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
Introduction to an Introduction to Approximate Bayesian Computation (ABC)
Last week I re-blogged a post introducing Approximate Bayesian Computation. I thought some of the content was a little foreign, so I wanted to give an intro to the intro. ABC core concept Say we have a process that is controlled by a parameter - say the slope in $latex y = m\cdot x+b$, or… Continue reading Introduction to an Introduction to Approximate Bayesian Computation (ABC)
PlantBiology2020 Online Workshop: Mathematical Modeling Across Scales in Plant Biology
The workshop will be online on July 31st from 2-4 pm EDT. I changed the format a little to facilitate this, read if you are curious.
Workshop on Computational Plant Biology at PB2020 & Opportunities for Participants
Last year I held a workshop on collaboration in computational plant biology at pb2019. We went through a few examples of how computational biology is used in a variety of situations, discussed challenges in collaboration and communication. Participants were matched with potential collaborators at the end of the workshop. I received a lot of feedback… Continue reading Workshop on Computational Plant Biology at PB2020 & Opportunities for Participants
How to teach yourself coding
I'm primarily a self-taught programmer. I have taken a handful of classes, which is precisely why I'm pro teach yourself. Having a vision for what you want to create with code makes everything so much easier. Pseudo code So, you have some idea about what you want to program. Start by writing pseudo-code. This is… Continue reading How to teach yourself coding
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
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: 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
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
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