File	Date	Author	Commit
DATA	2014-08-15	david knox	[6cf574] Initial commit
KnoxUtils.py	2015-07-03	Knox	[910829] Updates for consistency and added version into ...
README.txt	2015-07-10	Knox	[54b561] Modified to meet TCBB revisions required
SRB.py	2015-07-10	Knox	[c91b24] Modified to meet TCBB revisions required
SRB_Sample.ini	2015-07-03	Knox	[910829] Updates for consistency and added version into ...
SRB_Sample.mk	2015-02-07	Knox	[5ce5aa] Updated source and documentation to match manus...
SRB_Sample1.sh	2015-07-10	Knox	[c91b24] Modified to meet TCBB revisions required
SRB_Sample2.sh	2015-07-10	Knox	[c91b24] Modified to meet TCBB revisions required
SRB_Tutorial.pdf	2015-07-03	Knox	[702f04] Added note about JVM memory size for DIZZY
SRB_Visualizer.py	2015-07-10	Knox	[c91b24] Modified to meet TCBB revisions required

Read Me

#
# Copyright (2011-2015) University of Colorado
# All Rights Reserved
# Author: David Knox
#

The is the README file for the Stochastic Rule Builder (SRB).
A tutorial is available in the SRB_Tutorial.pdf file with detailed 
explanations of the applications and the parameters.

The SRB builds models using the SRB.py application.  
Models are simulated using the DIZZY simulation engine 
(available at: http://magnet.systemsbiology.net/software/Dizzy/1.11.4/download.html).
The results from the simulation can be visualized with a character representation
by the SRB_Visualizer.py application.  The KnoxUtils.py file provides a generic set 
of utility routines used in both the SRB and SRB_Visualizer applications.

We provide a set of sample files and data files for parameterization.
The files in the data directory provide the model builder and visualizer with
information required for parameters.  The sample files provided show an example
that models the IME4 region of a yeast genome.

Installation:
There are a number of libraries used by the SRB code base and must be installed prior to 
running the SRB application sample scripts.
	numpy
	pylab or scipy
	matplotlib
	Tamo
	
The SRB uses Dizzy as the rule simulator. Dizzy must be installed prior to  
running the SRB application sample scripts.  

Stochastic Rule Builder (SRB) software available at:
http://sourceforge.net/projects/stochasticrulebuilder/

TAMO available at:
http://fraenkel.mit.edu/TAMO/

DIZZY available at:
http://magnet.systemsbiology.net/software/Dizzy/


Running sample scripts:
The sample scripts must be edited to reflect the correct paths for SRB and Dizzy.

The Dizzy script for running models (runmodel.sh) must be edited to increase the memory
allocated in the Java Virtual Machine.  Change the -Xmx option to -Xmx4g to use 4 GB.