====== Discovering mixnet with a short practice ======
**(requires the installation of gnuplot and Cytoscape)**

  
# upload (remplacer ???? par le numero de version)\\
wget http://stat.genopole.cnrs.fr/_media/logiciels/mixnet/mixnet-1.????.tar.gz 


# extraction\\
tar zxvf mixnet-1.????.tar.gz



# licence\\
cd mixnet-1.0.0\\
more COPYING


# compilation and installation\\
./configure\\
make\\
make install

# you get an error if you are not root\\
# you should do the following\\

./configure --prefix=/yourhome/tmp\\
make install\\
export PATH=$PATH:/yourhome/tmp/bin


# help\\
# browse the web\\
mixnet -h\\
man mixnet


# Zachary karate club network\\
wget http://stat.genopole.cnrs.fr/_media/logiciels/mixnet/karate.spm\\
mixnet -q 4 karate.spm --undirected\\
xemacs karate_Q4.model\\
mixnet-cl karate_Q4.model\\
mixnet-cl karate_Q4.model\\
mixnet-cl karate_Q4.model --sum


# (suite) ICL\\
mixnet -q 1 -Q 15 karate.spm --undirected --improve\\
xemacs karate.likelihoods


# (suite) plot\\
gnuplot

<begin=gnuplot commands>\\
plot "karate.likelihoods"\\
plot "karate.likelihoods" with lines\\
plot "karate.likelihoods" index 0 w l\\
plot "karate.likelihoods" using ($0+1):($1) index 2 w l\\
<end=gnuplot commands>


# (suite) Cytoscape\\
mixnet-cl karate_Q4.model --cytoscape > karate_Q4.attributes\\
Cytoscape

<begin=Cytoscape clicks>\\
File->Import->Network from table ~> karate.spm\\
File->Import->Nodes attributes ~> karate_Q4.attributes\\
VizMapper->NodeColor then SelectValue->MixNetClass then SelectValue->DiscreteMapping\\
Layout->yFiles->Organic\\
<end=Cytoscape clicks>



# (suite) simulation\\
mixnet-sim karate_Q4.model -n 50 --undirected\\
mixnet-sim karate_Q4.model -i karate.spm --verbose --undirected > karate_simu.spm\\
mixnet -q 4 karate_simu.spm --undirected\\
mixnet-cl karate_simu_Q4.model --cytoscape > karate_simu_Q4.attributes\\
Cytoscape



# Newman football club network (optionnal)\\
wget http://stat.genopole.cnrs.fr/_media/logiciels/mixnet/football.spm\\
mixnet -q 1 -Q 20 football.spm --undirected --improve\\
gnuplot

<begin=gnuplot commands>\\
plot "football.likelihoods" using ($0+1):($1) index 2 w l\\
<end=gnuplot commands>



# Sporns macaque cortex network\\
wget http://stat.genopole.cnrs.fr/_media/logiciels/mixnet/cortex.spm

# (suite) Cytoscape\\
Cytoscape\\

<begin=Cytoscape clicks>\\
File->Import->Network from table ~> cortex.spm\\
Layout->yFiles->Organic\\
<end=Cytoscape clicks>



# (suite) ICL\\
mixnet -q 1 -Q 20 cortex.spm\\
mv cortex.likelihoods cortex.likelihoods.0\\
mixnet -q 1 -Q 20 cortex.spm -I . --improve\\
xemacs cortex_Q8.model



# (suite) plot\\
gnuplot

<begin=gnuplot commands>\\
plot "cortex.likelihoods.0" using ($0+1):($1) index 0 w l\\
replot "cortex.likelihoods" using ($0+1):($1) index 0 w l\\
plot "cortex.likelihoods" using ($0+1):($1) index 2 w l\\
<end=gnuplot commands>



# (suite) Cytoscape\\
mixnet-cl cortex_Q6.model --cytoscape > cortex_Q6.attributes\\
mixnet-cl cortex_Q8.model --cytoscape > cortex_Q8.attributes\\
Cytoscape\\

<begin=Cytoscape clicks>\\
File->Import->Nodes attributes ~> cortex_Q6.attributes\\
VizMapper->NodeColor then SelectValue->MixNetClass then SelectValue->DiscreteMapping\\
File->Import->Nodes attributes ~> cortex_Q8.attributes\\
VizMapper->NodeColor then SelectValue->MixNetClass then SelectValue->DiscreteMapping\\
Layout->CytoscapeLayout->DegreeSortedCircleLayout\\
VizMapper->NodeLabel then SelectValue->Degree\\
Layout->yFiles->Organic\\
<end=Cytoscape clicks>


[[:logiciels:mixnet|Back to MixNet Homepage]].