Cheese on cheese with a side of cheese, please.

Here I sit. I'm eating crackers that I bought at the lunch cart downstairs. They are cheese crackers with cheese spread between them. Pretty tasty. Pretty bad for me. They are also very hard to eat quietly. *CRUNCH CRUNCH CRUNCH CRUNCH*

If I would have bought food when I intended to, maybe I would have gotten a good salad or something. Unfortunately, I ran in to my adviser today. I would say this is the first time I've seen him in almost a month. He was wearing his usual leather jacket. The sleeves are slightly too long and he always hangs his arms at his side like they do not work. He looked tired. Hell, he always looks tired. He wants to meet with me. I said sure...

What am I going to say?! I need a brainstorming session. I need... ugh. I need sleep. And maybe more crackers.

In the mean time, I will continue to work on my math exam. I'm debating whether or not I should try to catch the professor in his office today. There is one question that is giving me particular difficulty... and I think everyone is having the same troubles. I'm going to be up all night. Maybe I'll actually go to Al's Breakfast in the morning. One things for sure, the meal I have there won't be as delectably cheesy as these crackers. Unless you can breed cheese and get eggs from it.

Ok, I'm done talking about crackers. I promise.

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!

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.