Computational Projects

  • Statistical Inference for Everyone

    Statistical Inference for Everyone is an introductory textbook on statistical inference, motivated by probability theory as logic. It is intended for a Statistics 101 audience.

  • pyndamics3: Python Numerical Dynamics Simulator

    • Pyndamics3 provides a way to describe a dynamical system in terms of the differential equations, or the stock-flow formalism. It is a wrapper around the Scipy odeint function, with further functionality for time plots, phase plots, and vector fields.
  • plasticity: synaptic modification in rate-based neurons

    Plasticity is a package with a convenient interface, used to run simulations of single cells and networks of neurons.

  • plasticnet + splikes: synaptic modification in rate and spike-based neurons

    This project aims at providing a simple-to-use neural simulator at a medium-level of complexity. This package combines both rate and spike-based models.

  • Natural Images

    This is a collection of natural images used in my research. It contains the original images, scripts for processing the images, as well as scripts to download some of the standard databases, such as the Olshausen and VanHateren image databases.

  • vacuum world

    This is my first semi-serious project in Python. Python is an awesome language, and this project is to help teach python for an AI and Robotics class.

  • PyNXC

    Python to NXC converter.

  • plasticity (Matlab version)

    Plasticity is a package of programs, with a convenient interface, used to run simulations of single cells and networks of neurons. It is used to explore BCM synaptic modification and Hebbian learning, amongst others.

  • $25 Thermal Cycler: A Programmable

    $25 Thermal Cycler is a very simple thermal cycler for performing PCR. The circuit itself costs a few dollars, and the control code can be easily run on a 486 running Linux. Go to the Thermal Cycler page to learn more about it.


    A simple class for doing Monte Carlo error analysis

  • Classy

    A simple python-based classification system, implementing Naive Bayes, RBF clustering, and others. Some data files can be found here.

Current and Potential Research Projects

  • Establishing the connection between rate-based and spike-based models of synaptic plasticity.
  • Estimating the oscillation time-scales in paleo-climate - comparison of models of temperature dynamics.
  • Dynamics of the immune system - the role of interaction and transmission rates.
  • Ebola dynamics and policy
  • Estimating Dose-Response curve parameters
  • Biochemistry of synaptic plasticity - entropy, energy, and dynamics.
  • Bayesian inference in economics resource limits
  • Extrasolar planets and the search for Earth-like conditions - analysis of Kepler mission data.
  • Oscillatory models in climate - comparison of methods
  • Deep learning
  • Environmental and economic dynamical systems