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?
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.
On Mon, Jun 30, 2008 at 1:22 PM, jky <jaf....@gmail.com> wrote:
> 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
-- ____________________________________________________________ Michael Smoot, Ph.D. Bioengineering Department tel: 858-822-4756 University of California San Diego
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.
> 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
> On Mon, Jun 30, 2008 at 1:22 PM, jky <jaf....@gmail.com > <mailto:jaf....@gmail.com>> wrote:
> 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
> -- > ____________________________________________________________ > Michael Smoot, Ph.D. Bioengineering Department > tel: 858-822-4756 University of California San Diego
-- 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: dsta...@umich.edu tel: (734) 615-5510 fax: (734) 615-6553 URL: http://stateslab.bioinformatics.med.umich.edu
> 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
> On Mon, Jun 30, 2008 at 1:22 PM, jky <jaf....@gmail.com> wrote:
> > 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
> --
> ____________________________________________________________
> Michael Smoot, Ph.D. Bioengineering Department
> tel: 858-822-4756 University of California San Diego
