SAMNet
Simultaneous Analysis of Multiple Networks (SAMNet) is a tool designed to identify key proteins undetected by high throughput biochemical experiments.
Contact: Sara JC Gosline sgosline@mit.edu
Copyright (c) 2012 Sara JC Gosline
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1- Python 2.5.2 or higher: http://python.org
2- Networkx 1.7 or higher: http://networkx.lanl.gov
3- NumPy: http://numpy.scipy.org
4- AMPL: http://www.ampl.com/DOWNLOADS/index.html
5- cplexamp or some other solver that will work with AMPL: http://www.ampl.com/CPLEX/#academic
1- Download code from source repository
2- Install ampl, cplexamp (or some other solver) and necessary python libraries
3- Investigate SAMNet run on the two datasets from Gosline et al. 2012. The yeast metal dataset from Jin et al. can be found in the ./data/yeast_metal subdirectory. The EMT dataset from Thomson et al. can be found in the ./data/human_emt data
4- Either run new results, or explore results included using the tools in the src/cytoscape directory
5- Also investigate GO enrichment tools in the src/go_enrichment directory.
6- To run on your own data, you'll need to parse it into the appropriate file formats: -protein weight files, formated like the *.phen files in the sample data directories, 1 for each commodity -mRNA expressiond ata, formated like the *.txt files in the sample data directories -a protein-protein interaction network in the networkx format, or you can use one of the ones provided -a protein-DNA interaction network, in the format of the *.tfa files provided -for more details type python src/samnet.py --h