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[[http://sites.google.com/a/brainconnectivitytoolbox.net/bct/Home  Brain Connectivity Toolbox: Lots of .m files at University of Indiana for quite a few good network functions/analysis tools]]
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[[http://sites.google.com/a/brainconnectivitytoolbox.net/bct/Home  Brain Connectivity Toolbox]]: Lots of .m files at University of Indiana for quite a few good network functions/analysis tools
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[[http://sites.google.com/a/brainconnectivitytoolbox.net/bct/Home  Lots of .m files at University of Indiana for quite a few good network functions/analysis tools]]
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[[http://sites.google.com/a/brainconnectivitytoolbox.net/bct/Home  Brain Connectivity Toolbox: Lots of .m files at University of Indiana for quite a few good network functions/analysis tools]]
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[[http://netwiki.amath.unc.edu/VisComms/VisComms  Our "generalized Louvain" MATLAB code]]
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[[http://netwiki.amath.unc.edu/GenLouvain/GenLouvain  Our "generalized Louvain" MATLAB code]]
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[[http://www.clips.ua.ac.be/pages/pattern  Pattern: A web mining & natural language processing system for Python]]
[[http://bit.ly/h2MqlO  Tim Chartier's code for creating twitter networks from a set of specified tweeters]]
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[[http://wwwrp.lip6.fr/~latapy/PP/walktrap.html  PonsLatapy "walktrap" method for community detection via optimizing modularity]]
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[[http://wwwrp.lip6.fr/~latapy/PP/walktrap.html  PonsLatapy "walktrap" method for community detection via optimizing modularity]]
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[[http://www.clips.ua.ac.be/pages/pattern  Pattern: A web mining & natural language processing system for Python]]
[[http://bit.ly/h2MqlO  Tim Chartier's code for creating twitter networks from a set of specified tweeters]]
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[[http://findcommunities.googlepages.com/  "Louvain" method for community detection via optimizing modularity]]
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[[http://findcommunities.googlepages.com/  "Louvain" method]] for community detection via optimizing modularity
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[[http://findcommunities.googlepages.com/  "Louvain" method for community detection via optimizing modularity]]
[[http://perso.uclouvain.be/vincent.traag/Vincent Traag]] has released his [[https://launchpad.net/louvainLouvain Community Detection]] software, including a variety of options
[[http://cs.unm.edu/~aaron/research/fastmodularity.htm  code that performs community detection by optimizing modularity ]] (by Aaron Clauset, Mark Newman, and Cristopher Moore) *[[Profiles/Mason]]: Note that this uses the "2004 version" of modularity maximization. That is, it's using the same modularity we know and love but it is ''not'' an implementation of Mark's 2006 eigenvector method to maximize modularity.
[[http://sourceforge.net/project/showfiles.php?group_id=74309&package_id=149722  code that identifies modules and quantifies modularity of a network using an application of the information bottleneck]] (by Etay Ziv, Manuel Middendorf, and Chris Wiggins; see also [[http://www.columbia.edu/~chw2/code.htmlWiggins' code page]])
[[http://netwiki.amath.unc.edu/VisComms/VisComms  Our "generalized Louvain" MATLAB code]]
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[[http://findcommunities.googlepages.com/  "Louvain" method for community detection via optimizing modularity]]
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[[http://cs.unm.edu/~aaron/research/fastmodularity.htm  code that performs community detection by optimizing modularity ]] (by Aaron Clauset, Mark Newman, and Cristopher Moore) *[[Profiles/Mason]]: Note that this uses the "2004 version" of modularity maximization. That is, it's using the same modularity we know and love but it is ''not'' an implementation of Mark's 2006 eigenvector method to maximize modularity.
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[[http://sourceforge.net/project/showfiles.php?group_id=74309&package_id=149722  code that identifies modules and quantifies modularity of a network using an application of the information bottleneck]] (by Etay Ziv, Manuel Middendorf, and Chris Wiggins; see also [[http://www.columbia.edu/~chw2/code.htmlWiggins' code page]])
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[[http://bit.ly/h2MqlO  Tim Chartier's code for creating twitter networks from a set of specified tweeters]]
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[[http://www.clips.ua.ac.be/pages/pattern  Pattern: A web mining & natural language processing system for Python]]
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[[http://sites.google.com/a/brainconnectivitytoolbox.net/bct/Home  Lots of .m files at University of Indianapolis for quite a few good network functions/analysis tools]]
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[[http://sites.google.com/a/brainconnectivitytoolbox.net/bct/Home  Lots of .m files at University of Indiana for quite a few good network functions/analysis tools]]
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[[http://www.insna.org/INSNA/soft_inf.htmlComputer Programs for Social Network Analysis]], maintained by the [[http://www.insna.org/INSNA]]
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[[http://www.insna.org/INSNA/soft_inf.htmlComputer Programs for Social Network Analysis]], maintained by the [[http://www.insna.org/INSNA]] (webpage didn't work on 3/25/10, so did they move it?)
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[[ConnectomeViewerhttp://www.connectomeviewer.org]], is an opensource Pythonbased software for visualization and analysis of networks occuring in structural and functional neuroimaging, integration of surface, voxel and tract data.
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[[http://www.connectomeviewer.orgConnectomeViewer]], is an opensource Pythonbased software for visualization and analysis of networks occuring in structural and functional neuroimaging, integration of surface, voxel and tract data.
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[[ConnectomeViewerhttp://www.connectomeviewer.org]], is an opensource Pythonbased software for visualization and analysis of networks occuring in structural and functional neuroimaging, integration of surface, voxel and tract data.
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[[http://netwiki.amath.unc.edu/VisComms/VisComms  Our network visualization code]]
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[[http://netwiki.amath.unc.edu/VisComms/VisComms  Our "Visualization of Communities in Networks" code]]
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[[http://netwiki.amath.unc.edu/uploads/Data/igraph_06.tar  igraph 0.6 beta]]
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[[http://netwiki.amath.unc.edu/VisComms/VisComms  igraph 0.6 bet]]
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[[http://netwiki.amath.unc.edu/uploads/Data/igraph_06.tar  igraph 0.6 beta]]
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[[http://netwiki.amath.unc.edu/VisComms/VisComms  igraph 0.6 bet]]
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[[http://netwiki.amath.unc.edu/VisComms/VisComms  Our network visualization code]]
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[[http://gephi.orgGephi]] is an opensource network visualizer for exploring graph topology and data, creating hires printable maps, and organizing your work. Its easy extensible framework provides an API for customizing layouts, data sources, statistics, manipulation tools and graphical rendering.
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[[http://wwwrp.lip6.fr/~latapy/PP/walktrap.html  Community detection in very large graphs, PonsLatapy method]]
[[http://findcommunities.googlepages.com/  "Louvain" method for optimizing modularity]]
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[[http://wwwrp.lip6.fr/~latapy/PP/walktrap.html  PonsLatapy "walktrap" method for community detection via optimizing modularity]]
[[http://findcommunities.googlepages.com/  "Louvain" method for community detection via optimizing modularity]]
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[[http://findcommunities.googlepages.com/  "Louvain" method for optimizing modularity]]
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[[http://www.codeplex.com/NetMap.NetMap]] class libaries to add network graphs to applications, including an Excel 2007 Template. Also available: [[http://www.artifexconsulting.com/2008/09/netmapgraphfordummiesplotting.html  a copy of the template for use with matrices]].
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[[http://www.codeplex.com/NodeXLNodeXL]] class libaries to add network graphs to applications, including an Excel 2007 Template. Also available: [[http://www.artifexconsulting.com/2008/09/netmapgraphfordummiesplotting.html  a copy of the template for use with matrices]].
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[[http://deim.urv.cat/~sgomez/multidendrograms.phpMultiDendrograms]] "A hierarchical clustering tool"
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[[http://paristraceroute.net/  Paristraceroute]
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[[http://paristraceroute.net/  Paristraceroute]]
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[[http://wwwrp.lip6.fr/~magnien/Diameter/  Very efficient diameter and average distance approximations.]]
[[http://wwwrp.lip6.fr/~latapy/Triangles/  Triangle and clustering coefficient computations in massive graphs.]]
[[http://wwwrp.lip6.fr/~latapy/PP/walktrap.html  Community detection in very large graphs, PonsLatapy method]]
[[http://wwwrp.lip6.fr/~latapy/FV/generation.html  Generation of simple connected random graphs with prescribed degree distribution.]]
[[http://wwwrp.lip6.fr/~latapy/Measurement/  Measuring Fundamental Properties of RealWorld Complex Networks]]
[[http://wwwrp.lip6.fr/~latapy/Bip/  Basic Notions for the Analysis of Large Twomode Networks]]
[[http://paristraceroute.net/  Paristraceroute]
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[[http://www.indiana.edu/~cortex/connectivity_toolbox.html  Lots of .m files at University of Indianapolis for quite a few good network functions/analysis tools]]
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[[http://sites.google.com/a/brainconnectivitytoolbox.net/bct/Home  Lots of .m files at University of Indianapolis for quite a few good network functions/analysis tools]]
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[[http://vbmod.sourceforge.net/vbmod]]: variational bayesian inference for network modularity, by Jake Hofman and Chris Wiggins.
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[[http://vbmod.sourceforge.net/vbmod]]: variational bayesian inference for network modularity, by Jake Hofman and Chris Wiggins. ([[http://link.aps.org/abstract/PRL/v100/e258701related paper]])
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[[http://vbmod.sourceforge.net/vbmod]]: variational bayesian inference for network modularity, by Jake Hofman and Chris Wiggins.
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[[http://www.cs.bris.ac.uk/~steve/networks/index.htmlCONGA and CONGO]]: Algorithms to detect overlapping communities in networks.
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[[https://nwb.slis.indiana.edu/community/?n=Main.HomePageNetwork Workbench]]
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see also [[DataFormats.Software]]
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[[http://www.codeplex.com/NetMap.NetMap]] class libaries to add network graphs to applications, including an Excel 2007 Template. Also available: [[http://www.artifexconsulting.com/2008/09/netmapgraphfordummiesplotting.html  a copy of the template for use with matrices]].
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[[http://cs.unm.edu/~aaron/research/fastmodularity.htm  code that performs community detection by optimizing modularity ]] (by Aaron Clauset, Mark Newman, and Cristopher Moore) [[Profiles/Mason]]: Note that this uses the "2004 version" of modularity maximization. That is, it's using the same modularity we know and love but it is ''not'' an implementation of Mark's 2006 eigenvector method to maximize modularity.
to:
[[http://cs.unm.edu/~aaron/research/fastmodularity.htm  code that performs community detection by optimizing modularity ]] (by Aaron Clauset, Mark Newman, and Cristopher Moore) *[[Profiles/Mason]]: Note that this uses the "2004 version" of modularity maximization. That is, it's using the same modularity we know and love but it is ''not'' an implementation of Mark's 2006 eigenvector method to maximize modularity.
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[[http://cs.unm.edu/~aaron/research/fastmodularity.htm  code that performs community detection by optimizing modularity ]] (by Aaron Clauset, Mark Newman, and Cristopher Moore]] [[Profiles/Mason]]: Note that this uses the "2004 version" of modularity maximization. That is, it's using the same modularity we know and love but it is ''not'' an implementation of Mark's 2006 eigenvector method to maximize modularity.
to:
[[http://cs.unm.edu/~aaron/research/fastmodularity.htm  code that performs community detection by optimizing modularity ]] (by Aaron Clauset, Mark Newman, and Cristopher Moore) [[Profiles/Mason]]: Note that this uses the "2004 version" of modularity maximization. That is, it's using the same modularity we know and love but it is ''not'' an implementation of Mark's 2006 eigenvector method to maximize modularity.
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!!!!Libraries and Packages
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!!!Libraries and Packages
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!!!!Specific Codes for Specific Tasks
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!!!Specific Codes for Specific Tasks
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[[http://www.insna.org/INSNA/soft_inf.htmlComputer Programs for Social Network Analysis]], maintained by the [[http://www.insna.org/INSNA]]
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[[http://cs.unm.edu/~aaron/research/fastmodularity.htm  code that performs community detection by optimizing modularity ]] (by Aaron Clauset, Mark Newman, and Cristopher Moore]] [[Profiles/Mason]]: Note that this uses the "2004 version" of modularity maximization. That is, it's using the same modularity we know and love but it is ''not'' an implementation of Mark's 2006 eigenvector method to maximize modularity.
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!!!!Libraries and Packages
[[https://networkx.lanl.gov/  NetworkX]] (by [[http://math.lanl.gov/~hagberg/  Aric Hagberg]] and Pieter Swart)
[[http://www.maths.strath.ac.uk/research/groups/numerical_analysis/contest  CONTEST]] (CONTrolable TEST matrices) "is a random network toolbox for MATLAB that implements nine models," developed and maintained by Alan Taylor and Des Higham.
[[http://www.stanford.edu/~dgleich/programs/matlab_bgl/MatlabBGL]] "is a Matlab package for working with graphs. It uses the [[http://www.boost.org/libs/graph/doc/Boost Graph Library]] to efficiently implement the graph algorithms. MatlabBGL is designed to work with large sparse graphs with hundreds of thousands of nodes."
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[[http://wwwpersonal.umich.edu/~mejn/cart/  Michael Gastner and Mark Newman's cartogram code]]
[[http://wwwpersonal.umich.edu/~mejn/percolation/index.html  Mark Newman and R. M. Ziff's Monte Carlo code for site and bond percolation]]
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[[http://www.clairlib.orgThe Clair library]] is a suite of opensource Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA).
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!!!!Specific Codes for Specific Tasks
[[http://cs.unm.edu/~aaron/research/fastmodularity.htm  code that performs community detection by optimizing modularity ]] (by Aaron Clauset, Mark Newman, and Cristopher Moore]] [[Profiles/Mason]]: Note that this uses the "2004 version" of modularity maximization. That is, it's using the same modularity we know and love but it is ''not'' an implementation of Mark's 2006 eigenvector method to maximize modularity.
[[http://wwwpersonal.umich.edu/~mejn/cart/  Michael Gastner and Mark Newman's cartogram code]]
[[http://wwwpersonal.umich.edu/~mejn/percolation/index.html  Mark Newman and R. M. Ziff's Monte Carlo code for site and bond percolation]]
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[[https://networkx.lanl.gov/  NetworkX]] (by [[http://math.lanl.gov/~hagberg/  Aric Hagberg]] and Pieter Swart)
[[http://www.maths.strath.ac.uk/research/groups/numerical_analysis/contest  CONTEST]] (CONTrolable TEST matrices) "is a random network toolbox for MATLAB that implements nine models," developed and maintained by Alan Taylor and Des Higham.
[[http://www.insna.org/INSNA/soft_inf.htmlComputer Programs for Social Network Analysis]], maintained by the [[http://www.insna.org/INSNA]]
[[http://www.clairlib.orgThe Clair library]] is a suite of opensource Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA).
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[[http://www.indiana.edu/~cortex/connectivity_toolbox.html  Lots of .m files at University of Indianapolis for quite a few good network functions/analysis tools]]
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[[http://sourceforge.net/project/showfiles.php?group_id=74309&package_id=149722  code that identifies modules and quantifies modularity of a network using an application of the information bottleneck]] (by Etay Ziv, Manuel Middendorf, and Chris Wiggins)
to:
[[http://sourceforge.net/project/showfiles.php?group_id=74309&package_id=149722  code that identifies modules and quantifies modularity of a network using an application of the information bottleneck]] (by Etay Ziv, Manuel Middendorf, and Chris Wiggins; see also [[http://www.columbia.edu/~chw2/code.htmlWiggins' code page]])
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"[[http://books.google.com/books?id=4Ty5xP_KcpAC&printsec=frontcover#PPA270,M1Software for Social Network Analysis]]" by M. Huisman & M. A. J. van Duijn, pp.270316 in Peter J. Carrington, John Scott, & Stanley Wasserman (Eds.) "Models and Methods in Social Network Analysis" (2005).
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[[http://roflvidz.infoFunny Videos]]
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[[http://roflvidz.infoFunny Videos]]
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[[http://cneurocvs.rmki.kfki.hu/igraph  The igraph software library for network analysis]], containing fast opensource implementations for many common algorithms in graph theory and network science. Written in C, but interfaces with R, Python and Ruby.
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[[http://en.wikipedia.org/wiki/Social_network_analysis_software  Social network analysis software page on wikipedia]]

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%white% [[http://fakeblogping5.infofake blog ping]], [[http://doorst5.infodoorst5]]; [[http://holiday100search.infoholiday 100 search]]: [[http://searcheslookup.infosearch lookup]]  [[http://searcheslookup.info/search.php?q=home+loanshome loans]]
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%white% [[http://fakeblogping5.infofake blog ping]], [[http://doorst5.infodoorst5]]; [[http://holiday100search.infoholiday 100 search]]: [[http://searcheslookup.infosearch lookup]]  [[http://searcheslookup.info/search.php?q=home+loanshome loans]]
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[[http://www.clairlib.orgThe Clair library]] is a suite of opensource Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA).
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[[http://cs.unm.edu/~aaron/research/fastmodularity.htm  code that performs community detection by optimizing modularity ]] (by Aaron Clauset, Mark Newman, and Cristopher Moore]] [[Profiles/Mason]]: Note that this uses the "2004 version" of modularity maximization. That is, it's using the same modularity we know and love but it is ''not'' an implementation of Mark's 2006 eigenvector method to maximize modularity.
[[http://wwwpersonal.umich.edu/~mejn/cart/  Michael Gastner and Mark Newman's cartogram code]]
[[http://wwwpersonal.umich.edu/~mejn/percolation/index.html  Mark Newman and R. M. Ziff's Monte Carlo code for site and bond percolation]]
[[http://sourceforge.net/project/showfiles.php?group_id=74309&package_id=149722  code that identifies modules and quantifies modularity of a network using an application of the information bottleneck]] (by Etay Ziv, Manuel Middendorf, and Chris Wiggins)
[[https://networkx.lanl.gov/  NetworkX]] (by [[http://math.lanl.gov/~hagberg/  Aric Hagberg]] and Pieter Swart)
[[http://www.maths.strath.ac.uk/research/groups/numerical_analysis/contest  CONTEST]] (CONTrolable TEST matrices) "is a random network toolbox for MATLAB that implements nine models," developed and maintained by Alan Taylor and Des Higham.
[[http://www.insna.org/INSNA/soft_inf.htmlComputer Programs for Social Network Analysis]], maintained by the [[http://www.insna.org/INSNA]]


