Math Modeling, Young Modelers

Modeling and Beyond: Meeting 10/2 and discussion with Dr Dreyer on membrane transport modeling

If you're a modeler, join us this Friday to talk about using physics-based models to discriminate different membrane transporter networks https://amoghpj.github.io/modeling-and-beyond/

Math Modeling, Misc, Young Modelers

Online Community for Modelers: Modeling and Beyond

MODELERS FACE A VARIETY OF CHALLENGES. Although the usefulness and appreciation of modeling as a field is always increasing, modelers today often experience a few setbacks. We often teach ourselves difficult concepts in an effort to innovate along any of the fields we operate in (coding, math, biology, statistics). We may complete our degrees in… Continue reading Online Community for Modelers: Modeling and Beyond

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.

Math Modeling, Opinion, Teaching

Diversity is good for science: Math and the status quo

A lot of people where I come from view diversity as a political thing. Some people think that having recruiting or retention preferences don't contribute to anything but some abstract social ideal. I've seen several things firsthand that counter that idea, but wanted to share one experience that specifically involves math (because its "objective"). I… Continue reading Diversity is good for science: Math and the status quo

Math Modeling

Jae Kyoung Kim – Analysis of dynamic data: from molecule to behavior – Mathematical and Computational Methods in Biology Workshop

MBI's online workshop on Mathematical and Computational Methods in Biology will be running all week! See the schedule here (https://mbi.osu.edu/events/mathematical-and-computational-methods-biology). It is also being live streamed here: https://video.mbi.ohio-state.edu/live. Dr. Kim likens simplification of complex biological networks to Picasso's progressive reductionism of a bull. I really enjoyed this talk by Dr Jae Kyoung Kim of KAIST.… Continue reading Jae Kyoung Kim – Analysis of dynamic data: from molecule to behavior – Mathematical and Computational Methods in Biology Workshop

Biology, Math Modeling

Map of mathematics: applications to biology and beyond

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

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

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