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Add SBML Events as Bioscrape Rules

Open WilliamIX opened this issue 4 years ago • 0 comments

This issue is to scope the possibility of allowing more general SBML events be incorporated into bioscrape as rules (possible called EventRules - but what might a better name be?). I note that I cannot call these Events because Events are a different kind of object in bioscrape Lineage.

What are SBML Events? These are assignments of Species, S, or Parameters, P, to some function which occurs due to a certain condition: If C(S, P): Then: S= F(S, P) & P= G(S, P)

How could this look in Bioscrape? Lineage already supports Division and Death rules based upon conditions C(S, P) >=< threshold. This code could be reused to produce 4 rule types:

SingleSpeciesEventRule: assigns a single species: IF C(S, P) >=< threshold, THEN: S_i = F(S, P). MultiSpeciesEventRule: assigns all species: IF C(S, P) >=< threshold, THEN: for i = 0...N: S_i = F_i(S, P). SingleParameterEventRule: assigns a single paremeter: IF C(S, P) >=< threshold, THEN: P_i = F(S, P). MultiParameterEventRule: assigns all species: IF C(S, P) >=< threshold, THEN: for i = 0...N: P_i = F_i(S, P).

@ayush9pandey Would this cover most SBML Events? Can we take a single SBML rule and systematically convert it into rules of this form? Similarly, can we take these rules and convert them into SBML events easily?

Also, I hate the EventRule class - what would a better name be?

WilliamIX avatar Jul 08 '20 22:07 WilliamIX