All our code is now on Github at our repo Emergent Behaviors in Biology. Some old code can be found below.

Bayesian Ising Approximation for Linear Regression.

This file contains mathematica notebooks for the figures in the paper as well as R code (be warned I wrote this quickly when I was first learning R and it was not used in the papers). In addition, we have C++ code for the soybean examaple There is also Matlab code for logistic regression.

Variational RG and Deep Learning .
The largely off the shelf Matlab code used to generate figures in variational RG paper can be found here

LIMITS Code .
Mathematica code for the LIMITS paper can be found here.