Synapse Act 2: a trio from https://penrose.ink

.dsl

type Synapse
type Channel
type Vesicle
type Glutamate
type Calcium
type NMDAR
type AMPAR

predicate InsideVesicle : Glutamate g * Vesicle v

predicate VesicleClosed : Vesicle v

predicate Initial : Synapse s

predicate IsDepolarized : Synapse s

predicate BindAMPA : Glutamate g * AMPAR a

.sty

forall Synapse A {
    A.axon = Rectangle {
      center: (0, 300)
      w: 800
      h: 100
      strokeWidth: 0
      color: hsva(155, 51, 100, 1)
    }
    A.axon.x = 0
    A.axonText = Text {
      string: "\text{Axon}"
    }
    
    A.dendrite = Rectangle {
      center: (0, -100)
      w: 800
      h: 100
      strokeWidth: 0
      color: hsva(185, 51, 100, 1)
    }
    A.dendriteText = Text {
      string: "\text{Dendrite}"
    }
    encourage centerLabel(A.axon, A.axonText)
    layer A.axonText above A.axon

    encourage centerLabel(A.dendrite, A.dendriteText)
    layer A.dendriteText above A.dendrite
}

forall AMPAR A; Synapse S {
  A.left = Rectangle {
    w: 10
    h: 50
    strokeWidth: 0
    color: hsva(291, 75, 100, 1)
  }
  A.right = Rectangle {
    w: 10
    h: 50
    strokeWidth: 0
    color: hsva(291, 75, 100, 1)
  }
  
  encourage equal(A.left.center[1], -50)
  encourage equal(A.right.center[1], -50)

  layer A.left above S.dendrite
  layer A.right above S.dendrite

  encourage nearPt(A.right, A.left.center[0] + 30, A.left.center[1])

  A.text = Text {
    center: A.left.center
    string: A.label
  }
  layer A.text above A.left
}

forall NMDAR N; Synapse S {
  N.left = Rectangle {
    w: 10
    h: 50
    strokeWidth: 0
    color: hsva(42, 75, 100, 1)
  }
  N.right = Rectangle {
    w: 10
    h: 50
    strokeWidth: 0
    color: hsva(42, 75, 100, 1)
  }

  N.magnesium = Circle {
    r: 10
    strokeWidth: 0
    color: hsva(212, 86, 60, 1)
  }
  
  encourage equal(N.left.center[1], -50)
  encourage equal(N.right.center[1], -50)
  encourage equal(N.magnesium.center[0], N.left.center[0] + 15)
  encourage equal(N.magnesium.center[1], -50)

  layer N.left above S.dendrite
  layer N.right above S.dendrite

  encourage nearPt(N.right, N.left.center[0] + 30, N.left.center[1])
  N.text = Text {
    center: N.left.center
    string: N.label
  }
  layer N.text above N.left
}

forall NMDAR N; Synapse S
where IsDepolarized(S) {
  override N.magnesium.color = hsva(0,0,0, 0)
}

forall Channel C; Synapse S {
  C.left = Rectangle {
    w: 10
    h: 50
    strokeWidth: 0
    color: hsva(0, 0, 50, 1)
  }
  C.right = Rectangle {
    w: 10
    h: 50
    strokeWidth: 0
    color: hsva(0, 0, 50, 1)
  }
  
  encourage equal(C.left.center[1], 250)
  encourage equal(C.right.center[1], 250) 

  layer C.left above S.axon
  layer C.right above S.axon

  encourage nearPt(C.right, C.left.center[0] + 30, C.left.center[1])

  C.text = Text {
    center: C.left.center
    string: C.label
  }
  layer C.text above C.left
}

forall Calcium C; Synapse S {
  C.icon = Circle {
    r: 10
    strokeWidth: 0
    color: hsva(0, 0, 50, 1)
  }
  layer C.icon above S.axon
  layer C.icon above S.dendrite
}

forall Glutamate C; Synapse S {
  C.icon = Circle {
    r: 10
    strokeWidth: 0
    color: hsva(41, 100, 100, 1)
  }
  layer C.icon above S.axon
  layer C.icon above S.dendrite
}

forall Glutamate G; Glutamate C {
  -- encourage repel(G.icon, C.icon, 0.2)
}

forall Vesicle V; Synapse S {
  V.icon = Circle {
    r: 40
    color: hsva(0,0,0,0)
    strokeColor: hsva(0,20,0,1)
    strokeWidth: 1
  }

  layer V.icon above S.axon

  encourage equal(V.icon.center[1], 250)
  V.blocker = Rectangle {
    center: (V.icon.center[0], V.icon.center[1] - 35)
    w: 50
    h: 20
    color: hsva(0,0,100,1)
    strokeWidth: 0
  }
  layer V.blocker above V.icon

  V.text = Text {
    center: V.blocker.center
    string: V.label
  }
  layer V.text above V.blocker
}

forall Vesicle V where VesicleClosed(V) {
  encourage equal(V.icon.center[1], 350)
  override V.blocker.color = hsva(100,0,0,0)
}

forall Vesicle V; Glutamate G
where InsideVesicle(G, V); VesicleClosed(V) {
  ensure contains(V.icon, G.icon)
}

forall Calcium C; Channel Ch; NMDAR N; Synapse S
where Initial(S) {
  encourage above(C.icon, Ch.left)
}

forall Calcium C; NMDAR N; Synapse S
where IsDepolarized(S) {
  encourage below(C.icon, N.left)
}

forall Synapse S
where IsDepolarized(S) {
  S.arrow = Arrow {
    start: (0, 200)
    end: (0, 0)
    thickness: 3.0
    color: hsva(0, 0, 80, 1)
  }
  S.depText = Text {
    string: "\text{depolarized}"
    center: (70, 100)
  }
}

forall Synapse S
where Initial(S) {
  S.arrow = Arrow {
    end: (0, 200)
    start: (0, 0)
    thickness: 3.0
    color: hsva(0, 0, 80, 1)
  }
  S.depText = Text {
    string: "\text{hyperpolarized}"
    center: (70, 100)
  }
}

forall AMPAR A; Glutamate G
where BindAMPA(G, A) {
  override G.icon.center = (A.right.center[0], A.right.center[1] + 20)
  layer G.icon above A.right
}

.sub

AutoLabel All
-- ACT 1 --

Synapse S

Initial(S)

Vesicle V1, V2
Glutamate G1, G2, G3
InsideVesicle(G1, V1)
InsideVesicle(G2, V2)
InsideVesicle(G3, V2)

VesicleClosed(V1)
VesicleClosed(V2)

NMDAR N1
AMPAR A1, A2
Channel Ch

-- ACT 2: CALCIUM BUILDUP --

Calcium C1, C2, C3, C4, C5

metadata.json

{"authorship":{"madeBy":"maxkrieger","name":"Synapse Act 2","avatar":"https://avatars.githubusercontent.com/u/2660634?v=4"}}