Run the bash scripts to recreate the figures from the paper. 

For example, fig1.sh will create the files Fig1A.png and Fig1B.png. sup1.sh will create supplemental fig. 1. 

Requirements:
	- matplotlib
	- scipy
	- MOGEN requires Java
	- ChromSDE requires MATLAB
	- HSA requires R

Chromosome3D can't be installed programmatically, so it must be installed according to the instructions here (https://github.com/multicom-toolbox/Chromosome3D) prior to running fig4.sh, fig5.sh, sup1.sh, sup2.sh, or sup3.sh. 

4/6/17: The ChromSDE website is currently inaccessible. Relevant portions of code have been commented out.