ecell4 Support PySB

Jul 11 '18 04:07 kaizu

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!

Jun 04 '19 16:06 ortega2247

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.

Jun 05 '19 04:06 kaizu

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?

Jun 06 '19 20:06 ortega2247

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?

Jun 07 '19 09:06 kaizu

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

Jun 07 '19 11:06 ortega2247