Network Simulation with Cytoscape

[jky]

Hi

I'd like to use Cytoscape to visualize neural networks - but have many
questions about it's potential role. Could Cytoscape also be used as a
pure simulation tool? Could it perform well enough compared to a Java
app written specifically for that purpose? Or would it be better to
use Cytoscape only for visualization? Finally, does Cytoscape support
updating the visual representation as state data changes?

Thanks
jky

[Mike Smoot]

Cytoscape is generally for visualization of networks.  Instead of building lots of analysis and simulation into Cytoscape, we let users write their own plugins to do their specific analysis.  So whether Cytoscape could be used as a simulation tool depends on whether a plugin exists to do what you want.  If you've already got a java app that does the simulation you'd like, then it would probably be best to use that for the simulation and Cytoscape for the visualization of the results.  Yes, Cytoscape can update its view as state data changes.


Mike

--
____________________________________________________________
Michael Smoot, Ph.D. Bioengineering Department
tel: 858-822-4756 University of California San Diego

[David J. States]

Cytoscape was designed for interactive editing and visualization rather than computationally efficient numerics.  In particular, if the simulation involves creating and destroying many networks, the Cytoscape data structures may run into problems.  On the other hand, the plugin interface lets you link in an arbitrary Java application so you can run your analysis in your own data structures and access  the visualization, annotation, analysis and link out functions of Cytoscape.

David

-- 
David J. States, M.D., Ph.D.
Professor of Human Genetics
Director of Bioinformatics Training Program
University of Michigan School of Medicine
Palmer Commons 2035B
100 Washtenaw Rd.
Ann Arbor, MI 48109 USA
email: dst...@umich.edu
tel: (734) 615-5510
fax: (734) 615-6553
URL: http://stateslab.bioinformatics.med.umich.edu

[jky]

Thank you very much for the replies, this answers my question
perfectly.

jky