Copyright (c) Nils Blüthgen and Bertram Klinger and Mathurin Dorel, 2013-

Gnu General Public Licence version 3 (GPLv3)

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The library contains the levmar-package (version 2.5) for optimization (c) by Manolis Lourakis
(see src/levmar-2.5/README.txt)

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This library can be used to model signalling perturbation data using models that are derived from
Modular Response Analysis using R. 

Requires the following C++ libraries to be installed (installation method depends on the OS): 

    ginac
    cln
    pkg-config (at least Mac OS)

And the following R packages: 

    Rcpp (>= 0.10.4)
    BH
    RhpcBLASctl
    Rgraphviz
    pheatmap
    lattice
    lhs
    parallel

You can install those packages in R with:

    source("https://bioconductor.org/biocLite.R")
    biocLite(c("Rcpp","BH","RhpcBLASctl","Rgraphviz","pheatmap","lattice","lhs","parallel"))

Unix (MacOS, BSD, GNU/Linux) installation guide:
    For a local installation, first create a folder for local R library in (e.g "home/<Username>/R")
    Open shell go to the folder of the package (“STASNet”)
    execute: R CMD INSTALL ./ (when recompiling use R CMD INSTALL --preclean ./)
    
    Note: for some newer OS versions you have to specify the c++ version:
    prior to installing the package execute:
    export PKG_CXXFLAGS='`Rscript -e "Rcpp:::CxxFlags()"` -std=c++11'

Have fun with it! 

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If you use this program in publications, please cite one of the following paper:

Dorel, M.; Klinger, B.; Sieber, A.; Prahallad, A.; Gross, T.; Bosdriesz, E.; Wessels, L. and Blüthgen, N.
Modelling Signalling Networks from Perturbation Data.
Bioinformatics, early online, 2018. [doi](https://doi.org/10.1093/bioinformatics/bty473) 
 
Klinger, B.; Sieber, A.; Fritsche-Guenther, R.; Witzel, F.; Berry, L.; Schumacher, D.; Yan, Y.; Durek, P.; Merchant, M.; Schäfer, R.; Sers, C. and Blüthgen, N.
Network quantification of EGFR signaling unveils potential for targeted combination therapy.
Molecular Systems Biology, 9: 673, 2013. [doi](http://dx.doi.org/10.1038/msb.2013.29)