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

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! Advertisements

Mathematical modeling is a relatively new field. You may be more aware of a subfield if 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 …

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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

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

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

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: First I ask them a series of … Continue reading

Originally posted on The Contemplative Mammoth:

As a professor, journal editor, reviewer, and mentor, I review a lot of writing. I come from a long tradition of mentors who focused on writing — during my PhD, I often heard stories of my grand advisor returning his students’ work covered in red line edits, and then…

When I started graduate school I had pretty low self-esteem. I wanted to study mathematical biology, but I still held on to some sexist self-directed beliefs about being bad at math and programming. This resulted in pretty strong imposter syndrome. I’ve had to teach to support myself through grad school (except a spring/summer semester). I … Continue reading

Recently there has been a lot of discussion around work-life balance in academia, particularly for early career researchers and students. It wasn’t until very recently that I personally began to be interested in this issue. Last year I wrote about how I never felt the need to reduce or alter my workload. At that point … Continue reading