README

Dynamic Factor Graphs for Gene Regulation Networks

This repository contains the Matlab code for our 2010 Genome Biology paper:
"Predictive network modeling of the high-resolution dynamic plant 
transcriptome in response to nitrate"
G Krouk, P Mirowski, Y LeCun, DE Shasha, G Coruzzi


The structure of the folders is as following:

* Arabidopsis/
contains the Matlab scripts that are called by the main, batch,
function. For instance, it contains scripts:
Script_Arabidopsis76_Leave1.m
Script_Arabidopsis76_Leave1_LARS.m
which are used for leave-out-last learning of the Arabidopsis GRN
using mRNA measurements from time points 0, 3, 6, 9, 12 and 15min
and uses the two last time points (15min and 20min) to evaluate the
out-of-sample trend.

* DFG4GRN/
contains all the code for our SSM,
minus the LARS library, which needs to be installed from the
bolasso.zip file.

* ClusterFrontend/
contains functions used for running the cluster code.


Please see Matlab file Tutorial.m for an example of how to run the code.