andy reagan only the interesting stuff

Maturity: An inforgraphic

Inspired by Will Paradis, I found this that I had made last year for his birthday:

REU: 2 Week Update

Figured I'd take a quick time out to write about how the first two weeks of research have been going.  As I've mentioned before, I love my group and it's awesome that a lot of them are into active things and cool people.  Getting to know them all has been a blast.

For me, the first week and a half was somewhat slow, because I'm working on the same project that I had been: building a discrete model of iron metabolism.  This is something that I thought I had finished during the semester, and was somewhat surprised when I learned that there were four of that are going to spend a whole summer working on it.  We're going to work on expanding it though, and perhaps revisit the ODE model.  So, we've been learning about the biology involved in iron metabolism, and how to build a discrete mathematical framework to describe this biology.  Here is a brief overview of our goals from the google group that Julia Chifman, our research advisor, has set up:

Welcome to the Iron metabolism Project!

Computational systems biology has brought many new insights to cancer biology through the quantitative analysis of molecular networks.

The goal of this project is to apply a systems biology approach to the understanding of intracellular iron metabolism in normal breast epithelium and the changes the network undergoes as cells transition to malignancy.

Our ultimate goal is to identify key nodal points that may represent new therapeutic targets in the future

Here is a picture of the core network:

After learning about those things, and personally gaining an even better understanding of the biology, we learned about making truth tables. It has been truly amazing how working with a group, explaining things, and being able to dedicate  time to thinking through issues has really deepened my understanding of modelling as a whole, the biology involved, and how it comes together.

This past Friday, Julia came to Blacksburg from MBI, and we set to work on truth tables (the first step in building a mathematical model).  But, we had problems, in that the tables we made did lead to networks that had single components with one fixed point, which had been the goal.  Jim, Emily, and I worked to fix the tables, by trying different effects while Paul worked on a program to automate the process all Friday afternoon, but we didn't get anything to really work out.  Over the weekend, we didn't get a chance to work on it, but instead went over our presentation for this week, which is supposed to always be on Monday but it was pushed back to Tuesday.

Today I was really excited because long story short (omitting all of the math and biology), I got the tables to work.  Paul was still programming, and Emily and Jim had moved on to the ODE model after we'd tried a few more things that didn't work.  What I ended up doing was to throw out the algorithm that Reinhard had developed to make the polynomials continuous, and instead do that part by hand for more control in making the tables better reflect biology.  This led me to making many tables, and after one (massively, I got 35 components when we're trying for one, the most we've ever got) failed attempt, I even surprised myself when my second try worked perfectly.  It's paining me a little to not be able to explain the methods in text sentences, but basically we're looking at the effect of a handful of protiens on the Labile Iron Pool (an intracellular pool of loosely bound iron, available to metabolism (which it needs to be, but too large of an amount is reactive and harmful to cells, so it is tightly controlled...hence the entire metabolic network to achieve this)), and using truth tables to describe the effect that different combinations of the levels of these protiens have on LIP.  But, we're not considering what LIP's current state is, just using an algorithm to make the current state move continuously to the new state, and this is the algorithm I tossed out by adding LIP's current state as an input to it's future state directly, and made the tables make more sense biologically, and it all worked out. This means that the table has 81 entries, instead of 27, but it is definitely better.  Now, Julia and I are going to see what Reinhard thinks about all of this (which includes throwing out his own polynomial algebra paper's algorithm because it doesn't make sense biologically (according to me)).

So, I'm excited, feeling like I've done some real research, and hope to accomplish much much more in 9 more weeks!!

Rafting, golfing, mowing, eating, riding, running, drinking, driving to Blacksburg

Well, the title pretty much covers what I've been up to since kayaking on the 23rd w Sam and Dan.

Tuesday, May 24th

First things first, I got up early to mow the lawn so I'd have time to get a new phone before going disc golfing.  I ended up getting the Droid PRO, and so far (6/2) I love it.  Much faster than my old phone and the blackberry keyboard is really nice.  And the batteries last two days.

After I got the phone, headed to Zdanowskis and we were off to play disc golf. I drove, but it really only took 25min to get there, not as bad as I remember.  After falling as much as three strokes behind, my consistently gigantic drives overcame Dan and John, for a four-stroke win on the day.  It was a gorgeous day out in Jamesville, and I actually played the whole thing barefoot.  There were some dude playing that were smoking and let us play on, it was funny when he told me "I've never heard a barefoot dude turn down a hit."

For dinner, I ate some delicious blackened talapia that my Dad aand Mom made, before going out for all you can eat wing night at Quaker Steak and Lube.  I drove again, and it was cool seeing people there from high school.  I didn't get all I could eat wings, but did eat an Atomic wing, rated at 150,000 SHU.

Wednesday

After spending about two hours deciding what we could all do together, my Mom, Bro, and I set out to play some mini-golf and get me a bread machine.  My Mom had one of those high school fundraiser discount cards, and it's actually a good deal at Fairmont Glen, which is where we went.  A single game pass is $7, and a three game pass is $14, and her discount was a BOGO three game pass.  So we got two three game passes, and a single game pass for the price of three single game passes!

We had the place to ourself, and its a really nice mini-golf place.  It's in the middle of busy commercial Fairmont, but set down into a quiet gully next to a stream.  Despite my Mom's four hole-in-ones, my consistent twos and threes (my only scores) were enough for an 11-point victory over Bro and Mom, who tied at 9 over par.   The "19th hole" is this thing you putt into so they get the ball back, that is a ramp the ball shoots off of, and it can go into the eyes, nose, mouth, or below a clown's face entirely. The eyes are a 4-stroke deduction, the mouth 2-strokes, and the nose is a free pizza and free game.  My competition swung away to no avail, and I used my superior patience and putt putt skill to send the ball directly into the nose!

I won a free game, pizza, bowling, an ice cream which I got right away and was delicious, wings, and some other stuff that I can't even remember.  Pretty sweet! From putt putt we went to Ra-Lins and got a bread machine, which has by 6/2 made four delicious loafs of honey whole wheat bread.  And on the way back we stopped for the free pizza, which my brother, Mom, and I split.

And then, I talked my Mom into going running with me at the park, which was great.  I beat up the soles of my feet wearing the Vibrams for 6 miles on cinder, but with some ice the feet were ready to go again.  It was the first time that I got to use my new Garmin Forerunner 310XT, and it's awesome.  Haven't had the slightest issue with it yet, which is soo amazing after being used to troubleshooting the powertap.  It transfers wirelessly to the computer, and auto-uploads the data, so after I finish an activity and set the watch next to my computer, it's uploaded by the time I'm done with a shower.  Here's the first run:

Thursday

I talked my Mom into rafting the Ninemile Creek, an idea that I'd heard about Kyle B, Tyler M, and Brian W attempting back in high school, and didn't get to do with Sam and Dan.  Well, it was good that Sam, Dan, and I stuck to Otisco Lake, because it was quite the adventure.

The creek was barely navigable, with huge trees down every hundred feet or so, making us portage our raft.  The whole trip covered 9 miles, which brought us only to Marcellus Park, and took 7.5 hours. It wasn't long before we ran into a huge pricker bush, and I got my arm all scratched up, and we put a slow leak into the raft.  For a while, I would stop and inflate every little bit just so we could keep going.  Eventually, we found a metal fishing boat that had been washed up ashore, and commandeered the vessel.  That allowed us to cruise on open water, because in a deflated raft and little current, it was slow going.  After many more miles, and the combined stubbornness of my Mom and I, we portaged the boat again and again before finally making it to park.  I was parched, and probably couldn't have gone too much farther without water, on such a hot day. I'm glad that we did it, and it'll definitely be an adventure to remember for my Mom and I.

Friday

Short bike ride, out downtown.

Saturday

Stuck around to maybe go up to Del's camp the next day, spend another day with the Fam, and go out with Dan and Dan for the night. Also went for a run: http://connect.garmin.com/activity/88592596

Sunday

Drove to BBurg, ran to the top of Brush Mtn and hammocked for the night. Here's the run link: http://connect.garmin.com/activity/89015500

Monday

Up really early, moved in! And of course, went for a ride: http://connect.garmin.com/activity/89110266