Give name to step

[pirbo]

Question raised by @jonathan-laurent.
In traces appear inital states, application of rules, application of perturbation and occurrence of an interesting pattern.
Stories (and potentially others) would like to have nice names to refer to them.

• rules in the forward direction can have a name.
• rules in the backward direction have hardwired the name 'name_of_the_forward_direction'_op
• occurrence of a new pattern names rely on a hack: If you've defined %var: 'foo' |a_pattern| you can use $TRACK 'foo' [true] instead of $TRACK a_pattern [true] AND, in this case, the step is called 'foo'.
• initializations cannot have names
• neither have perturbations

How to extend the syntax of kappa in order to be able to name everyone nicely?

[feret]

Interesting point. We have to be careful, because the names are likely to be used to define the notion of story isomorphism. If we do not want to change the syntax, - Initialization could be characterized by the agent and the views (state of the sites). - For some applications, it could be interesting also to distinguish according to the introduction time and according to the Location. I would not make difference between initialization and $ADD perturbation. (If we log time and/or location, this is already a way to distinguish them). I am not sure that I a aware of the semantics of $REMOVE perturbations. the Kappa encoding of the species (if they may not have side-effects) or the pattern (if they may) in a node with a different color may be good (with additional information as degradation time and Location, if requested). Otherwise, giving a name to each introduction, and each perturbation will be very heavy. Note that the solution that I propose will not distinguish along the introduction of the same view twice but in a different context (which is bad, but I can live with it), unless we ask for the Location. Cheers. Jérôme.

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Le 1 déc. 2016 à 16:55, Pierre Boutillier ***@***.***> a écrit : Question raised by @jonathan-laurent <https://github.com/jonathan-laurent>. In traces appear inital states, application of rules, application of perturbation and occurrence of an interesting pattern. Stories (and potentially others) would like to have nice names to refer to them. rules in the forward direction can have a name. rules in the backward direction have hardwired the name 'name_of_the_forward_direction'_op occurrence of a new pattern names rely on a hack: If you've defined %var: 'foo' |a_pattern| you can use $TRACK 'foo' [true] instead of $TRACK a_pattern [true] AND, in this case, the step is called 'foo'. initializations cannot have names neither have perturbations How to extend the syntax of kappa in order to be able to name everyone nicely? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#313>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AARts1Z3EZ3Opgj6uk71ngx3ZXSCkqMvks5rDu3vgaJpZM4LBjsd>.

[hmedina]

Here are my two cents:

• For reverse rule names, could we have two strings separated by a comma as the leading part of the rule line? This would be similar syntax to how we distinguish the forward and reverse rates. E.g.:
  'r+', 'r-' A(a),B(b) <-> A(a!1),B(b!1) @ 'γ+' {'k+':'n'}, 'γ-'
  When dealing with a variable horizon scope (e.g. 'n'), if KaSim is internally generating rules, I would suggest naming those rules based on the rule's value of 'n', e.g. 'r+_1', 'r+_2', 'r+_3', and so on. To avoid the possibility of naming conflict, we would ban the declaration of any variable a_n for all n if the user has defined a as a rule name.

• For perturbations, could we allow the user to give them a name? For repeating perturbations, the name could serve as a prefix. E.g.:
  %mod: 'A++' repeat ( [E] [mod] 10 ) do $ADD 1 A() until [false]
  And there would be perturbations named A++_1, A++_2, A++_3, and so on based on a counter of the number of times the perturbation has been triggered. The same ban would apply here as for rule names: banning the user from specifying a variable A++_n for all n if there is a repeating perturbation with the name A++.

• For the initialization specified with %init:, how about assigning default names? E.g.
  %mod: 10 A(a), B(b~o), C() would generate a name like initialization_A(a)_&_B(b~o)_&_C().