subway network maps

Q:

I’ve really enjoyed seeing your subway network maps. Our institute at Duke has an external review coming up, and I was wondering if any of the code you’ve developed might be applicable to visualize the published interactions within our institute as well as outside with other investigators across the Duke campus.

Thoughts, or is this still too early?

And I bet I’m not the only one who would be interested in this. Are you planning to publish this method? I would think many universities/groups would find this informative to understand where the interactions are happening across campus and where they aren’t happening enough.

A:
I am very enthusiastic that you find our analysis of publication
networks interesting. We just sent out a more extensive description
of this to the analysis group.

In relation to the software, we actually constructed a package for
doing literature networks and distributed some software associated
with it. It is called PubNet and it is available at
pubnet.gersteinlab.org. Unfortunately the web server does not work
that well as of late, mostly due to changes in the NCBI’s PubMed
system, but you can still download the software and do the queries
manually if you want to. I hope this is of use.

Pubnet

Q:

I just tried to access Pubnet again and it stopped at the parsing XML stage. Please let me know if this is my error or if the site is no longer functional.

A:

PubNet stopped functioning when NCBI changed their data APIs. We are working on fixing it.