A Network Analysis and Cytoscape Tutorial

I’ve finally completed a tutorial I’d long promised on network analysis and plotting graphs with Cytoscape, making use of the Network Analyzer tools to exemplify important concepts in graph theory! It’s probably riddled with errors, so thanks for any feedback and corrections here. It is also liberally dotted with screen captures, and I hope this provides a useful, in-depth introduction.


This accompanies my posts here on Locational Terms and Concepts in Network Analysis  and on my Thalaba Network Analysis Project.



The Digital Mitford’s Guide to 19th-Century British Postmarks, and How To Code Them in TEI

Sharing from our Digital Mitford Project Blog–a very helpful annotated guide to TEI encoding of the more challenging aspects of 19th-c. manuscript letters.

Digital Mitford

Here is a colorful, annotated series of powerpoint slides prepared by Greg Bondar, working from my notes on TEI coding, our photos of letters from the Reading Central Library (posted with their permission), and information from the canonical reference tome, Alcock and Holland’s The Postmarks of Great Britain and Ireland. (You really need to borrow the print book from a library-not enough of it is available online.) This should help us with identifying and encoding some of the more challenging aspects of 19th-century mansucript letters! Thanks, Greg!

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New Developments in the Thalaba Antisocial Network Analysis

Practical Matters: Working in Cytoscape:

See my Tutorial, An Introduction to Network Analysis and Cytoscape for XML Coders for a much more detailed explanation of how to read and make network graphs, and step-by-step advice on things you can do and try with Cytoscape’s network analyzer tools.

Sample .tsv file for import to Cytoscape:

Use import wizard to designate nodes and edges, and node + edge attributes for use in labelling info.

Eliminate self-loops and remove duplicated edges in Edit menu (or find ways to filter out unnecessary information that clutters your graph).

Use the Network Analyzer to calculate network statistics. Think about them. Choose among graphical layouts with care.

Of interest in my original graph was Betweenness Centrality of Nodes. Where does my network of places break (cutpoints)? Metaplaces were essential to network coherence.

Now, I’ve generated some new graphs to simplify our view of the places, eliminate the clutter of line-group nodes (moving that information to the edges). And I’m interested in Path Lengths of Edges (Average Shortest Path Length), and Closeness of Nodes.

Here’s a new network graph oriented to Closeness Centrality of Nodes (SVG output from Cytoscape).

I’m also measuring the Eccentricity of the Nodes–how far they are from each other, which produced a rather remarkable result: (SVG output from Cytoscape)

Day of DH 2014, and Pennsylvania Digital Humanists–Forming a Network?


There is a new Keystone DH Group forming on the Day of DH 2014 site, initially organized by Chris Long at Penn State University and Diane Jackaci at Bucknell University. It’s an effort to organize DH people from the state of PA together, and it could be good for interested Pennsylvanians to help build this and promote it. (Who knows–we could find ourselves pooling resources to organize a “PADH” conference or some such madness!) 
The group is organizing through Day of DH 2014, coming up next Tues. April 8. I’ve just signed up to participate in Day of DH and to join the Keystone DH group there (on the group pages). If you’re here with me in the state of PA, and you work on digital humanities projects you may want to sign up, too! 
Keystone DH Google Plus Community Page: : https://plus.google.com/communities/106531799213972398416
The Keystone Group seems to be just now forming–not many members yet: I know there are many more of us DH-istas here in PA, and it would be great to see us all form a supportive network! 


Digital Mitford Annual June Workshop Set: June 2, 3, and 4, 2014

Digital Mitford

Image Mary Russell Mitford in Pieces

We are calling for participants to join the Digital Mitford: the Mary Russell Mitford Archive, at http://mitford.pitt.edu. If you are interested in learning TEI coding and participating in a large-scale digital archive project now well underway, we are happy to orient you to the project as part of our June workshop series.

We are hosting our second of what we hope will be an annual series of face-to-face workshop sessions at the lovely Pitt-Greensburg campus, during the first week of June 2014. The dates are now set, so that we expect people to arrive on Saturday or Sunday May 31 / June 1, and depart on Thurs. June 5, with our workshops running during the days throughout Mon. – Wed. June 2 – June 4. (This is basically the same timing as last year’s launch workshops.)

Please share this message with any researcher whom…

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Digital scholarship in the humanities: Will post carry the same weight as publish?

Digital scholarship in the humanities: Will post carry the same weight as publish?

Pitt’s University Times interviewed me along with some other very fine people from across the university on digital humanities projects and their prospects for recognition as quality scholarship in academia.

Digital Mitford Annual June Workshop Set: June 2, 3, and 4.

Mitford Puzzle
Mary Russell Mitford in Pieces!

Calling all our Digital Mitford editors, and inviting new people to join us! We’re hosting our second annual Digital Mitford Projects Workshops at the beautiful Pitt-Greensburg campus again, in the first week of June. (Arrive Sunday June 1, depart Thurs. June 5). Details to come. We’re likely to have the cost of the residence on campus covered, but probably can’t cover travel funds on our own (waiting to hear from a grant application…) For now, we ask our editors and new editors to look about for local funding sources…and we’ll keep you posted! (Editors, look for a more detailed e-mail to follow soon.)