Cellular Automata

[Adam Treister]

Are there any Cytoscape apps to model networks based on cellular automata?  

I always get email from Wolfram Mathematica on Pi day (note that today's date is 3.14.16).  Stephen Wolfram's tome: A New Kind of Science is based on the premise that everything down to quantum physics is based on simple network functions.  Has anyone applied this to genetic or proteomic models?

Adam Treister

[Scooter Morris]

Hi Adam,
   I think ANIMO does something like that.  You want to give that a look.

-- scooter

[srikanth bezawada]

Hi Adam,

Were you able to find anything in that regard ?

Thanks,

Srikanth.

Try these Cytoscape apps!
CySpanningTree : apps.cytoscape.org/apps/cyspanningtree
Adj Exporter : apps.cytoscape.org/apps/adjexporter

TieDIE: apps.cytoscape.org/apps/tiedie

MClique : apps.cytoscape.org/apps/mclique

CyIsomorphism: apps.cytoscape.org/apps/cyisomorphism

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[Adam Treister]

Srikanth,

I followed thru the AMINO lead.  It’s a bridge to a program called UPPAAL which I got running as far as making a random walk thru a graph.  As I’m new to this, does anyone have a pointer to a template app (archetype?) where every time I hit the space bar, a function fires in each node that sets its selection from a threshold function of its neighbors selections.

Adam

[Mike Kucera]

You could implement your threshold function using the Filters API. It will run every time you click the "Apply" button in the select tab.