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This project will create a user-friendly modeling system for studying animal social aggregations. The model codifies the a new hypothesis that the animal's state, kinematics, and the group's emergent properties are dynamically linked together, with each one affecting the others. The model will be constructed using Object-Oriented MatLab.

PAMGuide is acoustic analysis software for the characterisation of the acoustic environment from sound recordings. PAMGuide can be used to produce calibrated spectrograms and statistical analyses of sound levels, and is provided in both MATLAB and R. A Tutorial on getting started with PAMGuide can be downloaded here: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12330/suppinfo PAMGuide was published as supplementary material to the following Open Access journal...

The Dynamic Multispecies Metabolic Modeling (DyMMM [dĭm]) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework was formerly known as the DMMM framework. Please use the following citation for bibliographical purposes: Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., & Lovley, D. R. (2011). Genome-scale dynamic modeling of the competition...

A matlab/octave based reaction transport model describing microbially mediated isotope fractionation processes in porous media.

Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.

The class libraries here provide infrastructure for creating simulations of low energy nuclear physics experiments, as well as some useful working programs that do simple simulations and analysis of experiments performed with magnetic spectrographs.