python scripting

[David Epstein]

Hi everyone,

I am new to Cytoscape and am interested in learning more about python
scripting. I can create nodes and edges. But, how do I create and
alter attributes, focus and zoom the view, set and apply filters, and
alter selections?

Also, are most people storing data in physical files rather than a
relational database?


-david

[swaraj basu]

Hello,
you can create nodes from cytoscape editor in the cytoscape
control panel.

[Keiichiro Ono]

Hi.
In general, Cytoscape Scripting feature uses JVM implementation of
scripting languages, such as Jython, JRuby, or Rhino. You can
directly access Cytoscape public Java API from scripting languages:

http://chianti.ucsd.edu/Cyto-2_6_3/javadoc/

Thanks.
Kei


2009/10/23 David Epstein <davi...@umich.edu>:

--
Keiichiro Ono ko...@ucsd.edu

Cytoscape Core Developer Team: http://www.cytoscape.org/
UCSD School of Medicine Trey Ideker Lab: http://chianti.ucsd.edu/idekerlab/

[David Lawrence Epstein]

Hi Keiichiro,

Thank you for your earlier response. I'm looking through the javadocs.
Are there more example scripts online or available besides those
listed at the site:

http://cytoscape.wodaklab.org/wiki/ScriptingPlugins#Python_.28New.21.29

I may be able to do more if I can see how others have accomplished
basic tasks.

-david