Moving

Moving...

Can't talk...

*runs and starts packing*

Thoughts on Gradschool (Part 4 of Many)

Events of late have made me ponder my existence as a graduate student at the University of Minnesota. In my opinion, I have been failing most splendidly at adopting the life of a grad student. Granted, the flooding in my office and other events in my life have not helped, but I can't use that as an excuse. I must be willing to devote myself entirely to my research. I must be willing to spend all day, every day, in my office, at my computer, working. Thinking about new ideas... developing new software... forgetting about friends and fun and food.

For the first month or so of this semester, I have rarely spent a full day in my office. A full day to me involves coming in during the morning, before a first class, and staying until at least dinner time. Last semester, I was in my office (not including class time) from approximately 9 or 10 am to 9 or 10 pm. Full day, me working... not necessarily enjoyable, but that was mostly because I'd forget to bring food.

I dunno. Is this a sign? Do I really not feel attached to my work? Do I even belong in graduate school? My classes frustrate me, my adviser pisses me off, my research is going nowhere... *sigh*

I apologize to blog readers for this rant.

I need to get my head on straight and decide what the fuck I am doing. And soon...

Thoughts on Grad School (Part 3 of Many)

*drum roll*

Introducing....

THE INVISIBLE ADVISER!

*symbol crash*

...ABLE TO ADVISE GRAD STUDENTS WITHOUT THEM EVER SETTING FOOT INSIDE HIS OFFICE!

*symbol crash*

...DROPPING DOUGLAS ADAMS REFERENCES WITHOUT BATTING AN EYE!

*begins kicking drums*

...CAPABLE ONLY OF COMMENTING ON FULL LaTeX DOCUMENTS WITH ENOUGH MERIT TO BE PUBLISHED!

*a foot goes through the bass drum*

...AGREEING TO GROUP MEETINGS ONLY WHEN AN ADVISEE HAS PROVEN TO HAVE IDEAS OF INTELLECTUAL MERIT AND IS WILLING TO PRESENT THEM!

*symbols crash to the floor*

...FAILING TO ADVISE. PERIOD!

"To paraphrase Douglas Adams, you are not merely "professional thinkers"; you are research assistants -- paid to
think, yes, but also to translate these thoughts into publishable pages of LaTeX."

Thoughts on Gradschool (Part 2 of Many)

It is currently 3pm CST. I just sat for HALF AN HOUR in the bowels of Walter library, waiting for my adviser to show up for our scheduled weekly meeting. No emails, no note, no phone call... Instead I plunked around on the internet in the weird reception area near his temporary office. Several weird looks were passed around and I eventually left, laptop in hand, head down.

I walked the stretch of half frozen pavement from Walter to the still-damaged EE/CSci building and made my way to the sixth floor. As soon as I sat at my computer, the professor that runs the lab in which I am temporarily stationed came in. He asked me about if I was going to switch advisers.

"If you were to assign a percentage to how likely you are going to switch advisers, what would it be?"

Probability. One of the many banes of my existence. Therefore, I feel I must make a pros and cons list, weight them accordingly, and come up with a real solid percentage estimate. After all, I am a scientist of sorts.

Unfortunately, I have several options. These include:

• Continue to be a part of my adviser's lab and get a Ph.D.
• Continue to be a part of my adviser's lab and get a Masters
• Switch to another lab and get a Ph.D.
• Switch to another lab and get a Masters
• Transfer to Penn State and get a Ph.D.
• Transfer to Penn State and get a Masters
  
• Transfer to Penn State after getting a Masters and get a Ph.D.

Damn.

Beck - Walls

I've seen Beck perform live... in fact, I saw him live before I was really into any of his work. This song is from the album Modern Guilt, which I believe is his most recent album. This song has been stuck in my head all day. I just love the instrumentation. Lyrics are pretty good too. Enjoy.



Beck- Walls

Some days we get a thrill in our brains
Some days it turns into malaise
You see your face in the veneer
Reflected on the surface of fear
Because you know we're better than that
But some days we're worse than you can imagine
And how am I supposed to live with that
With all these train wrecks coming at random

Hey what are you gonna do
When those walls are falling down
Falling down on you

Hey what are you gonna do
When those walls are falling down
Falling down on you

You got warheads stacked in the kitchen
You treat distraction like it's a religion
With a rattlesnake step in your rhythm
We do the best with the souls we've been given
Because you know we're nothing special to them
We're going some place they've already been
Trying to make sense of what they call wisdom
And this riff raff ain't laughing with them

Hey what are you gonna do
When those walls are falling down
Falling down on you

Hey what are you gonna do
When those walls are falling down
Falling down on you

Birthday, etc, etc.

Today is Valentine's Day. Have you had your allotted amount of chocolate today? I know I have. However, mine wasn't in the form of candies, but birthday cake.

That's right, it was my birthday two days ago. My mother got me the most delicious cake possible. Chocolate cake with bananas and cream cheese icing, all topped with ganache and fancy lettering. She also announced that she got me a gazelle (yes one of those horrible work out machines sold on the teevee) as a birthday present, but it has not come yet. Cake and work out machinery... oh mom.

I've had enough cake in the last few days. Tara, Whitney, and I baked six cakes on Tuesday. That's right six. Six boxes of cake mix, six pans, sick minds. Most people have seen the rainbow cake instructions that have been floating around the internet. I decided that was what I wanted to make. Three cakes were made with just coloring, and three cakes were made with coloring AND gelatin. Both kinds of cake were decidedly amazing. The gelatin cake did not have a cake-like consistency upon baking, but still was like eating gummy fruity pebbles. Mmm.

It was a hit at my Star Wars role playing group Thursday night. I supplied two cakes and a backpack full of hard liquor... both went over well. All-in-all, a very good birthday.

Hopefully my 24th year on the planet will be an eventful one. I'm going to be cliche and make a list of the things I accomplished in my 23rd year:

• Graduated
• Quit my job
• Saw Andrew Bird and Tim and Eric
  
• Said goodbye to my grandpa
• Moved (twice)
• Got my ears pierced
• Went on a diet (successfully)
• Stopped playing WoW (and haven't picked it back up)
• Started grad school
• Broke up with Adam
• Went to a dance club (verdict: awful)
• Visited the power-spot
• Helped redecorate two rooms at my parents house
• ... can't think of any more right now

Hopefully my list will be better this time around.

Andrew Bird - The Happy Birthday Song

Had to post it. The best birthday song ever.



The Happy Birthday Song:

when i wake up
in the morning,
pour the coffee,
and i read the paper,
and i slowly,
and so softly,
i do the dishes.
i feed the fishes.
sing me happy birthday
sing it like it's going to be your last day.
like it's hallelujah,
don't let it just pass on through ya
it's a giant and long cliché,
and that's why i want you to sing it anyway
sing me happy birthday
'cause hell, what's it all about?

sing me happy birthday,
happy birthday.
it's gonna be your last day,
gonna be your last day.

sing me happy birthday,
happy birthday,
like it's going to be,
going to be your last day.

the last instant message

(2:31:55 PM)
you took everything you wanted,
a roommate,
the circle of friends of a pervert you previously hated,
and you refused to even explain what was going on
for months
after you told me you hated me
and didn't want to talk,
and now you are the one with issues?

---

I gave you everything you wanted,
a best friend,
a confidant,
a whipping post,
I took it all in stride for as long as I could
and then I snapped.
For years, I tried to reconcile my feelings
I tried to convince myself that you were a good boyfriend
and somehow I was the bad one.
I don't want to talk.
We both have a lot of healing to do.

---

you have no conscience
I am proud

---

I don't love you anymore
I am happy.

Devotchka - The Clockwise Witness

I keep hearing this song on The Current. It sounds a lot like Andrew Bird, who is probably my favorite artist besides The Beatles. I might have to buy this album.




The Clockwise Witness:

It don't look right
In broad day light
It don't feel right
to me
If you win the rat race
If you come in first place
Then a rat is all you will be

How long will this take?
How long must I wait?
My heart is sinking
What were we thinking?
I can't fake this anymore

In this moment
of atonement
can you ever forgive me?
Is there something hovering?
It seems to be governing
everything once dear to me

Oh and how long........

On my walk through campus this morning

Walking through the city after a first winter's rain.
Snowbanks are all that remain of the once superfluous drifts of white.
Winter's cache is now visible after the ranks have receded
Socks, pens, pamphlets, and various undesirables
Miscellany washed up on the banks with the ebb and tide of snow.
Autumn's leaves make a special tea in the puddles and cracks
Brown from their essence and the dirt and salt that once encased the ground.
The world begins to breathe again,
Exhaling the familiar putrid odors of spring.
Even though it is only February,
I can feel the clutch of winter loosening
And the joy of summer warm my soul.

Writing my Thesis

I had a meeting today. It was one of the usual meetings... you know, the kind where everybody talks and nobody listens. My adviser, nodding with his usual glazed-over glances and deciding certain things were amazing ideas and others are crap... Immediately assuming that our most recent paper was rejected because we did not pitch it as compiler theory...

After some banter, he looked at me and said: You need to start writing your thesis.

I'm sure the expression on my face noticeably changed. My eyes widened and my mouth drew back slightly in a smirk. I swallowed the lump in my throat, leaned back in my very comfortable desk chair and said "Yeah, I suppose I should get started on that."

He wants me to write section two of my thesis... not the sparkly, pitch that is section one (in which you try to convince the reader that your research really is valid and interesting). Section 2: The background material... the stuff that perhaps you didn't research directly, but is needed to understand the meat (sections three through infinity) of your thesis. Basically, all of the things I have read and done since September, condensed into one place; explained concisely and succinctly in black and white with as little bloodshed as possible.

Oh
My
God
.

I suppose it is a good idea. I have been striving towards being able to explain all of the prior research in this area well enough so that I can get ANYONE to understand it (even readers of this blog... if you exist). So, over the next month or so, I plan on writing SECTION TWO of my thesis, which feels incredibly pompous without a section one.

I hope to write some blog entries on the things I feel are necessary to this magical section two. These include:

-Synthetic Biology overview (kinda done)
-Simulating biochemistry (kinda done)
-Computing with biochemistry
-Rate independence
-Iterative/Clocked computation
-Technology mapping (depending on how far we get with it this semester)

Then again... If I were only doing my masters right now, writing section two would be like writing the entirety of my thesis. Either way, this will be beneficial to my general understanding and progress towards a degree.

*sigh* Onwards! Upwards! And not towards the guillotine!

Little Joy: Next Time Around

Had to post a song today. Little Joy is one of the side projects of The Strokes members. This is the side product of Strokes drummer Fabrizio Moretti. He dated Drew Barrymore, you know. I think that Little Joy is pretty fab. :-p




Next Time Around:

One to many goals
The measure of your worth
Can sink your weight in gold
Sat by the ivory sail
The further out you look
The further out you'll be

It's not enough to set the curve
With nothing ventured, nothing learned
The words I've said again, still die

I'll belong to you, it's how it's meant to be

Settle on your own
Sweeping dust from stone
With the letter "ohm"
Back where the hours roam
The simplest things they buy the thrill
Just by noticing at will

It's not enough to set the turn
With nothing ventured nothing learned
It's how it's always been

(In Portuguese)
E onde a sorte ha de te levar, saiba o caminho e o fim mais que chegar
E quiera o dia ser, gentil a tua mao, aberta pra quem e

I'll belong to you, it's how it's meant to be
It's how it's always been

Simulation of Biochemical Reactions

In 1977, Daniel T. Gillespie published the paper that in essence starts the work in my field. Titled "Exact stochastic simulation of coupled chemical reactions" this work lays the foundation for stochastically simulating chemistry. In a biochemical system, reactions occur at random. In order to properly model this system, we must express it in terms of probabilities. The Stochastic Simulation Algorithm, or SSA, is a simulation technique that involves concepts of Monte Carlo simulation and Markov Chains.

In essence, a set of reactions is expressed as matrix of probabilities. Each reaction is assigned a probability, based on the number of reactants available, the number required for the reaction, and the rate of the reaction. These probabilities are lined up on the zero to one interval. Then, a random number generator is used to "select" which reaction fires. The process repeats until an end condition or when all reactions can no longer occur. Often, the reactions for a system are simulated many times to get a "mean" response.

The formulas for the probability of a reaction occurring is as follows:

We calculate the alpha value for each reaction. Using these values, we can determine the probabilities that each reaction will fire. This system gets very complicated with large numbers of reactants and reactions.

Next blog entry about my research: I will give a basic example using this method.

My First "LAN"

I digress from the research and grad school themed posts to bring you one STRAIGHT OUT OF FUN LAND. Last night, I had an epic evening.

(Random thought: You know how you can say "evar" and put some sort of internet spin on the meaning of the word ever? I think epic has started to become overused and we need a new spelling/saying of it as well. Maybe EPUC or something.)

After a very long afternoon chasing keys (long story, won't go into it), I finally embarked on my role-playing, taco-eating, mountain dew-drinking, zombie-killing evening. Nobody reads my blog, but okay, I will admit it. I am a nerd. There, I said it. I've recently joined a tabletop role playing game known as Star Wars Saga Edition (or SWSE) for short. Think of it as a Star Wars themed Dungeons and Dragons. We role dice and talk about star wars and it's pretty cool. There are usually tacos involved as there is a Taco Bell near the house we generally play at. All-in-all, it is good times.

I've also been playing some video games with the guys involved in SWSE. One of these video games is Left 4 Dead. Here is a brief synopsis: Zombie invasion. You and three other players (Yes this is where the 4 comes from) must shoot and esplode your way through several levels of zombies before you can meet up with the rescue convoy. There are general "horde" zombies, and there are special zombies. These are hunters, smokers, tanks, boomers, and witches. These throw in more interesting situations than just BANG BANG BANG KILL ZOMBIES RAWR.

Anyway, this is a game created by Valve. There are several achievements you can unlock, one called ZOMBIE GENOCIDEST in which you must kill 53,595 zombies. This is a cumulative number and can be achieved over weeks or months of play. From a total zombie kill number of approximately 22,000, he was bet that he couldn't reach the magical 53,000 number in 24 hours. So, after SWSE, we travelled back to Moose's apartment and got ready for a VERY long day. We started playing at about 1am and basically played for 8 hours straight with a very specific strategy, running the starting area of one level OVER AND OVER again. I would not fire shots, and he would basically get all of the shots and kills from explosives. After lots of mountain dew and caffiene, by 9:30am, he had over 51,000 kills. EPUC.

At 9:30, I brought Moose to class and we called it "a night." I crawled into my bed at about 11am, but have been unable to sleep due to random techno music coming from one of the neighbors.

Perhaps I'll post about stochastic simulation later today if I still cannot sleep.

"Adverntures in Synthetic Biology"

For anyone that is interested, there exists a comic that talks about the field of Synthetic Biology. It can be found here on the Nature website. The corresponding article is also very helpful in understanding the field. In fact, it was one of my references on my NSF Fellowship application.

The term Synthetic Biology is generally used when it applies to chemists, biologists, geneticists, and other lab grunts working on creating synthetic biological components. This means that they are either changing the DNA of bacteria or creating man-made proteins or some other process that requires a wet lab and advanced knowledge in genetics/biology/chemistry. These Synthetic Biologists take their knowledge in biology and use it to create new functionality.

My research is also lumped into the realm of synthetic biology, and we do the exact opposite. We take our knowledge of computing and other fields and use it to create models for new functionality. I am *not* a biologist, chemist, or geneticist. My knowledge only goes a small way beyond the intro classes I was required to take in my undergrad degree. The papers we write don't claim we know any of the biochemistry behind the research, but propose that the long-standing models used are sufficient proof that our computation would work in vivo.

The third side of Synthetic Biology runs right in the middle. There are researchers at MIT and other places that work on creating repositories of standard parts. This could be a set of reactions or a chain of DNA for E.Coli that performs a known function and could theoretically be used in another design. A Synthetic Biologist could feasibly go to one of these databases and pick the correct part for their project, "plug it in," and away they go.

Hopefully that made some sense. I'll go into detail about my research in specific later. Feel free to add comments if there are questions.

Adviser Meeting

I've come to realize a few things about my adviser since I met him back in Spring 08.

• He's a night owl. This man has a schedule that is approximately 7-8 hours behind everyone elses. He would need a night job if he was not an intellectual.
• He's a procrastinator. Papers and proposals get put off until the last minute. And, as my dad would say, at the last minute, he makes sure it really is the last minute. If it isn't, resume procrastination.
  
• He has idyllic visions for our research together. He believes that I can get the majority of the work needed for my dissertation done by May.
• He shifts from optimism to pessimism at the drop of a pin. Paper writing has been particularly manic as he decides the paper is amazing/crap from day to day.
• He is not my style. I would rather work with someone who is a "planner." I'd rather have things ready to go ahead of time than barely on time.

At my meeting, we talked about the following things: explaining our contributions better, mapping a yeast library, future papers, module locking, indicator molecules, classifying what we know, implementing other functions in verilog, parsing, web interfaces, Chad & Megan (whom I've never met), level sensitivity and consuming, upcoming conferences, stochastic modules, experimental labs, research brochures, and BICB people.

The notes I scribbled in my notebook are essentially that list. I gathered that he wants me to do... research... about stuff... and write papers... and be a general wreck for another three months...

I've got a lot on my plate for the upcoming semester... and I actually need to pass/finish my classes this time. Keeping a 3.3GPA in grad school is going to be harder than I thought.

If I have the chance, I'm going to write an overview of my research as a series of blog posts this week. It might help me in the long run. Hopefully I can explain it properly.

Thoughts on Gradschool (Part 1 of Many)

I write this lab from the "top" floor of the Electrical Engineering and Computer Science building. I am sitting alone in a lab I first entered approximately an hour ago. I now have a key to this lab. In this lab, I have a desk, a chair, and a computer.

I am here for several reasons. The most obvious is the fact that my normal lab/office/room-where-I-spend-my-time is in SHAMBLES. Okay, that's a bit of an exaggeration... but the point is that I can no longer spend my time in said room. Why? Because sometime on Thursday night, a pipe burst in the penthouse (7th floor) of the EE/CSci building, sending tendrils of water through the North side of the building. Floors one through five experienced extensive damage. My office on the fourth floor has damage to the carpetting and walls. This damage is apparently minor compared to some of the damage experienced in other parts of the building. I would post pictures, but venturing in these areas requires an escort... and the escort certainly won't let me wander.

Funny part is, most of the damage is exclusive to the electrical engineering side of the building. This is exemplified by the following piece of evidence. On my escorted way to my office this morning, I walked past the EE and CSci department offices. These offices are neighbors. They say hi and exchange small talk on a regular basis. Walking past the CSci office, I noticed two differences: There was only one lady in my immediate vision, and there was a fan blowing on the carpetting. However, walking past the EE office, I noticed that it was no longer an office, but an empty room in which even the carpetting and ceiling panels had been removed.

Ok, returning from that birdwalk, I will now list another reason why I am in this lab. The long and short of it is that I am being "encouraged" to join this lab group. The professor that runs this lab is involved in the BICB (Biomedical Informatics and Computational Biology) program (more on BICB later). He is an expert in databases and would be a very good fit in an adviser for me. This may be the first step to becoming one of his advisees.

I will take these changes in stride. Chances are, I will be a member of this lab for at least a week, perhaps more. The knowledge of the CSci peoples in this lab would be invaluable for my research. This is the kind of knowledge that my current adviser lacks.

THIS IS THE KIND OF KNOWLEDGE THAT I NEED IF I'M GOING TO MAKE IT OUT OF GRAD SCHOOL BY THE TIME I'M THIRTY.

Anyway, the events of late will definitely make me evaluate my situation. Hopefully my next post will be about my actual research topics.

Late-night Minneapolis in February

Excuse the shaky image... my camera takes horrible night shots. The picture above is from the back door of my apartment. The new 35W bridge is in this picture. Instead of the normal royal blue, the bridge is a beautiful amethyst purple (Perhaps for the first day of February?). Behind that is the Minneapolis skyline. I spend time staring at this view almost every night.

Minneapolis is an interesting place. It has been my home for four years. Hopefully I will post some stories about Minneapolis later.