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KarrLab / wc_sim

A multi-algorithmic simulator for whole-cell models
MIT License
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Improve NRM submodel #86

Open artgoldberg opened 4 years ago

artgoldberg commented 4 years ago
  1. remove reaction_index from self.dependencies[reaction_index] and eliminate the if at line 207
  2. discuss how to choose between SSA (the Direct Method) and NRM in a model
  3. add logging to the NRM submodel
  4. consider this NRM submodel optimization: compute dependencies on species shared with continuous submodels dynamically; no dependency exists if the slope has been 0 since the last reaction was executed. (don't need to look further back, because if the slope was non-0 before the previous reaction, then the propensity would have been calculated then)
artgoldberg commented 4 years ago

Did 1.