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Changed line 26 from:
[[http://sites.google.com/a/brain-connectivity-toolbox.net/bct/Home | Brain Connectivity Toolbox: Lots of .m files at University of Indiana for quite a few good network functions/analysis tools]]
to:
[[http://sites.google.com/a/brain-connectivity-toolbox.net/bct/Home | Brain Connectivity Toolbox]]: Lots of .m files at University of Indiana for quite a few good network functions/analysis tools
Changed line 26 from:
[[http://sites.google.com/a/brain-connectivity-toolbox.net/bct/Home | Lots of .m files at University of Indiana for quite a few good network functions/analysis tools]]
to:
[[http://sites.google.com/a/brain-connectivity-toolbox.net/bct/Home | Brain Connectivity Toolbox: Lots of .m files at University of Indiana for quite a few good network functions/analysis tools]]
August 03, 2012, at 05:51 PM by Mason - fixed typo in url (thanks to Charlite Brummitt for pointing this out)
Changed line 44 from:
[[http://netwiki.amath.unc.edu/VisComms/VisComms | Our "generalized Louvain" MATLAB code]]
to:
[[http://netwiki.amath.unc.edu/GenLouvain/GenLouvain | Our "generalized Louvain" MATLAB code]]
Deleted lines 47-50:
[[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://www-rp.lip6.fr/~latapy/PP/walktrap.html | Pons-Latapy "walktrap" method for community detection via optimizing modularity]]
Deleted lines 55-56:
[[http://www-rp.lip6.fr/~latapy/PP/walktrap.html | Pons-Latapy "walktrap" method for community detection via optimizing modularity]]
Added lines 63-66:

[[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]]
Changed line 35 from:
[[http://findcommunities.googlepages.com/ | "Louvain" method for community detection via optimizing modularity]]
to:
[[http://findcommunities.googlepages.com/ | "Louvain" method]] for community detection via optimizing modularity
Added lines 35-45:
[[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/louvain|Louvain 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.html|Wiggins' code page]])

[[http://netwiki.amath.unc.edu/VisComms/VisComms | Our "generalized Louvain" MATLAB code]]

Deleted lines 59-60:
[[http://findcommunities.googlepages.com/ | "Louvain" method for community detection via optimizing modularity]]
Deleted lines 67-69:
[[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.

Deleted lines 70-71:

[[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.html|Wiggins' 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]]
February 04, 2011, at 09:52 AM by 129.67.187.18 -
Changed line 26 from:
[[http://sites.google.com/a/brain-connectivity-toolbox.net/bct/Home | Lots of .m files at University of Indianapolis for quite a few good network functions/analysis tools]]
to:
[[http://sites.google.com/a/brain-connectivity-toolbox.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.html|Computer Programs for Social Network Analysis]], maintained by the [[http://www.insna.org/|INSNA]]
to:
[[http://www.insna.org/INSNA/soft_inf.html|Computer 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?)
March 09, 2010, at 11:16 AM by 140.182.250.191 -
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[[ConnectomeViewer|http://www.connectomeviewer.org]], is an open-source Python-based software for visualization and analysis of networks occuring in structural and functional neuroimaging, integration of surface, voxel and tract data.
to:
[[http://www.connectomeviewer.org|ConnectomeViewer]], is an open-source Python-based software for visualization and analysis of networks occuring in structural and functional neuroimaging, integration of surface, voxel and tract data.
March 09, 2010, at 11:16 AM by 140.182.250.191 -
Added lines 29-31:

[[ConnectomeViewer|http://www.connectomeviewer.org]], is an open-source Python-based 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]]
to:
[[http://netwiki.amath.unc.edu/VisComms/VisComms | Our "Visualization of Communities in Networks" code]]
October 25, 2009, at 06:21 PM by 72.130.190.23 -
Deleted lines 67-68:

[[http://netwiki.amath.unc.edu/uploads/Data/igraph_06.tar | igraph 0.6 beta]]
October 25, 2009, at 12:58 AM by 72.130.190.23 -
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[[http://netwiki.amath.unc.edu/VisComms/VisComms | igraph 0.6 bet]]
to:
[[http://netwiki.amath.unc.edu/uploads/Data/igraph_06.tar | igraph 0.6 beta]]
October 25, 2009, at 12:54 AM by 72.130.190.23 -
Changed line 69 from:
[[igraph 0.6 beta]]
to:
[[http://netwiki.amath.unc.edu/VisComms/VisComms | igraph 0.6 bet]]
October 25, 2009, at 12:53 AM by 72.130.190.23 -
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[[igraph 0.6 beta]]
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[[http://netwiki.amath.unc.edu/VisComms/VisComms | Our network visualization code]]
September 22, 2009, at 04:45 AM by 89.224.42.36 - Added Gephi software
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[[http://gephi.org|Gephi]] is an open-source network visualizer for exploring graph topology and data, creating hi-res printable maps, and organizing your work. Its easy extensible framework provides an API for customizing layouts, data sources, statistics, manipulation tools and graphical rendering.
Changed lines 36-38 from:
[[http://www-rp.lip6.fr/~latapy/PP/walktrap.html | Community detection in very large graphs, Pons-Latapy method]]

[[http://findcommunities.googlepages.com/ | "Louvain" method for optimizing modularity]]
to:
[[http://www-rp.lip6.fr/~latapy/PP/walktrap.html | Pons-Latapy "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]]
June 30, 2009, at 12:05 PM by 76.188.251.164 -
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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.artifex-consulting.com/2008/09/netmapgraph-for-dummies-plotting.html | a copy of the template for use with matrices]].
to:
[[http://www.codeplex.com/NodeXL|NodeXL]] class libaries to add network graphs to applications, including an Excel 2007 Template. Also available: [[http://www.artifex-consulting.com/2008/09/netmapgraph-for-dummies-plotting.html | a copy of the template for use with matrices]].
Added lines 29-30:

[[http://deim.urv.cat/~sgomez/multidendrograms.php|MultiDendrograms]] "A hierarchical clustering tool"
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[[http://paris-traceroute.net/ | Paris-traceroute]
to:
[[http://paris-traceroute.net/ | Paris-traceroute]]
January 20, 2009, at 08:25 AM by ML - added complexnetworks.fr links
Added lines 30-42:
[[http://www-rp.lip6.fr/~magnien/Diameter/ | Very efficient diameter and average distance approximations.]]

[[http://www-rp.lip6.fr/~latapy/Triangles/ | Triangle and clustering coefficient computations in massive graphs.]]

[[http://www-rp.lip6.fr/~latapy/PP/walktrap.html | Community detection in very large graphs, Pons-Latapy method]]

[[http://www-rp.lip6.fr/~latapy/FV/generation.html | Generation of simple connected random graphs with prescribed degree distribution.]]

[[http://www-rp.lip6.fr/~latapy/Measurement/ | Measuring Fundamental Properties of Real-World Complex Networks]]

[[http://www-rp.lip6.fr/~latapy/Bip/ | Basic Notions for the Analysis of Large Two-mode Networks]]

[[http://paris-traceroute.net/ | Paris-traceroute]
Changed line 26 from:
[[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]]
to:
[[http://sites.google.com/a/brain-connectivity-toolbox.net/bct/Home | Lots of .m files at University of Indianapolis for quite a few good network functions/analysis tools]]
November 17, 2008, at 02:19 PM by 209.131.60.67 -
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[[http://vbmod.sourceforge.net/|vbmod]]: variational bayesian inference for network modularity, by Jake Hofman and Chris Wiggins.
to:
[[http://vbmod.sourceforge.net/|vbmod]]: variational bayesian inference for network modularity, by Jake Hofman and Chris Wiggins. ([[http://link.aps.org/abstract/PRL/v100/e258701|related paper]])
November 17, 2008, at 02:15 PM by 209.131.60.67 -
Added lines 42-43:

[[http://vbmod.sourceforge.net/|vbmod]]: variational bayesian inference for network modularity, by Jake Hofman and Chris Wiggins.
November 01, 2008, at 03:50 PM by Steve Gregory - CONGA and CONGO
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[[http://www.cs.bris.ac.uk/~steve/networks/index.html|CONGA and CONGO]]: Algorithms to detect overlapping communities in networks.
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[[https://nwb.slis.indiana.edu/community/?n=Main.HomePage|Network Workbench]]
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[[Amazon Books]]
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see also [[DataFormats.Software]]
Added line 35:
[[http://www.codeplex.com/NetMap|.NetMap]] class libaries to add network graphs to applications, including an Excel 2007 Template. Also available: [[http://www.artifex-consulting.com/2008/09/netmapgraph-for-dummies-plotting.html | a copy of the template for use with matrices]].
Changed lines 26-27 from:
[[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.
Changed line 26 from:
[[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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!!!!Overviews
to:
!!!Overviews
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!!!!Libraries and Packages
to:
!!!Libraries and Packages
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!!!!Specific Codes for Specific Tasks
to:
!!!Specific Codes for Specific Tasks
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!!!!Overviews
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[[http://www.insna.org/INSNA/soft_inf.html|Computer Programs for Social Network Analysis]], maintained by the [[http://www.insna.org/|INSNA]]
Changed lines 10-13 from:
-----

[[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:
!!!!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."
Changed lines 20-23 from:
[[http://www-personal.umich.edu/~mejn/cart/ | Michael Gastner and Mark Newman's cartogram code]]

[[http://www
-personal.umich.edu/~mejn/percolation/index.html | Mark Newman and R. M. Ziff's Monte Carlo code for site and bond percolation]]
to:
[[http://www.clairlib.org|The Clair library]] is a suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA).
Added lines 24-31:
!!!!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://www-personal.umich.edu/~mejn/cart/ | Michael Gastner and Mark Newman's cartogram code]]

[[http://www-personal.umich.edu/~mejn/percolation/index.html | Mark Newman and R. M. Ziff's Monte Carlo code for site and bond percolation]]

Deleted lines 33-39:
[[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.html|Computer Programs for Social Network Analysis]], maintained by the [[http://www.insna.org/|INSNA]]

[[http://www.clairlib.org|The Clair library]] is a suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA).
Added lines 15-16:

[[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.html|Wiggins' code page]])
Added lines 2-4:

"[[http://books.google.com/books?id=4Ty5xP_KcpAC&printsec=frontcover#PPA270,M1|Software for Social Network Analysis]]" by M. Huisman & M. A. J. van Duijn, pp.270-316 in Peter J. Carrington, John Scott, & Stanley Wasserman (Eds.)
"Models and Methods in Social Network Analysis" (2005).
Deleted lines 21-22:

[[http://roflvidz.info|Funny Videos]]
April 11, 2008, at 07:14 PM by 85.241.91.49 -
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[[http://roflvidz.info|Funny Videos]]
February 29, 2008, at 10:31 AM by 84.3.51.82 - Added igraph library
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[[http://cneurocvs.rmki.kfki.hu/igraph | The igraph software library for network analysis]], containing fast open-source implementations for many common algorithms in graph theory and network science. Written in C, but interfaces with R, Python and Ruby.
Added lines 1-4:
[[http://en.wikipedia.org/wiki/Social_network_analysis_software | Social network analysis software page on wikipedia]]

-----

Deleted line 1:
%white% [[http://fakeblogping5.info|fake blog ping]], [[http://doorst5.info|doorst5]]; [[http://holiday100search.info|holiday 100 search]]: [[http://searcheslookup.info|search lookup]] | [[http://searcheslookup.info/search.php?q=home+loans|home loans]]
Added line 2:
%white% [[http://fakeblogping5.info|fake blog ping]], [[http://doorst5.info|doorst5]]; [[http://holiday100search.info|holiday 100 search]]: [[http://searcheslookup.info|search lookup]] | [[http://searcheslookup.info/search.php?q=home+loans|home loans]]
Added lines 14-15:

[[http://www.clairlib.org|The Clair library]] is a suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA).
Added lines 1-13:
[[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://www-personal.umich.edu/~mejn/cart/ | Michael Gastner and Mark Newman's cartogram code]]

[[http://www-personal.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.html|Computer Programs for Social Network Analysis]], maintained by the [[http://www.insna.org/|INSNA]]