MATLAB: From the Basics

In addition to working on modeling my Parkinson’s pathways this summer, I’ve been developing some new analytical methods for our lab to use in the future. This includes switching everyone over to modeling in MATLAB, which has a steeper learning curve than PLAS, the program we had been using previously. My lab is a mix of chemistry and neuroscience majors, so it is possible that some of them have no coding experience at all. Jumping right into modeling a huge system can be intimidating, especially if you’re learning coding basics, a language, and how to model all at the same time.  I’ve been trying to create a small tutorial on MATLAB and coding to ease their way into the modeling process.

Since this is a chemistry lab, despite the fact that our space is filled with computers, I’ve kept the tutorial as specific to biochemical systems theory modeling as possible. I’ve created a small example system in CellDesigner, our pathway visualization program, and modeled it in MATLAB with extensive explanations of what each line of code is accomplishing. I also made a more general document that explains basics like loops, functions, matrices, and what to do if you get an error. It was a bit challenging to try and think back to all the problems I was having when I was first developing the code, and addressing those issues in a way that makes sense to someone with no coding experience. I’m really looking forward to having someone test run the tutorial and point out all the obvious omissions. I’ve been thinking about this code for so long that I’m sure there’s something I do automatically now that does not make sense if you’re seeing the code for the first time.

Comments

  1. Woah, this is so cool! I’ve been wanting to teach myself MATLAB for a while, but haven’t had a pressing use for it yet, so I’ve mostly been experimenting with R. I’d love to try out your tutorial some time!