Automorphism Cytoscape app

9 views
Skip to first unread message

srikanth bezawada

unread,
Apr 21, 2016, 5:29:59 PM4/21/16
to cytoscap...@googlegroups.com
Hi,

I'm working on a Cytoscape app which finds all symmetries in a network (Automorphism). Any ideas on how to represent the output ?


Thanks,
Srikanth.B.

Martin Cerny

unread,
Apr 22, 2016, 6:36:05 AM4/22/16
to cytoscap...@googlegroups.com
Hi,
well, it sounds difficult :-) It also depends on what you expect the user to need to learn from the automorphisms. For a general understanding of the structure of the automorphisms, I guess you could show a minimal set of generators for the automorphism group. You could have the original graph coloured and for each such generator show how it transforms the colors (or numbers if there are too many vertices) in a separate graph in the network..., graying out the nodes that do not change for this generator. You could also let the user to filter only the generators of a given cycle size. But I do not know if this is computationally tractable.

I have also heard there are methods to find a drawing of a graph that displays some of the automorphisms as rotational/reflection symmetries in the drawing, but I have not read the papers:
http://www.sciencedirect.com/science/article/pii/S030439759900239X
http://link.springer.com/chapter/10.1007%2F3-540-45848-4_16

Well, thats my 5 cents, hope it does not ignore some fundemental thing about automorphisms - group theory is definitely not my strongest :-)

Good luck with the app!
Martin Cerny

--
You received this message because you are subscribed to the Google Groups "cytoscape-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-disc...@googlegroups.com.
To post to this group, send email to cytoscap...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-discuss.
For more options, visit https://groups.google.com/d/optout.

srikanth bezawada

unread,
Apr 25, 2016, 8:30:54 PM4/25/16
to cytoscap...@googlegroups.com, cer...@gmail.com
Hi Martin,

Thanks for the descriptive answer and references. I'm also new to this topic, so not really sure :-) 

Thanks,
Srikanth.
Reply all
Reply to author
Forward
0 new messages