A simple, small toolbox for estimating parameters in ODE-based models. The main usecase is to estimate parameters in models where parameters depend heavily on experiment-specific settings.

• Assimulo (http://www.jmodelica.org/assimulo, in progress) and SciPy for numerical integration of differential equations.

• SymPy for automatic derivation of forward sensitivity equations, useful when doing gradient-based optimization.

• SciPy (http://www.scipy.org/), nlopt (http://ab-initio.mit.edu/wiki/index.php/NLopt), and geo_lsqt (http://arxiv.org/abs/1201.5885) for optimization and parameter estimation.

• matplotlib for plotting and visualization.

Heavily inspired from sloppycell (Sethna group).