This code introduces how to perform parameter estimation for a system of differential equations in R. First, the necessary packages and data are imported using code previously introduced in a previous post. R code available here. Due to computational constraints, the mathematical model we are using to fit to the data includes product inhibition. If product inhibition doesn't… Continue reading Introduction to modeling: parameter estimation in R

# Tag: teaching tools

## Introduction to modeling and coding in R

After introducing students to a simple mathematical model describing enzyme kinetics, I introduced them to coding and modeling in R. Coding is traditionally done by first describing some coding 'rules', including ending the line with semicolons or how to define a variable. Personally I found these methods ineffective and frustrating. I took a few classes… Continue reading Introduction to modeling and coding in R

## Modeling demo: enzyme kinetics

When using this demo, students can alter the reaction rate, substrate, or enzyme concentrations. The simulation motivates understanding what a basic mechanistic model of enzyme kinetics would consist of. After running a simulation, the predicted dynamics of the product and substrate are plotted. The model behind the simulation is: $latex \frac{dS}{dt} = - r*E*S\\ \frac{dE}{dt} =… Continue reading Modeling demo: enzyme kinetics