Computation, Math Modeling

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.

Biology, Computation, Data analysis, Math Modeling

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

Computation, Data analysis

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

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, 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

Biology, Computation, Data analysis, Math Modeling, Misc, Statistics, Visualization

Ask me anything!

Ask me anything anonymously (or non-anonymously) using this Google form: https://goo.gl/forms/JIAIGvvLYATAuEjv2 You can also ask questions on the blog or on the Plantae BDCI network!

Computation, Statistics

Introduction to Bayesian Statistics, Part 3

The two most popular Markov chain Monte Carlo sampling algorithms are Gibbs sampling and Metropolis Hastings. These algorithms produce Markov chains. Numbers inside a Markov chain are dependent on only the previous number. In the context of sampling, we check the probability of the proposed value based on only the probability of the current value,… Continue reading Introduction to Bayesian Statistics, Part 3

Biology, Computation, Math Modeling

Why do we need mathematical modeling in biology?

Mathematical modeling is a relatively new field. You may be more aware of a subfield of biology called bioinformatics or computational biology. These tend to deal with larger data sets, studying them using more algorithmic methods. Computational biology also refers to mathematical biology, or an even mixture of mathematics and computer science as applied to… Continue reading Why do we need mathematical modeling in biology?