Matlab implementation of the DUNE PPI network evolution model
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README.md
RT_save_figures_Cvk.m
RT_save_figures_E2.m
RT_save_figures_Q.m
RT_save_figures_bvk.m
RT_save_figures_d.m
RT_save_figures_f1.m
RT_save_figures_frag.m
RT_save_figures_gcc.m
RT_save_figures_loss.m
RT_save_figures_nvk.m
RT_save_figures_pb.m
RT_save_figures_pk.m
RT_save_figures_plambda.m
RT_save_figures_px.m
final_snapshot.m
pointmutation.m
ppi.m
ppi_dyn.m
ppi_import.m
std_dyn.m
std_stat.m
std_tracking.m
trackstats.m

README.md

ppi.m is an implementation of the DUNE (DUplication & NEofunctional- ization) model of eukaryotic protein-protein interaction network evolution. Please see http://ppi.tinybike.net for project details. To run, this script requires several supporting files:

  • ppi_import.m (data import, requires adjacency matrix as input file)
  • pointmutation.m (neofunctionalization/assimilation events)
  • timedepstats.m (updates dynamical properties at specified intervals)
  • trackstats.m (updates degree and betweenness "tracking" values)

In addition to these, the MatlabBGL package: http://www.mathworks.com/matlabcentral/fileexchange/10922 and Louvain modularity algorithm: https://sites.google.com/a/brain-connectivity-toolbox.net/bct/ are also required.

The following files can be used to calculate various statistics and plot several static and dynamic quantities obtained from the simulation, but are not required to run ppi.m:

  • std_dyn.m (calculates dynamical statistics)
  • std_stat.m (calculates static end-state statistics)
  • std_tracking.m (calculates degree and betweenness "tracking" statistics)
  • ppi_dyn.m (prepares dynamical quantities for plotting)
  • RT_save_figures_bvk.m (betweenness vs degree)
  • RT_save_figures_nvk.m (nearest-neighbor degree vs degree)
  • RT_save_figures_Cvk.m (clustering coefficients vs degree)
  • RT_save_figures_E2.m (second-largest eigenvalue evolution)
  • RT_save_figures_px.m (closeness distribution)
  • RT_save_figures_plambda.m (walk matrix eigenvalue distribution)
  • RT_save_figures_pb.m (betweenness distribution)
  • RT_save_figures_pk.m (degree distribution)
  • RT_save_figures_gcc.m (global clustering coefficient evolution)
  • RT_save_figures_Q.m (modularity coefficient evolution)
  • RT_save_figures_d.m (diameter evolution)
  • RT_save_figures_f1.m (largest component evolution)

Jack Peterson (jack@tinybike.net)

License: LGPL