Suggestion: use py-perl5 for more seamless bridge to BNGL2.pl #22

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1. ASinanSaglam commented on Sep 16, 2021

   

   ASinanSaglam

   on Sep 16, 2021

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   This is a fantastic idea and I'll try to add this as soon as I can
2. ASinanSaglam

   added

   enhancementNew feature or requestNew feature or request

   on Sep 16, 2021
3. jonrkarr commented on Sep 16, 2021

   

   jonrkarr

   on Sep 16, 2021

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   To elaborate, we would want to use this to execute multiple simulations (with different parameter values or initial conditions) without re-parsing the .bngl file for the model.

   Here's the main things we would want

   1. Parse a model file to a data structure that represents the model (this would be a instance of a py-perl5 class)
   2. Use that data structure to execute a simulation (without exporting the data structure to a .bngl file and BNGL2 then parsing that file)
   3. Make basic changes to that data structure for the values of parameters, compartment sizes, and initial counts of species

   If BNGL2 already has methods for the above, this might be fairly easy. Instantiating a bridge from Python to BNGL2 and then letting users use whatever API BNGL2 exposes might be sufficient. To make it more user friendly, it might be helpful to wrap this into Python methods rather than asking users to navigate the BNGL2 Perl API.
4. jrfaeder

   added a commit that references this issue on Jul 20, 2026

   🧹 [code health improvement] Remove actionable TODO in libsbml2bngl.py (…

   ...

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