Address issues noted in wc_lang.expression_utils

KarrLab / wc_sim

A multi-algorithmic simulator for whole-cell models

MIT License

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Closed jonrkarr closed 4 years ago

jonrkarr commented 5 years ago

put dict of submodels in dynamic_model
give abstract compartments control over their volumes
can a reaction's reactants and modifiers be contained in multiple compartments
ensure that all related objects made before their using objects in DynamicModel.init()
handle any multiplicity of StopConditions; allow execution to choose among multiple StopConditions, or use them all

jonrkarr commented 5 years ago

Done

Volume is now a function in wc_lang; wc-sim only needs to calculate the mass of each compartment
wc_lang allows the reactants, products, and modifiers of each reaction to be in 1 or multiple compartments

Todo

put dict of submodels in dynamic_model
give abstract compartments control over their volumes
ensure that all related objects made before their using objects in DynamicModel.init()
handle any multiplicity of StopConditions; allow execution to choose among multiple StopConditions, or use them all

artgoldberg commented 4 years ago

Done

put dict of submodels in dynamic_model
ensure that all related objects made before their using objects in DynamicModel.init()
handle any multiplicity of StopConditions

To do later