(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>

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