The stereotype of math is of a white-haired professor writing equations on a blackboard. Usually the professor doesn't care about real life or applications. But math is a really broad field. Made by Dominic Walliman. You can purchase here, and download different dimensions here. In the above map, different theoretical or 'pure' concepts have their… Continue reading Map of mathematics: applications to biology and beyond

# Category: Biology

## 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

## 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

## 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

## 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

## 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

## 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!

## 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?

## Model Complexity in Mathematical Biology

Most biological systems consist of many moving parts that happen at slightly different timescales. A true-to-life biological model of a sub-network might include dozens of parameters and biological species, regardless of the scale. Constructing a model with an appropriate level of complexity is one of the challenges in mathematical biology. Why is model complexity an… Continue reading Model Complexity in Mathematical Biology

## Infographic: Light Memory in Plants

Available here.