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.
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Assimulo (http://www.jmodelica.org/assimulo, in progress) and SciPy for numerical integration of differential equations.
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SymPy for automatic derivation of forward sensitivity equations, useful when doing gradient-based optimization.
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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.
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matplotlib for plotting and visualization.
Heavily inspired from sloppycell (Sethna group).