cell_cycle 0.1.1 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -29,7 +29,12 @@ And a more complex one, developed at Virginia Institute of Technology, and calle
 
     require 'cell_cycle/virginia_tech'
 
-This one
+You can then try
+
+    run!
+
+The current version of the Virginia Tech cell cycle takes a long time to execute, but
+once the waiting is over, you can display the results
 
 ## Contributing
 

data/lib/cell_cycle/simple.rb

@@ -6,7 +6,7 @@
 # phase. Cdc20A represents the APC (Anaphase Promoting Complex). When present,
 # it degrades the cell cycle enzyme machinery.
 
-require 'cell_cycle'
+require_relative '../cell_cycle'
 
 # Constants that control the cell cycle settings.
 S_phase_duration = 12.h
@@ -30,12 +30,12 @@ Cdc20A_end = 20.min
 =end
 
 # Figure them out as numbers in seconds.
-Sα = S_phase_start.in :s
-Sω = S_phase_end.in :s
-Aα = A_phase_start.in :s
-Aω = A_phase_end.in :s
-Cdc20Aα = Cdc20A_start.in :s
-Cdc20Aω = Cdc20A_end.in :s
+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
+Cdc20A_s = Cdc20A_start.in :s
+Cdc20A_e = Cdc20A_end.in :s
 
 # Timer place
 Timer = Place m!: 0
@@ -54,18 +54,18 @@ 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_ϝ = Transition assignment: -> t { t > Aα && t < Aω ? 1 : 0 },
+A_phase_f = Transition assignment: -> t { t > A_s && t < A_e ? 1 : 0 },
                        domain: Timer,
                        codomain: A_phase
-S_phase_ϝ = Transition assignment: -> t { t > Sα && t < Sω ? 1 : 0 },
+S_phase_f = Transition assignment: -> t { t > S_s && t < S_e ? 1 : 0 },
                        domain: Timer,
                        codomain: S_phase
-Cdc20A_ϝ = Transition assignment: -> t { t < Cdc20Aω || t > Cdc20Aα ? 1 : 0 },
+Cdc20A_f = Transition assignment: -> t { t < Cdc20A_e || t > Cdc20A_s ? 1 : 0 },
                       domain: Timer,
                       codomain: Cdc20A
 
 # Include the A transitions in the CELL_CYCLE net.
-CELL_CYCLE << A_phase_ϝ << S_phase_ϝ << Cdc20A_ϝ
+CELL_CYCLE << A_phase_f << S_phase_f << Cdc20A_f
 
 def CELL_CYCLE.default_simulation
   simulation time: 0..36.h.in( :s ),

data/lib/cell_cycle/version.rb

@@ -1,5 +1,5 @@
 module CellCycle
-  VERSION = "0.1.1"
+  VERSION = "0.1.2"
   # 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/lib/cell_cycle/virginia_tech.rb

@@ -3,7 +3,7 @@
 # Generic cell cycle published in Csikasznagy2006agm. Mammalian constants used.
 # Initial state was obtained as described in Csikasznagy2006agm.
 
-require 'cell_cycle'
+require_relative '../cell_cycle'
 
 # == TRICKS =====================================================================
 
@@ -42,8 +42,8 @@ CASE = 1; G2_MODULE = true
 # cell_cycle/virginia/mammalian_constants.rb
 # ==============================================================================
 
-begin; require_relative 'virginia_tech/mammalian_constants'; rescue LoadError
-  require './virginia_tech/mammalian_constants'
+begin; require_relative 'virginia_tech/parameters'; rescue LoadError
+  require './parameters'
 end
 
 # begin

data/lib/cell_cycle/virginia_tech/{mammalian_constants.rb → parameters.rb}

@@ -5,7 +5,6 @@
 # PUBLICATION ID: Csikasznagy2006agm
 # ==============================================================================
 
-
 require 'sy'; require 'y_nelson' and include YNelson
 
 # Golbeter-Koshland function used in Csikasznagy2006agm.
@@ -121,9 +120,6 @@ DATA = {
   CycD⁰:     { BY: 0.108,  MA: 0.5,      FY: 0.05,  G2: nil,  XE: nil   }
 }
 
-# We choose the mammalian parameter set.
-PARAMETER_SET = :MA
-
 # Singleton method that chooses a given set of constants. Constants starting
 # with "K" are considered rate constants in min⁻¹. All values are converted to
 # floats (Using #to_f method). Using eval, the keys are defined as constants
@@ -141,5 +137,8 @@ def DATA.choose which
   }
 end
 
+# Mammalian parameter set will be chosen.
+PARAMETER_SET = :MA
+
 # Choose the parameter set.
 DATA.choose PARAMETER_SET

data/test/simple_test.rb

@@ -22,12 +22,12 @@ describe :simple_cell_cycle do
     A_phase_end.must_equal 17.h
     Cdc20A_start.must_equal 22.h
     Cdc20A_end.must_equal 1.h
-    CELL_CYCLE.A_tt.names.must_equal [ :A_phase_ϝ, :S_phase_ϝ, :Cdc20A_ϝ ]
+    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 ),
                                 step: 1.min.in( :s ),
                                 sampling: 20.min.in( :s )
-    sim.simulation_method.must_equal :pseudo_euler
+    sim.simulation_method.must_equal :basic
     sim.run!
     sim.recording.marking( S_phase, A_phase, Cdc20A ).plot
     sleep 15

data/test/virginia_test.rb

@@ -11,7 +11,7 @@ describe "virginia tech cell cycle" do
     require './../lib/cell_cycle/virginia_tech'
   end
 
-  # TODO: This is how far I came.
+  # TODO: There are unwritten tests for some cell cycle modules.
 
   describe "basic elements" do
     it "should have basic interface places" do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cell_cycle
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-15 00:00:00.000000000 Z
+date: 2016-06-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -60,7 +60,7 @@ files:
 - lib/cell_cycle/simple.rb
 - lib/cell_cycle/version.rb
 - lib/cell_cycle/virginia_tech.rb
-- lib/cell_cycle/virginia_tech/mammalian_constants.rb
+- lib/cell_cycle/virginia_tech/parameters.rb
 - test/simple_test.rb
 - test/virginia_test.rb
 homepage: ''
@@ -83,7 +83,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: A model of eukaryotic cell cycle.