What pre-medical students can learn from the humanities

As I finish writing my final lab report for my Intermediate Physics Lab, the fall semester of my sophomore year comes to a slow, much-needed end. I've taken some time to reflect on the impact my classes have had since the beginning of the year. This semester, unlike those of my freshman year, has been markedly different in several ways. For one thing, all my classes were either directed towards my physics or my philosophy degree; none of them were pre-medical requirements. This was a huge breather for me, not because it was less work or I had the chance to be lazy, but because I had more time to develop as a person.

The Uncertainty of Stochastic Models and Human Mortality

Stochastic models help us predict events that deal with uncertainty. We can use them to do cool things like predicting the levels of noise in gene expression [1]. The randomness of genetic mutation, epigenetic factors, and other biological mechanisms that influence genetic expression isn't something that we look at as some sort of black box that we can never know. Not only is it a truly remarkable demonstration of concepts that are inherent to theoretical physics in the messy world of biology, but I loved how these types of models incorporate the epigenetic factors that we have previously deemed "unpredictable" on the gene expression scale.


Float like a butterfly; sting like a bee.

Your hands can't hit what your eyes can't see.

For this reason, we have to be careful when feeding numbers into our computer. Check out what happens when you ask a basic math question to Python:

Pictured: the folly of man

Promoting the discussion of Ethics

The time is 6:30 am.  I'm outside my residence hall, having completed my morning run. I look around me and see faces and lights begin to appear. People in cars and buses slowly move into the empty streets. The chirps of birds and songs of the bugs break the desolate wasteland of the hour before. The dark void of isolation is warm as always. The sun will shine, and the world is mine. In the morning, I tell world that I'll be there when you wake up. I own the world in everything I do during the day. Time and tide wait for no man because time had better catch up with me. 

Programming for Particle Physics - Monte Carlo simulations and Markov Chains



Call me Ishmael. Some years ago - never mind how long precisely - having little or no money in my purse, and nothing particular to interest me on shore, I thought I would sail about a little and see the watery part of the world. 

I'll tell you a story from my ongoing adventure in physics.

The Importance of Hashing

People who are just beginning to code make a lot of mistakes and do a lot of stupid things. I once used to struggle with parsing thorough every line of a file before I learned that it would be much easier to use split-functions and similar lists. One common mistake people make is that they need to store large amounts of data and parse through them every time they need to access that information. But, with a bit more expertise, those newbies can throw away those "for" loops and sort-methods. There's a new kid in town. And his name is "Hashing."

Longest Common Subsequence and NumPy

Perl may be crafty and efficient like a ninja, Ruby may be written like a prose or work of fiction, but, for most purposes, Python, with its simplicity and elegance, is usually my weapon of choice when it comes to programming languages. (To be frank, as long as it's not some cryptic code like Fortran that should probably be waiting for the rain to wash it away, it floats my boat.) With my knack for mathematics, I had been reconstructing various equations and theorems from scratch in most of my scripts. Recently, I've begun to embrace NumPy to give me more functionality for purposes like matrices and arrays, but also that I can do all the things my MATLAB friends do without too much effort to learn extra languages.

Comparing genome alignment methods

One of my current projects in the Matthew Hahn Lab is to investigate the effectiveness of a few different full-genome alignment methods. My mentor and I have been studying a new program called progressiveCactus, and comparing its output to other alignment methods. By comparing the number of indels (that is, insertions and deletions) between different species, we can compare the effectiveness of different genome-alignment methods. But my work has mostly been spent struggling to figure out how to get programs to run, and deciding the best way to parse output files.

Genetic Inversions, Bill Gates, and Pancakes

Imagine that you are a waiter running back and forth in your breakfast restaurant. Your life is constantly moving between the kitchen and the seating area in your usual "flow". Most days you have to work very hard to make ends meet, so you don't have time to sit back and smell the roses or rose the smells. It's a shame that your work prevents you from studying the world around you through mathematics and algorithms. Every now and then, a guest orders a stack of pancakes, but, when the cook hands you the plate of pancakes, you're a bit disappointed because the pancakes aren't stacked by size.
what is this madness

Helping other students with Undergraduate Research Awards and Opportunities

My university recently featured me on their webpage for their new Office of Competitive Awards and Research for my recent REU at Cornell University. It's definitely exciting to get press coverage. And it looks like REU's are definitely the gift that keeps on giving.

"Memory Palaces (Method of Loci)" or "Memorizing a Deck of Cards in a Minute" or "Why You Have an Amazing Untapped Memory"

I like hobbies. Hobbies are fun. Especially when they're challenging.

How do I prepare myself for research internships (or how do I do well in my research lab)?

When I entered college, I was obsessed with science and getting involved in research, but I didn’t know how to join a lab, let alone what exactly it was I wanted to research. I was particularly fascinated by understanding biology through math, so I joined a bioinformatics lab.

When I joined, I was overwhelmed. I had never written a programmed anything before in my life. But I put hours and hours of effort into learning the programming skills and research techniques throughout the semester, and, before the end of my freshman year, I was accepted to a bioinformatics REU at Cornell University. Having said that, it didn’t come easy, but I’d like to share some thoughts on excelling in your research so you can find new opportunities.

Unplug and Recharge - my poster presentation and what I've learned form my internship

I've officially finished my research internship at the Boyce Thompson Institute. After several stressful nights of analyzing my data, putting it into a readable form, and drawing conclusions, I whipped together a poster that shows my results. From my RNA-Seq analysis of the tomato genome, I collected a lot of information about lncRNAs and cisNATs and their involvement in the ripening of the tomato.

Building a Heap

Binary heaps are binary trees that are sorted in such a way that the parent leaf is either greater or lesser than both of its child nodes. When the root node is the greatest and each parent is greater than its children, then it's a max heap. In the opposite scenario, we have a min heap. When presented with an array, we simply line up each element in the array from left to right, top to bottom in a binary tree format. 

Testing graphs for bipartiteness

Graphs are amazing.

de Brujin graphs and Velvet Optimiser

I'm working with the Velvet Assembler as part of my virus identification project. When I'm not trying to write a perl module to complement the already-bulky script files that I'm working with,  I like to do something that I usually wish most other bioinformatics scientists I've met would do as well: I like to delve into the mathematics behind the program.

Suboptimal Alignment Algorithm

Despite the existence of the Lalign program which could find internal duplications between two strings, I've developed my own algorithm for carrying out a similar function as part of this Rosalind problem.

Perl

Ever since I got to Ithaca at the Boyce Thompson Institute, I've had to learn how to program in Perl, a  less elegant version of my weapon of choice, Python.

An underscore? Next, you'll be telling me to use goto and watch the world burn.

Any way the wind blows

Dear blog, my source of reflection,

One thing that has occurred to me is that, in order to keep moving ahead in life, you need to routinely ask yourself why you are doing the things you do. For example, I've loved science since I don't even know when, but I never really ask myself why I want to grind my nose in research or go to med school (if I even still want to). Let's face it. I wasn't born with an undying love for what I do. If the high school freshman I once was had seen my bioinformatics research projects that I'm currently doing, I would have gone running for the hills in any direction other than science.

Getting work done

It is not enough to be industrious; so are the ants. What are you industrious about? - Henry David Thoreau

My new scorecard


I crawled out of bed on a warm, brisk Monday morning, waiting for my energy to kick in and let me go out for a run before work today. Waking up at my normal time on Monday mornings after staying up late on the weekends always felt like coming home jet lagged from a trip to India. "I just need to drink some water...my room is 200 degrees and counting," I thought to myself. With the fan on the highest setting, my room still felt like a sauna that just lulled you to sleep before you could even try to get up again. I'd consider leaving the window open all the time, but that would leave my room to damage from rain if it would occur during the night.

Back to the lab again

I don't know what's worse. The fact that I slept for maybe 10 hours last night or the fact that I don't feel too guilty about it. I thought I was going to "take a nap" around 7:00 pm, but ended up sleeping until midnight. At that point, I decided to just "nap" for four or five more hours. It certainly doesn't help that my dorm room is like a billion degrees Celsius and I can't open the window. Maybe I've just been lazy cuz I've been getting hyped over the new Smash Bros game that's coming out in the next year or so. During my waking hours, I've been watching video after video and obsessing over each post about Smash Bros anyone makes on the internet.

Beginning my summer research internship - on bioinformatics and math and everything

What do you get when you combine running and nature, two of my favorite interests?

Pictured: nature
Cornell University, aka, the place where everyone runs and worships trees. Last Saturday I moved into a residence hall with ~20 other students as part of a Research Experience for Undergraduates (REU) with the Boyce Thompson Institute, where I'll be using computers, science, and computer science to study the DNA of tomatoes. When I was applying for summer internships, I thought this one sounded interesting, but I never realized how much I really loved Cornell and its atmosphere until I got here. Everything about being at a small, private school seems different than at the state college I attend. Even though its summer (which means the campus is mostly empty of students and there isn't much going on), I still feel like I'm a student who truly belongs here. It makes me excited to do research, and I'm definitely going to miss it when I return at the beginning of August. 

New kid on the blog

This is a blog I made. I'll try to put stuff in it as I surf the internet so I don't feel like I'm being unproductive as I read articles on the internet. I'll also write about stuff that happens to me.