You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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?
The text was updated successfully, but these errors were encountered:
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?
The text was updated successfully, but these errors were encountered: