2020-11-29 17:43:20 +01:00
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#lang scribble/manual
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2023-08-08 17:22:03 +02:00
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@(require scribble/example racket/sandbox
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(for-label typed/racket/base
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(submod "../rs.rkt" typed)))
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@(define rs-evaluator
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(parameterize ([sandbox-output 'string]
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[sandbox-error-output 'string]
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[sandbox-memory-limit 500])
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(make-evaluator 'typed/racket #:requires '((submod "rs.rkt" typed)))))
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@(define-syntax-rule (ex . args)
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(examples #:eval rs-evaluator . args))
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@(define-syntax-rule (deftypeform . args)
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(defform #:kind "type" . args))
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@(define-syntax-rule (deftype . args)
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(defidform #:kind "type" . args))
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2020-11-29 17:43:20 +01:00
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@title[#:tag "rs"]{dds/rs: Reaction Systems}
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2023-08-08 17:22:03 +02:00
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@defmodule[(submod dds/rs typed)]
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2020-11-29 22:12:01 +01:00
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This module defines reaction systems and various tools for working with them.
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@section[#:tag "rs-basics"]{Basic definitions}
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2023-08-08 17:22:03 +02:00
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@deftype[Species]{
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A synonym of @racket[Symbol].
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}
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2023-08-08 17:40:44 +02:00
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@defstruct*[reaction ([reactants (Setof Species)]
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[inhibitors (Setof Species)]
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[products (Setof Species)])]{
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A reaction is a triple of sets, giving the reactants, the inhibitors,
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and the products, respectively.
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}
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@deftype[Reaction]{
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The type of the instances of @racket[reaction].
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}
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2023-08-09 11:29:09 +02:00
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@deftype[ReactionName]{
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A reaction name is any @racket[Symbol].
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}
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2023-08-08 18:09:24 +02:00
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@defproc[(make-reaction [r (Listof Reaction)]
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[i (Listof Reaction)]
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[p (Listof Reaction)])
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Reaction]{
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A shortcut for constructing @racket[Reaction]s using list syntax
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instead of set syntax.
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@ex[
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(make-reaction '(a b) '(c d) '(e f))
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]}
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2023-08-08 18:28:25 +02:00
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@defproc[(enabled? [r Reaction] [s (Setof Species)]) Boolean]{
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A @racket[Reaction] is enabled on a set of species if all of its
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reactants are in the set and none of its inhibitors are.
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@ex[
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(enabled? (make-reaction '(a b) '(c d) '())
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(set 'a 'b 'e))
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(enabled? (make-reaction '(a b) '(c d) '())
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(set 'a 'b 'c))
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(enabled? (make-reaction '(a b) '(c d) '())
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(set 'b 'e))
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]}
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2023-08-08 18:34:40 +02:00
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@deftype[ReactionSystem]{
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2023-08-09 11:29:09 +02:00
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A reaction system is a dictionary mapping @racket[ReactionName]s to
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@racket[Reaction]s.
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2023-08-08 18:34:40 +02:00
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}
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2023-08-09 11:29:09 +02:00
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@defproc[(list-enabled [rs ReactionSystem] [s (Setof Species)])
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(Listof ReactionName)]{
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2023-08-09 11:15:43 +02:00
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Returns the list of the names of reactions of @racket[rs] enabled on
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@racket[s].
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@ex[
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(let ([rs (hash 'a (make-reaction '(x) '(y) '(z))
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'b (make-reaction '(x y) '() '(z)))])
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(values (list-enabled rs (set 'x 'y))
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(list-enabled rs (set 'x))))
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]}
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2023-08-10 01:07:41 +02:00
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@defproc[(union-products [rs ReactionSystem] [as (Listof ReactionName)])
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(Setof Species)]{
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Returns the union of the product sets of the given reactions listed in
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@racket[as] in @racket[rs]. If no reactions are supplied, returns the
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empty set.
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@ex[
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(union-products (hash 'a (make-reaction '(x) '(y) '(z))
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'b (make-reaction '(x y) '() '(z)))
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'(a b))
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]}
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2023-08-09 11:15:43 +02:00
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2023-08-10 16:19:58 +02:00
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@defproc[(apply-rs [rs ReactionSystem] [s (Setof Species)])
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(Setof Species)]{
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Applies the reaction system @racket[rs] to @racket[s].
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@ex[
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(let ([rs (hash 'a (make-reaction '(x) '(y) '(z))
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'b (make-reaction '(x y) '() '(z)))])
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(apply-rs rs (set 'x)))
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]}
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2023-08-08 18:34:40 +02:00
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2020-11-29 22:12:01 +01:00
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@section{Org-mode interaction}
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This section contains some useful primitives for
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@hyperlink["https://orgmode.org/"]{Org-mode} interoperability.
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2023-08-10 16:30:02 +02:00
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@defproc[(str-triple->reaction [lst (List String String String)]) Reaction]{
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Converts a triple of strings to a reaction.
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@ex[
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(str-triple->reaction '("a b" "c d" "e f"))
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]}
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2023-08-10 16:46:32 +02:00
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@defproc[(ht-str-triples->rs [ht (HashTable ReactionName (List String String String))])
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ReactionSystem]{
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Converts a hash table mapping reaction names to triples of strings to
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a reaction system.
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@ex[
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(ht-str-triples->rs (hash 'a (list "x y" "" "k i")
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'b (list "" "x y" "t j")))
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]}
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2023-08-10 18:05:22 +02:00
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@defproc[(read-org-rs [str String]) ReactionSystem]{
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Reads a reaction system from an Org-mode style string.
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@ex[
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(read-org-rs "((\"a\" \"x t\" \"y\" \"z\") (\"b\" \"x\" \"q\" \"z\"))")
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]}
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2023-08-10 16:30:02 +02:00
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2020-11-29 22:12:01 +01:00
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@section{Dynamics of reaction systems}
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The dynamics of reaction systems is typically defined as @emph{interaction
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processes}. An interactive process of a reaction system is a sequence of
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states driven by a sequence of contexts in the following way. The reaction
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system starts with the initial context. Then, at every step, the result of
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applying the reaction system is merged with the next element of the context
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sequence, and the reaction system is then applied to the result of the union.
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If the sequence of contexts is empty, the reaction system cannot evolve.
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