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ecell / ecell4

An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
https://ecell4.e-cell.org/
GNU General Public License v3.0
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Support PySB #16

Open kaizu opened 6 years ago

ortega2247 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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