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Dynamical Systems
Math lecture notes
Measure Theory
Personal scripts and software
An R package for efficient phylogenetics on large trees.
Database and software for mapping prokaryotic taxa to metabolic functional groups
MCM (Microbial Community Modeler)  
A computational framework for modeling microbial communities using dynamic flux balance analysis of genome-based cell models, in the context of a dynamical environment. Classical functional group models are also supported.
peacots (Periodogram Peaks in Correlated Time Series)  
An R package for detecting cyclicity in time series using the Ornstein-Uhlenbeck model as a (non-cyclic) null hypothesis.
Simona v1.0  
C++ Implementation of the Barnes-Hut tree-algorithm for N-Body simulations with electric and newtonian-gravitational force fields. Also bundled is a creator program for generating start values for astronomically relevant N-body mechanical systems.
STDP v1.0  
Simple data-plotting gnuplot-interface for FORTRAN 90. Compatible with gnuplot 4.2.
STPlot v2.6  
Open source C++ API for plotting with gnuplot. Supports multiple plots within one window, multiple graphs within one plot, 2D plots, 3D surface plots, histograms, heat maps with hierarchical clustering, vector field phase portraits and circular network plots. Maximum compatibility with gnuplot 4.6.5 and ISO C++98. Includes example code and a thorough user guide.