to lock my bike I wasn't paying attention again, and saw a good spot under a tree. I go over, and start to lock it against a rack. As I'm about to do this I notice that the rack is moving. Then I realize, it's not moving, it's just COVERED with caterpillars! I look over at the next rack, and see the same thing, and my eyes follow up the spokes of the wheel to the handle bars, which look like moving foam. My alarm is increasing. I look at the seat, it's moving too! Then I muster up the courage to lift my head, and I'm in a veritable forest of hanging caterpillars!!!!!! How I managed to miss all of them while walking in, I am unsure. But now all I see is a slalom course to dodge these long squirmy fellas hanging from their little webs, thinking they're all sneaky and that I'll be their free taxi to another tree!

I pretty much started spazzing out. I screamed (more like shrieked, I have a horribly piercing scream), and run out of there, Ryan came over and saved Penelope before I dropped her on the ground, and I rip off my helmet and start dancing in a circle to get off the phantom caterpillars. I was so disturbed! With my newfound adrenaline I ran over under the safety of the overhanging walkway and left my bike at a rack over there. Some think they are super clever and hang over the edges of those as well! EW EW EW! Carol showed me a Stanford Daily paper that said they are here until GRADUATION! Possibly even LATER!!!!

So on Monday and Tuesday I rode in, but on Wednesday I had another Stanford South Africa Student Seminar Series. NO ONE CAME on the Stanford end. It was just me, Betty Chang (the coordinator on the Stanford end) and Konrad Scheffler (the speaker) who gave an excellent talk, and the South Africa students via video-conference. Apparently we have a budget for food, so I plan on bribing the students with Izzy's Bagels next time to get them to show up. Unfortunately NO ONE has volunteered to give a talk to the students, so I'm pretty unhappy. I will have to start more serious harassment.

On my rides in to campus I have noticed some strange behavior.
1) People like to walk on the street, even when there is a sidewalk available, and they are always either on the phone, listening to music, or smoking.
2) Just like you are defined by your surroundings, your dislike of other people is defined by your vehicle. I hate bikers when I'm in a car, and I had cars when I'm on a bike.
3) Riding through campus during the hours of 10 and 4 is a bad idea. All the students wander aimlessly and are not paying attention, and people on bikes are either too slow, or too reckless.
4) Of course I am always right ;)

My best experience so far has been the fire line which is a no parking zone...for cars. The lane is probably too narrow to allow any cars or fire trucks to get through because it is LINED with bikes on either side!!! In any case, I love riding my bike. It clears my mind, it makes me feel happy, and most of all, it's an easy way to squeeze in some exercise that really only costs me about an extra 30 minutes of time every day, although I must admit the helmet hair leaves much to be desired!!! Maybe I'll keep a blow dryer in my desk. That would be really funny...or really reasonable.

All good things (like spring break) must come to an end

On Monday I got some work done, a haircut, and promptly lost my cell phone. That last part is pretty crummy. On the plus side it gave me a reason that prevented me from doing anything on Monday night, instead I just stayed at home and did work. On Tuesday we had lunch, then headed back to the bay area. It rained and snowed on the ride up AND I hit not one but TWO tumbleweeds, at which point I gave up and let Ryan drive. He, on the other hand, got a ticket for speeding, so I felt really bad that I wasn't driving! We'll see what happens.

Me and my sister's dogs, isn't Spencer (the black and white one) so chubbo? It's so cute!

Ryan and his speeding ticket.

Rainbow welcoming us back to the bay area!

Wednesday I had lab meeting, followed by a talk with Gill. He didn't seem particularly happy with my progress, and was a bit worried about finishing over the next two weeks (at which point I should be switching over to the Batzoglou lab). I spoke with Russ the next day who suggested that I should just go ahead and begin working with Serafim sooner, which Gill agreed was right as well. So I will still be meeting with Serafim next week, and jump right into the work! I will also only be taking one class. It just seems right to do it that way.

On Wednesday night we went to dinner with Tiffany, the accepted student from Duke. She was out here for a Google scholarship weekend. She is still deciding between Harvard Systems Biology and our program. They are so different I am quite surprised that she is struggling. She said many people she knew were going to be in Boston, so I am wondering if that is weighing heavily on her decision. This seems like it should only indicate that there is something pretty important that continue to draw her toward Stanford. We will see! I hope she just goes with her gut in the end, but as I mentioned before, I think it's pretty important to go with the choice that leads to fewer distractions, although having distractions would likely make you more immune to these.

On Thursday night we went to dinner for our friend Hye Jin's birthday (I've known her since 6th grade) and also got to see another friend since back then, Hannah! She just started school in the bay area as well (everyone comes here eventually)! We went to this Iraqi place called Yaya's, and basically got the waiter's number for Beth, and left hers for him as well. He called while we went out afterwards! He seems like a total sweetheart! He's from Sonoma! He put up with our antics pretty nicely.

Friday was Julie Schnitzer's going away party! I'm particularly sad that she is leaving. She was the very first person I met when I got here at the beginning of the year, and she took the time to sit down and show me how the Marguerite worked, and what the best way was to get to the bookstore. She was also telling me how she lived in San Diego and just made me feel completely at home and happy! She's not moving terribly far but it will be sad not seeing her on a daily basis! She claims she will be around so I hope to get to see her at times :)

Mark Musen made a funny!

As usual there was food and wine available there, but there was so much left, and the uncorked wine cannot be taken away, so it is given to the grad students (of course). Amar Das pointed out we had a great life at BMI! We have free food and wine, constantly, showers in the bathrooms, couches, desks, a plasma TV, what more could we ask for?! We lead pretty cushy grad lives! So naturally we took the leftover food, and I ate it (at the right, I'm serving the tray to my fellow BMIer Kaustubh Supekar). The best part was when Rosalind Ravasio brought the wine bottles over to David, Genaro and myself. How could we let the lovely wines go to waste?! Besides, what better way to make students productive than by bribing them with food, wine, and televisions :).

David with the booty!

Ryan and I went up to the city that evening for a dinner with Julie's sister who is in town (I called her MiniFitt and her friend Megan, MiniFittFriend-Jule's last name is Fitt). We had a pretty good time, but had to get back at a relatively decent hour. However, the next day I tried to do some work but just ended up recovering from the last week, month, quarter. I will be getting my cell phone on Monday which is highly necessary! I really hope to be refreshed when classes start, at the moment I am highly unmotivated. I am finishing up some work for a publication with Ben, and doing a literature search for Serafim, but at least I only have one class!

In recovery under the supervision of Nurse Scoots.

Finally, Sunday was my cousin Micah's "12th" birthday party. I says that his actual 12th birthday was cancelled and so he will not celebrate his 31st. I got some dirt from my aunt, who does not remember why exactly it was cancelled, but said that Micah was naughty somehow, and so that was how he was punished. The birthday was a nice barbecue in the park in San Mateo. It was really nice, with tons of friends of Micah's, some of Vincy's family, and of course Ryan and I. We got to play some Bocce ball, and eat some delicious food, and there was also this massive cake covered in sugar!!! It had big balls of frosting of top of it. I didn't eat it but I was thinking about it the whole time! Paula, one of Micah's friends (who is actually considering doing a professional MS from BMI!!!!!) pointed out that there is a place that does Bocce ball and dinner around the area! We are planning on going it should be SO much fun!

We also went on the Monkey bars, which turns out to have been my downfall. We had fun swinging around and everything, but this morning I woke up and I am basically immobile. My back hurts TERRIBLY! As a sophomore in high school, during the tennis season, we were playing a game against a local high school and I tried to hit an overhead smash, which somehow totally killed my back! I couldn't even stand up straight! So my mom took me to the doctor's office who basically gave me some super strong ADVIL and sent me home. It has been mostly okay since then. It definitely is not a perfect situation, so I do Pilates to strengthen my "core" and take some strain from my back, but of course as I have been inconsistently able to sleep 8 hours, I often find myself lagging on these exercises as well! Which is terrible!

Ryan setting a bad example

So now I am feeling the consequences! The doctor prescribed me the same pills again. I was offered a shot of some pain killer, which could make me loopy, so I was not interested. Ryan swears by percocet which he had after an operation, but I took Vicodin once after getting my wisdom teeth removed, and unless it is TOTALLY necessary, I will avoid it at all costs! All I did was sleep!!! Although that is basically all I can do at the moment anyways! We'll see...I have a class tomorrow that I cannot miss, so I will go in for that, and hopefully I will survive!!! Mostly...I just cannot handle being home like this all day, I feel like I'm missing out on the whole world. I also have a lot of work to do. At least it has made reading papers easy. For my work with Serafim he wanted to me to read 2-3 papers, it's more like 6-7 at this point!