Indomitable Spirit

29-04-2008 Notes

kmdaily — Tue, 29 Apr 2008 22:54:24 +0000

Meeting with waterman

Discussed Wnt signaling pathway
Wnt is ligand, binds to receptor (Frizzled, 7-pass), activates cascading pathway
One part near the end of this are TCF family of DNA binding proteins, have C-terminal domain that binds beta-catenin (activator) as well as HMG-NLS domain
Beta-catenin accumulation → constitutively active TCFs → abberant regulation
Regulate (by activation at least) cell cycle proteins, what else?
Particular member of the family (TCF1) has extra DNA binding domain (other than HMG group that all in the family share) in E-tail (called C-clamp)
Does having C-clamp allow it to bind to other targets, or more strongly to some known targets?
For some reason, mutations show up first (often) in intestines/colon
Microarray performed by Waterman lab (unpublished) shows genes differentially expressed in cancer cells with different forms of TCF expressed (one normal, one missing beta-catenin domain), both with C-clamp
Look at expression difference, expect constitutively active version w/o B-cat domain to have genes increased in activity

2008-04-28

kmdaily — Mon, 28 Apr 2008 15:32:32 +0000

Xiaohui’s class

Went over phastcons scoring method

One state models phylogenetic tree of conserved regions (with different states for codon position)

One state models non-conserved regions (multiple types of background

AIML talk

Discussion of modeling txn reaction, metabolic, etc. networks

Using machine learning (SVM, kernels) to get edges in the matrices

ODES governing these systems

Waterman project

Updated graph image generation in R of stats about motifs, genes

Downloaded PhastCons scores and RP scores for the new motif Nate described (more flexibility in 3′ end - instead of RCCG)

Generated stats images for original motifs

Yay warm weather!

kmdaily — Fri, 16 Feb 2007 21:19:31 +0000

Man, it sucks to be a Hoosier, given that its -20 degrees and we lost to Purdue. Unless your in California, then its only half as bad, because its 83 degrees right now. Wearing jeans today was a bad choice.

TVs and porn stars

kmdaily — Mon, 12 Feb 2007 23:30:49 +0000

So the other day, I bought a TV…from an Internet porn star. I responded to an ad on Craigslist for a TV/DVD player for a good price. The responding email came from the domain www.beautydestroyed.com (NSFW)…and it indeed was her. Unfortunately the tuner was not working, so I got it for even cheaper. Only in California…

Colts rule and being injured sucks

kmdaily — Sat, 10 Feb 2007 21:38:57 +0000

So I sprained my ankle last Saturday, and its no fun. It’s really hard to not be able to do the things I’m used to - just basic tasks getting around the apartment, and especially not being able to work out! No Tae Kwon Do for a couple weeks, no basketball, no running…I’m getting really restless! At least I had an exam last week, so spent lots of time studying! But Super Bowl Sunday was still awesome, a keg of beer does wonders for injuries and ailments. Yay Indiana! Be sure to check out my photos soon, I’ll have some of the Super Bowl party soon. What a success that was! We set up Ramzi’s apartment like a sports bar - had a projector and 5 other TV’s around the apartment, foosball, grilled food, and lots of beer! Lots of friends made it, and when the Colts won my friend Chayan poured a beer on my head! We also played a popular Swedish game called Kubb. What fun!

More Hoosier goodness - the 24th ranked Indiana Hoosiers just beat Illinois today! Go IU! I got to see the end of the game after #2 UCLA lost to the Mountaineers. Anyways, thats enough for now!

Another quarter begins…

kmdaily — Sat, 13 Jan 2007 05:26:01 +0000

and I already feel behind. I’m taking two real classes this time, Algorithm Design and Probabilistic Learning. The PL course is already tough, starting with the first homework…I thought I knew something about probability models, but apparently not. So I’m getting reaquainted rather quickly. It is an exciting class though, and the instructor seems really good and well organized. Other than that, I’m playing tennis, doing TKD, and trying to get back into shape. I’ve started running more, as well as increasing my core workout. I’ve started at a 7 minute mile, and trying to get that down to 6:30 before the end of the month. The tennis class is good as well, lots of challenging players taking it.

I also went skiing for the first time over Winter Break, that was an experience! Thanks Melissa for trying to teach me, and staying somewhat patient. I can at least get down the mountain in one piece!

Not much else going on, hoping to find some time to go ski again, but need to get some winter clothes first!

Research is going, although it has been stalled over break. Going to start in earnest now!

Edit: Why is it warmer in Indiana than in SoCal right now?!?! WTF, mate…

long update

kmdaily — Fri, 27 Oct 2006 17:32:51 +0000

Don’t worry, I am not on fire. That is 100 miles to the northeast of me. However, The western winds have brought the smoke here, so the air smells like wood smoke, and its very hazy.

I work in the lab of Pierre Baldi, a prominent computer scientist working on bioinformatics and chemical informatics projects. I am working with a sub group of this lab on the system called ChemDB, which is a database of ~4 milliion chemical structures. Right now, I am working on comparing different similarity measures of molecules - if you have two molecules, how do you determine how similar they are? This project is well underway, and I have some results. The project I have lined up next is to examine some data structures to support fast searching of the database.

My advisor has ~15 students working under him (that’s a lot!) Some of them that I work/hang out with frequently are Ramzi (from Lebanon) and Chayan (from Albuquerque). Ramzi’s girlfriend Kristina (from Sweden) is also around a lot. Some other people I’ve met work in machine learning such as Lars (from Deutschland), Dave, and Todd.

I just finished my 5-week surfing class yesterday! I’ve learned how to maneuver on the board, and can stand up and go straight on my own waves. Surfing is a lot of fun, but it will have to take the backseat for a while, because I don’t have a board or a wetsuit, and its getting a little cold for going without. I met a lot of great people through the class, we all went out to a bar last night after the class. Two of the instructors are brothers about my age who have been teaching surfing for 10 years. Two of the students (Rupert and Joe) are from the London area, and they brought with them some other British friends to the bar. There is a girl from Spain (Maria), and one other girl (Alexandra) that I know. The other people in the class didn’t really stick around to party! Hopefully we will get together again to surf (or drink!)

I am still doing Tae Kwon Do, right now through a class through the Rec Center at UCI. It is going well, although unfortunately more geared toward sparring than I would like. I am really enjoying learning the sport aspect of TKD, but I miss the traditional part that I know from IUTKD (the people aren’t as cool either, but they are awesome too!) I did start learning the Tae Guk forms though, so I will have something to teach you IUTKD’ers when I come back! One of the girls in the class is also supposed to teach me Hap Ki Do forms (from Jin Pal Hap Ki Do) There are about 15 people in the class, with 1/2 being black belts. However, about 1/2 of the black belts haven’t trained for over 5 years and are just coming back. The other half are really good and have been training for an average of 10 years. I am also involved (partly) in getting a TKD sparring club up and running. I’ll probably end up as the webmaster! Go figure. Our goal is to join the Pac West Tae Kwon Do Conference and have a competitive team. So, we are trying to recruit (there have to be people with a 70% Asian population on campus!) and find a coach.

I have also started training in Iaido, the Japanese art of simultaneously drawing and cutting with the samurai sword. Check out a video here. This is much different than the physically strenous activity of TKD, and is much more internal. A short explanation is this art is like Wild West dueling: two people with swords, whoever draws and cuts faster walks away, and the other person is dead. The stresses in this art are focus and concentration, etiquette (lapses of this are the main reason for getting into a duel in the first place!), posture, and body control. The instructor is David Otaguro, who has been practicing for about 15 years. The style of Iaido we do is Suio-ryu Iaido, one of the oldest schools of Iaido in existence, and one of the Japanese martial arts known as Koryu, or ancient arts. This means there are written, verified records of the art over a ~~period of at least 500~~ (Thanks David!) lot of years. The art of Suio-ryu Iaido was developed in the early 17th century. According to our instructor, there are only about 700 people in the world practicing this art, and UCI has the largest group in the United States. The head of the art is Katsuse Yoshimitsu Kagehiro, who has come to UCI to teach as well as groups of students going to Japan to learn from him.

So I think this is enough of an update for now!

Long overdue update

kmdaily — Wed, 11 Oct 2006 08:00:41 +0000

So, a quick message for the people that actually read my blog - I’ll update it soon! For now, check out my new pictures at http://picasaweb.google.com/kmdaily. I’ll summarize them for you later!

Maria sharapova commercial

kmdaily — Thu, 31 Aug 2006 19:01:52 +0000

Commercial being aired during the US Open (Oh So Funny!) with the song “I’m So Pretty” from West Side Story:

http://www.youtube.com/watch?v=P-_CgWugraA

Woah….

kmdaily — Thu, 31 Aug 2006 18:30:30 +0000

I just found out that in the community room at my apartment complex we have a 70″ Sony HD Television….wow. I am watching US Open in high def, and it is awesome. I don’t think I’ll be buying a TV anytime soon. I am reserving this room for every Colts game that I can get out here…which is frustrating. It turns out we have a Fox Sports Grill restaurant, but they won’t know until tomorrow if they will carry the game vs. the Bengals. Otherwise I will be calling every sports bar around to find the game.

Otherwise, things are good, getting situated just fine. I got a bunch of furniture for my room, check out the pictues page. I’ll be getting my computer monitor (19″ flat widescreen) sometime today. Super excited, I haven’t had a desktop monitor in over a year!

I’ve been working out too, at the beach. Early mornings are nice, the beach opens at 6 am, and I can drive and park about a 5 minute walk from the beach. Since I’m old and go to sleep really early, I can get up around then to go! Practicing forms on the beach is very serene and peaceful, and a good workout on the legs and balance as well. I need to start working out the upper body though if I want to be able to surf!

Next week I start “working”. I’ll only be taking two classes (Research Seminar in Informatics, and Machine Learning), but these don’t start until September 22. Most of my time will be focused on research. I’m going to start my reading list of papers, books, etc. to start narrowing down a research topic, and meet with my professor (Pierre Baldi) to discuss.

I’ll also be in a Tae Kwon Do class, which meets just as IUTKD Club is finishing up (4:00-5:20 PST). So it will feel like I’m there, just a little late. Check out the class and the video about it and the instructor (he’s pretty awesome). Hopefully I’ll also be able to take the Surfing class!

Anyways, I’m going to watch a little more US Open tennis then run some errands on campus.