andy reagan only the interesting stuff

Poconos!

I took an invitation from David Henry to come down and spend the final two days of my Thanksgiving break (I ought to rename is Thanksgiving "adventure") exploring where he grew up: in the woods in the Pocono Lake Preserve. David's Dad, John, is the manager of the Pocono Lake Preserve and that means that they live on the preserve and have access to / maintain / build some awesome trails around the lake. It's a beautiful area, and I really enjoyed my stay there. His house is nice, and I actually slept under the rock wall in David's room. Yeah, for real.

Turns out that David is only 3 hours away from Syracuse which is really cool, and it's right on my way down 81 to Tech, so it was a chance to break up my drive as well. On Saturday after I got there at noon, we ate lunch, went on a mountain bike ride, watched the virginia tech football game while eating more delicious leftover thanksgiving food, and then hung out before going to bed. The ride was great, we got muddy and spent a lot of time not necessarily riding, but drinking out of natural springs, fixing suspension bridges, riding over logs and clearing trees from the trail. It was sweet.

There are some gorgeous views of the lake along the mountain bike trails, and that was cool. The riding there is awesome. I need to work on getting over trees, but I'm sure a few more rides that include downed trees all over and I'd really have the hang of it (was getting much better after two rides). David broke out some crazy trials mode, that I've only imagined seeing people do on the trails, and that was really amazing.

To best avoid the crazy thanksgiving traffic down 81 (it took Stephanie 7+ hours to make a 4hr drive back to Tech on Sunday), David and I opted to leave much later, and it worked! We hit about 20 minutes of traffic in PA, that was just congestion from lots of cars, but it was smooth sailing in VA!! Pretty sweet. Since we weren't leaving until 4, we had all day to go out on an even more epic mountain bike ride too! We rode pretty hard for like 3 hours, circumnavigating the lake. It was awesome, we got covered in mud, and hit like most of the trails out there. Could ride for days in those woods.

Not really saying half of what I have to say here, but it was a really awesome couple days. And thanks again to David's parents John and Amy for the meals and having me stay!

An Introduction to LaTeX

Personally caving under Dr. Brown's requirement to type math homework, after spending too many late nights fighting with equation editor in MS Word, I learned and am now a huge fan of LaTeX. It's what mathematicians write papers (and books) in, and makes typing math homework a breeze. It is usually quicker than writing homework by hand, once you get the hang of it.

The learning curve was somewhat harsh to me, so without too much help on the interwebs, I'm here to help. I've made a short video intro to LaTeX that should hopefully get you rolling on your first homework assignment in 15 minutes.

1. Download and install MikTeX: http://lmgtfy.com/?q=download+miktex
2. Download and install WinShell (or equivalent): http://lmgtfy.com/?q=download+winshell
3. Download this demo file.
4. Watch this video!!

REU Conclusions, Being home and the Great Race

The same day as the aforementioned Draper Mile marked the conclusion of the MSSB REU which was my job for the summer, and I miss everyone in the program but am excited as well for the opportunity to continue this research.  I took the two weeks I had at the end of summer, and went home.  This year for the Great Race, my Mom was the captain of Team Reagan, and we recorded the best race I've ever been in, by nearly 7 minutes.  Now I'm back at school, and have 20 minutes to burn before a class so here goes.

REU Conclusions

This past summer, if you hadn't heard, I spent doing mathematical biology researching at the Virginia Bioinformatics Institute, located on Virginia Tech campus.  The program was a Research Experience for Undergraduates, specifically in Modeling and Simulation of Systems Biology and was sponsored by the NSF. Thank them.

I got to work with Dr. Julia Chifman as a mentor, who obtained her Ph.D in Math from University of Kentucky, now at the Mathematical Biosciences Institute and the work was done under our program director, Dr. Reinhard Laubenbacher of VBI and VT.  On my team was Jim Brunner (UMich), Paul Vines (Roanoke), and Emily Hendryx (Angelo State).  Our team was awesome, and the research we did in making a discrete model of iron metabolism was very well received by the biologists at the Wake Forest Cancer Biology Department who study iron metabolism and cancer.

Spending 8hrs/day getting up close and personal with a discrete model, I learned a great deal. Jim had greater experience coming in with ODE models, which are in general much more popular, and towards the end of our time got frustrated with the shortcoming of the discrete modeling framework. This current semester I am taking a graduate class in Mathematical Modeling of Biological Systems that, from the looks of it so far, will focus entirely on ODE's.  I am very interested to gain this perspective.

I titled this conclusions, and so there are some that I can share. I have made a decision to study applied mathematics in graduate school as a result of this experience. Math can be very useful in giving us more information about real systems, and this is what I want to do.  The specific application of mathematics is something with which I am still struggling, and am still hesistant about going into math biology specifically. For one, biology isn't my favorite subject and doing research in biology increased my level of frustration with the understand we do have of biology.  There are many experiments that are done, and we are able to elicit the functions of many protiens, but there is still so much that is unsure.  Some of the other applications of math that I find appealing are climate modeling and traffic modeling.  These are both very real problems that face us, and they're not isolated from each other. Looking at different schools and figuring out which ones to apply to is actually quite difficult, and I sent my GRE scores to VT, Boulder, Univ Maryland, and Univ of Minnesota.  One professor who I have found specifically whose research sounds very interesting is Dr. Chris Danforth at the Univ of Vermont: http://www.uvm.edu/~cdanfort/main/research.html.

Being Home

After the program had concluded, with our final Research Symposium, I came home pretty quick. The Draper Mile was that night, and I headed home on Saturday. I got a late start, at something like 10:30 in the morning so it made for a long day of driving but I made it home safe n sound.

My two weeks at home were very much like a vacation, as both of my recent trips home have been.  I lounge around, eat great food, ride and run like that's my job, and go out downtown with my friends.  I ended up playing more disc golf this break than I did going to dtown SYR, and it was good.  The first Sunday I was back, Sam from Bport came and visited, and her and Dan and I went and played a nice round of disc golf. Unfortunately it was one of my few losses of the season (I ended the summer series a half game down), but Sam was there so we could make fun of how Dan looks like he's going to fall every time he throws .

Not much unlike coming home in the beginning of summer (whence I was told that I had been signed up for a bike race and a 5K the coming weekend), my Mom captained a team for the Great Race. I'm really glad that she took the initiative, in making this my 7th consecutive great race and with my broski Kyle paddling, we dropped 7min off our previous best time.  Losing only by 30sec the year before, this year we were second by 5min, as the other team in our age category had brought in a ringer in the kayak that with a 18ft kevlar machine put 5 minutes into Kyle.

It was also exciting to see that my Dad is getting back into great shape, only 6 months after having a heart attack.  We got to go on some great walks, and my Garmin Connect "Walk with @rumblinstumblin" (classified as Speed Walking) will testify to this shape, 2 miles in less than 30 min is a pretty mean pace.  And my Mom is in as good of running shape as ever, and she came out and put the hurt on me a little at the end of one of my longer runs, as I had to tell her to slow down more than once!

One of the biggest things that happened while I was home was that my parents bought lake property on Skan Lake, and it is awesome.  When my Dad told me over the phone as I was driving home that he and Mom "found some lake property they were going to put an offer on" all I could do was chuckle because oh how many times I'd heard that. But they did it, and are currently closing on 5 acres with shared access to a 280ft lakefront. The property itself is wooded, and I love it. Would be a perfect place to build a cabin. I'm less fond of my Dad's idea to buy a 10k pop-up and haul that thing in, but he's also looking at building a garage-house that would be cool. Problem is that it all adds up with a septic and well, and then up goes the assessment.  It's just hard to now have the land, and not want to build on it.  But I think they'll be patient.

I looked at my title again for the rest of what I was going to talk about and saw great race, but I already talked about that. Perhaps some other things to mention there are that my Mom suprised me again coming in at just over 23 minutes.  My Garmin data puts me at winning a minute with no transistion time, but with our high number (longer transisition) and the volunteers making my brother walk that whole 1/4 mile, it took 3 minutes for just the handoffs and I had come in two minutes behind the leader in 13th place.  And it was definitely the transisitions, because on the course I caught up to two guys that were going hard enough that it seemed they could stick with me after awhile.  This was after passing roughly 100 people (I passed 120-some total), which is crazy. I'm almost over the yellow line, laying down 24-ish MPH whizzing by, and ocassionaly weaving through, a literal crowd of bikers to the right.  The two guys could in fact hold my draft (do 30% less work than I was) but after two miles of this, when we got to a hill, I wanted to let them do some work and pull up. It's not even as much more work to be on the front on the hill, but instead (feeling fresh from drafting off me for so long), the one dude sprinted around me and the other followed him. Like, really, what was he thinking? That I had caught him, pulled him for 2 miles, and that now he was just going to leave me in the dust? Annoyed, I reeled them back in, and sat on their draft for 15 seconds before sprinting around them so they wouldn't have a chance to sit in my draft. Recovering from my attack, one of them made their way up to me, a guy from Skan who races for Notre Dame.  He was actually cool, and would take a short pull when I asked him to.  His pulls were very short, and 19MPH instead of the 22 I was doing, but he was doing what he could. And he wasn't a jerk and let me come into the transisition area first after pulling hard into it (it was downhill going into it). But his time was a minute faster than mine, when I know mine should've beaten his by at least 30sec (I had to first catch him), so that little anecdote just speaks to our transistions. But, we still wouldn't have been able to catch the team in our category ahead of us. Luckily we bead the team the guy that I helped was on, because they were actually in the same category haha.

That's all for now!!