Software Packages, Tools, and Scripts

SEEDS: Stochastic Ecological and Evolutionary Dynamics System

SEEDS is an open-source computational platform for studying the ecological- and evolutionary dynamics of digital populations and communities. SEEDS is a plugin-based system that is designed to be easily used and extended. More information, source code, examples, and documentation are available at the SEEDS development site.


pushoverr is an R package for sending push notifications to mobile devices. It can be used to send messages when jobs are done. Find more information and documentation at pushoverr’s development site.


PlateTools is an open-source Python package for reading, manipulating, and analyzing microplate data. More information, source code, scripts, and documentation are available at the PlateTools development site.

Plotting Themes and Scripts

ggplot2 themes, scripts, etc.

I frequently use the excellent ggplot2 package for R to produce plots and graphics, and I’ve made my themes, scripts, and other materials available as an R library named ggplot2bdc.

Guides, HOWTOs, Tips, and Tricks