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

Misc, Opinion

Happy New Year!

Last year was very eventful for me. I've been a bit busy to write many blog posts but I'm ready to get back into it. Over the next year I'll be writing about my experiences in grad school, postdoc, and the transition; as well as some of the projects I've been working on and coding… Continue reading Happy New Year!

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


Five common writing mistakes new scientists make

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 I experienced the same when I turned in my first drafts. My own students now know that this is something they can expect from me: close reading and detailed feedback. It’s how I grew as a writer, myself! I still remember comments from individual reviewers about bad habits in my manuscripts (thanks, Reviewer #3!), and I hear myself passing on my advisor’s comments (in his voice, even!) as I edit my students’ work.

As I’ve found myself doing more and more editing lately, I’ve started noticing patterns — common issues that tend to disproportionately show up in student and early career…

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