Support PySB

[kaizu]

No description provided.

[ortega2247]

Hi! I work in the Lopez lab at Vanderbilt University, we are one of the labs that maintains and develops PySB. I would be more than happy to help with this issue!

[kaizu]

Thank you, @ortega2247 ! That sounds great!
Let me check the recent updates in PySB. If you have any idea for good collaboration with PySB, please let me know.

[ortega2247]

I checked the ecell4 tutorials and saw that now you support rule-based modeling. I am not sure what was your plan for supporting PySB, but maybe we could start by building a translator to convert pysb models to ecell4 models and vice versa?

[kaizu]

This issue is first planned for a hackathon with The Systems Biology Institute.

a translator to convert pysb models to ecell4 models and vice versa

Yes, that's what we supposed to do. It would be good to support PySB as well as SBML in ports.py.
Should we start from https://github.com/pysb/pysb/tree/master/doc/examples ?
Is there any other list of the models for testing?

[ortega2247]

ohh a hackathon sounds fun. And yes this is a list with multiple pysb examples: https://github.com/LoLab-VU/pysb/tree/master/pysb/examples