About Me, Misc, Teaching

Scientific web apps

Recently I've been thinking about developing scientific web apps. I wanted to discuss my experiences with making web apps, and an overview of what I've made. A more technical/development discussion will follow in a subsequent post. I was introduced to R Shiny at a gerrymandering workshop a few years ago. Since then, I've created a… Continue reading Scientific web apps

Computation, Math Modeling, Teaching

Hardy-Weinberg population simulator

As a grad student, I was a TA for the introductory biology labs at LSU. The second semester lab had some modules on evolution, including a population simulator. This simulator was developed about 20 years ago, and was difficult to install, as well as having a layout that was unfamiliar to the students. When I… Continue reading Hardy-Weinberg population simulator

Math Modeling, Opinion, Teaching

Diversity is good for science: Math and the status quo

A lot of people where I come from view diversity as a political thing. Some people think that having recruiting or retention preferences don't contribute to anything but some abstract social ideal. I've seen several things firsthand that counter that idea, but wanted to share one experience that specifically involves math (because its "objective"). I… Continue reading Diversity is good for science: Math and the status quo

Biology, Computation, Data analysis, Math Modeling, Teaching

Introduction to modeling: parameter estimation in R

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

Computation, Math Modeling, Teaching

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

Biology, Computation, Math Modeling, Teaching

Modeling demo: photosynthesis

This demo is intended to help students understand the connection between photosynthetic pigment function, light energy, and plant growth. The relative absorption of 8 wavelength ranges can be modified to represent an absorption spectra. These absorption spectra could be simplified to include one or two specific colors, or approximate an absorption spectra obtained in lab.… Continue reading Modeling demo: photosynthesis

Biology, Math Modeling, Teaching

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

Biology, Computation, Teaching

Interview: Technology as a tool in teaching quantitative biology

Shelby Scott and Miranda Chen recently published the article Technology as a tool in teaching quantitative biology at the secondary and undergraduate levels. You can find the paper here. In this interview, the authors describe what they see as the next steps for integrating quantitative methods into biological curriculum and tons of online resources to get you started. This information will help… Continue reading Interview: Technology as a tool in teaching quantitative biology