cell_cycle 0.1.2 → 0.1.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/cell_cycle/simple.rb

@@ -9,6 +9,7 @@
 require_relative '../cell_cycle'
 
 # Constants that control the cell cycle settings.
+Cell_cycle_duration = 24.h
 S_phase_duration = 12.h
 S_phase_start = 5.h
 S_phase_end = S_phase_start + S_phase_duration
@@ -30,10 +31,11 @@ Cdc20A_end = 20.min
 =end
 
 # Figure them out as numbers in seconds.
-S_s = S_phase_start.in :s
-S_e = S_phase_end.in :s
-A_s = A_phase_start.in :s
-A_e = A_phase_end.in :s
+Cc_duration_s = Cell_cycle_duration.in :s
+S_start_s = S_phase_start.in :s
+S_end_s = S_phase_end.in :s
+A_start_s = A_phase_start.in :s
+A_end_s = A_phase_end.in :s
 Cdc20A_s = Cdc20A_start.in :s
 Cdc20A_e = Cdc20A_end.in :s
 
@@ -54,21 +56,40 @@ CELL_CYCLE << Timer << Clock << A_phase << S_phase << Cdc20A
 # Assignment transitions that control the state of the places A_phase, S_phase
 # and Cdc20A.
 # 
-A_phase_f = Transition assignment: -> t { t > A_s && t < A_e ? 1 : 0 },
-                       domain: Timer,
-                       codomain: A_phase
-S_phase_f = Transition assignment: -> t { t > S_s && t < S_e ? 1 : 0 },
-                       domain: Timer,
-                       codomain: S_phase
-Cdc20A_f = Transition assignment: -> t { t < Cdc20A_e || t > Cdc20A_s ? 1 : 0 },
-                      domain: Timer,
-                      codomain: Cdc20A
+A_phase_f = Transition domain: Timer, codomain: A_phase,
+                       assignment: -> timer {
+                         cc_progress = timer % Cc_duration_s
+                         if cc_progress > A_start_s and cc_progress < A_end_s
+                           1
+                         else
+                           0
+                         end
+                       }
+
+S_phase_f = Transition domain: Timer, codomain: A_phase,
+                       assignment: -> timer {
+                         cc_progress = timer % Cc_duration_s
+                         if cc_progress > S_start_s and cc_progress < S_end_s
+                           1
+                         else
+                           0
+                         end
+                       }
+Cdc20A_f = Transition domain: Timer, codomain: Cdc20A,
+                      assignment: -> timer {
+                        cc_progress = timer % Cc_duration_s
+                        if cc_progress < Cdc20A_e or cc_progress > Cdc20A_s
+                          1
+                        else
+                          0
+                        end
+                      }
 
 # Include the A transitions in the CELL_CYCLE net.
 CELL_CYCLE << A_phase_f << S_phase_f << Cdc20A_f
 
 def CELL_CYCLE.default_simulation
-  simulation time: 0..36.h.in( :s ),
+  simulation time: 0..48.h.in( :s ),
              step: 1.min.in( :s ),
              sampling: 20.min.in( :s )
 end

data/lib/cell_cycle/version.rb

@@ -1,5 +1,5 @@
 module CellCycle
-  VERSION = "0.1.2"
+  VERSION = "0.1.3"
   # TODO: Once Net class is made a subclass of module, I can define
   # VERSION constant directly on it. If it turns out plausible.
 end

data/test/simple_test.rb

@@ -23,13 +23,16 @@ describe :simple_cell_cycle do
     Cdc20A_start.must_equal 22.h
     Cdc20A_end.must_equal 1.h
     CELL_CYCLE.A_tt.names.must_equal [ :A_phase_f, :S_phase_f, :Cdc20A_f ]
-    # the simulation should look good
-    sim = CELL_CYCLE.simulation time: 0..36.h.in( :s ),
+    # The simulation should look good
+    sim = CELL_CYCLE.simulation time: 0..48.h.in( :s ),
                                 step: 1.min.in( :s ),
                                 sampling: 20.min.in( :s )
     sim.simulation_method.must_equal :basic
     sim.run!
-    sim.recording.marking( S_phase, A_phase, Cdc20A ).plot
+    sim.recording.marking( S_phase, A_phase, Cdc20A )
+      .plot title: "Test of the simple cell cycle simulated for " +
+              "48 hours. Please visually inspect for correctness.",
+            ylabel: "Marking of S_phase, A_phase and Cdc20A [0 or 1]"
     sleep 15
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cell_cycle
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.3
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-22 00:00:00.000000000 Z
+date: 2016-06-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler