Cytoscape plugin development with some Python code inside

[Guillaume Dumas]

Hi!

can we embed Python script into a Cytoscape plugin without having to install the Jython Scripting Engine?

If not, is there a dependency management in the App store?

Thanks for the help!

Cheers,

Guillaume

[Keiichiro Ono]

Hi Guillaume.

Due to the many known limitations in Jython, we decide to implement
language-agnostic RESTful API instead of maintaining each JVM
scripting language runtimes.
If you want to use Python for driving Cytoscape, there are some examples:

http://nbviewer.ipython.org/github/idekerlab/cy-rest-python/blob/develop/index.ipynb

Cookbook:
http://nbviewer.ipython.org/github/idekerlab/cy-rest-python/blob/develop/basic/CyREST_Cookbook.ipynb

Tutorials:
https://github.com/idekerlab/cyREST/wiki/VIZBI-2015-Tutorial
https://github.com/idekerlab/sdcsb-advanced-tutorial/wiki

Please let me know if these cannot cover your use cases.

Thanks,
Kei

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Keiichiro Ono
http://keiono.github.io/

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