====== MixNet ======

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This program implements the variationnal EM algorithm for directed and undirected networks.

===== Running mixnet =====
  
mixnet -q <int> -Q <int>  <filename.spm>  [options]

Main options are:
    *  - -undirected : Specifies that the network is undirected
    *  - -improve : Performs improvements of unsatisfying models


For a complete options list:

mixnet -h 
man mixnet


===== Post-treating the results ===== 
MixNet provides two Perl programs:

    * **mixnet-cl** c From a MixNet .model file, displays the class of each nodel and creates file for Cytoscape
    * **mixnet-sim** From a MixNet .model file, simulate a network


===== Reading the pdf documentation ===== 

    * {{:logiciels:mixnet:mixnet-doc.pdf|Implemented algorithms}}


===== A short practice ===== 

    * [[:logiciels:mixnet:practise|A few lines to discover mixnet]]


===== References ===== 
[1] Daudin J.J, Picard F, Robin S, [[http://hal.inria.fr/inria-00070186/en/|A mixture model for random graphs]], Rapport INRIA n°5840, 2006 .


[2] M.Mariadassou , J.J.Daudin, V.Lacroix, V.Miele, F.Picard, S.Robin, M.F.Sagot, Uncovering structure in biological networks, RIAMS, 2006.

[3] Daudin, J.-J., Picard, F.Robin, S.,  Mixture model for random graphs, Statistics and Computing, 2008.

[4] Picard F, Miele.V., Daudin J.J, Robin S, [[http://www.biomedcentral.com/1471-2105/10/S6/S17/abstract|Deciphering the connectivity structure of biological networks using MixNet]], BMC Bioinformatics, 2009 


===== Project Team ===== 

    * Statisticians: Jean-Jacques Daudin, Franck Picard, Stéphane Robin.
    * Developers: Mark Hoebeke, Vincent Miele.

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