Our project on social (citation and collaboration) networks in British and German political science involves networks with hundreds and thousands of nodes (scientists and articles). At the moment, our data come from the Social Science Citation Index (part of the ISI web of knowledge), and we use a bundle of rather eclectic (erratic?) scripts written in Perl to convert the ISI records into something that programs like Pajek or Stata can read. Some canned solutions (Wos2pajek, network workbench, bibexcel) are available for free, but I was not aware of them when I started this project, did not manage to install them properly, or was not happy with the results. Perl is the Swiss Army Chainsaw (TM) for data pre-processing, incredibly powerful (my scripts are typically less than 50 lines, and I am not an efficient programmer), and every time I want to do something in a slightly different way (i.e. I spot a bug), all I have to do is to change a few lines in the scripts.
After trying a lot of other programs available on the internet, we have chosen Pajek for doing the analyses and producing those intriguing graphs of cliques and inner circles in Political Science. Pajek is closed source but free for non-commercial use and runs on Windows or (via wine) Linux. It is very fast, can (unlike many other programs) easily handle very large networks, produces decent graphs and does many standard analyses. Its user interface may be slightly less than straightforward but I got used to it rather quickly, and it even has basic scripting capacities.

The Missing Manual

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