Software recommended for creating BioPAX from scratch

[Kozo Nishida]

Hi BioPAX community,

Let me know if you have any recommendations for software to create a BioPAX file from scratch.
I installed 

https://github.com/PathwayCommons/chibe

but that did not allow me to create BioPAX from scratch.

Regards,

Kozo

[Augustin Luna]

Programmatically, using Paxtools may work for you:
https://github.com/BioPAX/Paxtools

# Example Code
https://gist.github.com/cannin/b6f7ba64e1156b001282
https://gist.github.com/cannin/b6f7ba64e1156b001282#file-firstmodel_1-groovy

Augustin Luna

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[Gary Bader]

Hi - I've also found that ChatGPT can do it, but you need to be specific with your prompts.

Best,
Gary

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[Quirin Manz]

Hi, 

I came across the python package pybiopax, which can be used for this task.

See the related issue and the corresponding notebook.  

Best,
Quirin

[Augustin Luna]

Yes, if you're a Python user, the pybiopax would be good to try as
suggested by Quirin.

Augustin Luna

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