This is a readme file explaining the main feautres of the matlab package 
multiSw.zip. The software is meant to be working software and is largely 
non-optimised and uncommented; the purpose is to illustrate how the model 
works, not to release commercial-grade software. 

The package contains two demo files to reproduce the results in the paper. 
demoToyMulti.m first generates synthetic data (using MSDataGenerateMulti.m); 
the simulated TF profiles and connectivity are stored in variables extField and
X respectively. parameters are stored in a structured variable params (with 
extensions A, lambda, b and sigma). The other demo file (demoYeastMultiAlt2.m) 
first loads the data from Tu et al. Both files then call the file 
MSOptimizeMulti.m which performs the saddle-point optimisation by calling the 
subsidiary functions. The results are saved at the end of the procedure.