Synthetic Biology and Microsoft

So, back a year or so ago, I was a full-fledged grad student studying synthetic biology.

Well... it turns out Microsoft is also in on the synthetic biology game. And I believe they've done something similar to what I was researching. They've made a "synthetic biology programming language."

Check it out for yourself here.

The feeling is mutual, but it still hurts.

I regret to say that I'm not willing to supervise you any more on
research projects.

He laid it down in simple words

He laid it down in simple words...
I can't.
I just can't.
You've given me nothing.
Produced nothing.
There is no indication
Your undergrad...
Must be
Your personal life.
Not cut out.
Bad grades.
It's over if you get a C.
No funding.
No job this summer.
Get good grades and give me papers.
Then everything will be back on track...
He didn't disagree when I said I felt like a failure.

Paper woes

Turns out neither of my papers from last semester were accepted.

If you are interested in reading the latest one, you can find it here.

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!

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.

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.