Week 1 - Alex

Post 1: Setting Expectations

I will begin shadowing on July 1, when I get back from my computational biology summer program. In the meantime, I plan to use this blog to summarize my thesis project progress and experience in the summer computational biology program. I will make up for missing these first three weeks, by continuing to work with my clinical mentor, Dr. James Ip, after the program is over. I am working in Dr. David Christini’s lab in New York, whose lab is across the street from where Dr. Ip works. Below, I’ve listed my focus for each week of the summer, which will also be the topic of my blog post that week.

• June 10: Wrapping up my Spring 2019 research, traveling to Norway
• June 17: First week of the Simula program in Norway – mostly lectures
• June 24: Second week of the Simula program in Norway – lectures and a group project
• Weeks of July 1-July 29:  Shadow Dr. Ip
• Weeks of July 8-15: Simula program in San Diego 

Who knows, I may continue to write weekly summaries after the week of the 15th. It’s a good way to document progress and help me appreciate my accomplishments. 

The first three days of this week, I worked on my thesis project. I recently converted a commonly-used computational model from Matlab to Python. I did this for a couple of reasons: 

1. I prefer to learn Python programming skills
2. Our lab uses evolutionary algorithms to optimize parameters in the model. There are a few Python well-established and easy-to-use libraries for implementing evolutionary algorithms.

I was able to quickly convert the bulk of the model to Python. Then, I spent about three days trying to find a Python ODE solver similar to the Matlab implementation. Most of the SciPy solvers I tried took 100x to 200x the steps of the ode15s method. Eventually, I implemented a solver that produced something similar, but still took 10x as long as the Matlab solver. I wrote a Stack Overflow question in hopes of getting some direction. 

I received answers to my question on Stack Overflow, and was able to get help from someone who authored a Python integrator that compiles systems of ODEs to C code, before performing the integration. This implementation resulted in a  10x speed increase, compared to the Matlab implementation. If you review the conversation on GitHub, you will see that the person went above and beyond to help me implement this solution. 

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Yesterday, I left for Norway to attend the 2019 Simula School for Computational Physiology. At this point, I know a few of the lecture topics and a project that I will complete over the next two weeks, and for a couple weeks in August. The projects aligns with thesis project. I will be working with a group to simulate drug effects on 3D micro tissues using computational models of cardiomycyte electrophysiology. I have a few pieces of pre-reading, which include the computational model that I mentioned above.

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When I return from Norway, I will work with Dr. Ip on one of his ongoing research projects (I have been added to the IRB). Also, I may work with a few physicians who specialize in ECG reading to develop machine learning software to diagnose patient with abnormal readings.