cell_cycle 0.0.3 → 0.1.1

checksums.yaml

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

@@ -6,8 +6,7 @@
 # phase. Cdc20A represents the APC (Anaphase Promoting Complex). When present,
 # it degrades the cell cycle enzyme machinery.
 
-require 'y_nelson' and include YNelson
-require 'sy'
+require 'cell_cycle'
 
 # Constants that control the cell cycle settings.
 S_phase_duration = 12.h
@@ -50,7 +49,7 @@ S_phase = Place m!: 0
 Cdc20A = Place m!: 1
 
 # Include them in the CELL_CYCLE net.
-CELL_CYCLE = Net() << Timer << Clock << A_phase << S_phase << Cdc20A
+CELL_CYCLE << Timer << Clock << A_phase << S_phase << Cdc20A
 
 # Assignment transitions that control the state of the places A_phase, S_phase
 # and Cdc20A.

data/lib/cell_cycle/version.rb

@@ -1,3 +1,5 @@
 module CellCycle
-  VERSION = "0.0.3"
+  VERSION = "0.1.1"
+  # 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 'sy'; require 'y_nelson' and include YNelson
+require 'cell_cycle'
 
 # == TRICKS =====================================================================
 
@@ -419,52 +419,35 @@ finalize # YNelson command that finishes the net from the prescribed commands.
 # ==============================================================================
 
 
+CELL_CYCLE.merge! net   # This is quite fragile, since it assumes that no places
+                        # and/or transitions have been created before requiring
+                        # the cell cycle gem.
 
 
+# Net that defines cell growth, to be used eg. for testing or separate use.
+CELL_GROWTH_NET = Net()
+CELL_GROWTH_NET << Mass << Cell_growth << CycD <<
+  transition( :CycD_ϝ ) << CycB << ActCycB <<         # cyclin B
+  Ck_license << Cytokinesis << License_cocking        # cytokinesis
 
+# cell growth
+def CELL_CYCLE.default_simulation
+  simulation time: 0..96.h.in( :s ),
+             step: 5,
+             sampling: 300
+  # FIXME: This method #default_simulation doesn't work, and I don't know why,
+  # while standard way of simulation works. I can just use the standard way
+  # of simulation by simply calling run! command, and fix this later.
+end
 
-
-
-
-
-
-
-
-
-
-
-
-
-=begin
-
-# === Whole CELL_CYCLE Nelson net ===
-
-CELL_CYCLE = Net() << A_phase << S_phase << Cdc20A
-
-# === Cell growh net ===
-
-CELL_GROWTH_NET = Net() <<
-  Mass << Cell_growth << CycD << transition( :CycD_ϝ ) << # cell growth
-  CycB << ActCycB <<                                      # cyclin B
-  Ck_license << Cytokinesis << License_cocking            # cytokinesis
-
-set_step 5                                               # simulation settings
+set_step 5
+set_target_time 96.h.in( :s )
 set_sampling 300
-set_target_time 3600 * 24 * 4
-
-new_simulation
-
-
-pm                            # prints marking of the newly created simulation
-simulation.step!              # peforms a single simulation step
-pm                            # prints marking again
-
-# simulation.run! upto: 3600    # we can run 1 hour of this simulation
-
-recording.plot                # and plot the recording
 
-# and do other things with the recording, such as resampling,
-# feature extraction, saving to a file, reconstruction of a new
-# simulation object at a given time etc.
+# I commented this out, I don't really want to run this lengthy simulation upon
+# requiring the gem.
+# run!
 
-=end
+# Note: Possible things to do with the recording, such as resampling, feature
+# extraction, saving to a file, reconstruction of a new simulation object at
+# a given time etc.

data/lib/cell_cycle.rb

@@ -1,5 +1,16 @@
 # encoding: utf-8
 
-# YSupport is a collection of methods used  in Y gems.
-# 
-require "cell_cycle/version"
+# Mammalian cell cycle model. 2 versions available at the moment,
+# 'cell_cycle/simple' and 'cell_cycle/virginia_tech'. This is the
+# common 'cell_cycle.rb' file.
+
+# Require dependencies.
+require 'sy'
+require 'y_nelson' and include YNelson
+
+# Define the empty CELL_CYCLE net (its contents is to be added by
+# the particular implemented cell cycle types).
+CELL_CYCLE = Net()
+
+# Cell cycle version.
+require_relative "cell_cycle/version"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cell_cycle
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.1.1
 platform: ruby
 authors:
 - boris