File	Date	Author	Commit
src	2011-05-07	Logan J Everett	[237c56] v1.0 beta
COPYING	2011-05-07	Logan J Everett	[237c56] v1.0 beta
Makefile	2011-05-07	Logan J Everett	[237c56] v1.0 beta
README	2011-05-07	Logan J Everett	[ad8343] Added NAR reference to README file.
example.conf	2011-05-07	Logan J Everett	[237c56] v1.0 beta
example_simple.conf	2011-05-07	Logan J Everett	[237c56] v1.0 beta
make.conf	2011-05-07	Logan J Everett	[237c56] v1.0 beta

Read Me

Copyright 2009 Logan J. Everett, Sridhar Hannenhalli

MONSTER is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

MONSTER is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with MONSTER (called COPYING).  If not, see 
<http://www.gnu.org/licenses/>.

For questions related to the original MONSTER source code, contact:
Logan J. Everett: loganje@mail.med.upenn.edu OR loganism@gmail.com

If you use MONSTER in your published work, please cite:
Everett LJ, Jensen ST, Hannenhalli S. "Transcriptional regulation 
via TF-modifying enzymes: an integrative model-based analysis"
Nucleic Acids Research, 2011. PMID: 21470963
<http://www.ncbi.nlm.nih.gov/pubmed/21470963>

TO INSTALL:
 - Download and Install GNU Scientific Library (GSL): 
	<http://www.gnu.org/software/gsl/>
	Make sure the library is installed in the g++ library path
 - Download and BOOST: <http://www.boost.org/>
	You do not need to compile boost separately, only header 
	packages are used. Store these files in the g++ include path, 
	OR change this line in make.conf:
	INC_FLAGS = -I <path/to/boost>
 - Run "make" to compile the code

TO RUN:
 - See example.conf for a full model example, or example_simple.conf 	
   for a TF-only model example
 - All input files should be tab-delimited text with labels in the 
   first row and first column
	The very first data cell can be blank, or any text you want:
GENES	SAMPLE1	SAMPLE2	SAMPLE3	...
GENE1	5.123	4.435	3.942	...
GENE2	1.23	7.03	7.78	...
...
	- For expression data, columns should correspond to samples, and 
	  rows correspond to genes (see above).
	- Expression for Target genes, TFs, and modifiers should be in 
	  separate files with the same sample order and labels
	- TF-Gene Prior Matrices should have columns corresponding to 
	  the TFs and rows corresponding to the target genes (same 
	  labels as in the expression data)
	- Mod-TF Prior Matrices should have columns corresponding to the
	  Modifiers and rows corresponding to the TFs (same labels as in 
	  the expression data)
 - RUN: ./monster my.conf
	Where "my.conf" is any config file you create.