cell_cycle 0.0.2 → 0.0.3

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data/README.md

@@ -4,21 +4,32 @@ Cell cycle model.
 
 ## Installation
 
-Add this line to your application's Gemfile:
+You can install it by
 
-    gem 'cell_cycle'
+    $ gem install cell_cycle
 
-And then execute:
+## Usage
 
-    $ bundle
+This gem contains two versions of cell cycle. Both of them contain an engine,
+a Petri net whose execution results in cycling, and 3 output places: A_phase,
+S_phase and Cdc20A.
 
-Or install it yourself as:
+Simple version of the cell cycle is called by:
 
-    $ gem install cell_cycle
+    require 'cell_cycle/simple'
 
-## Usage
+You can then try
+
+    s = CELL_CYCLE.default_simulation
+    s.run!
+    s.recording.print
+    s.recording.plot except: [ Timer ]        # relies on Gnuplot
+
+And a more complex one, developed at Virginia Institute of Technology, and called by:
+
+    require 'cell_cycle/virginia_tech'
 
-TODO: Write usage instructions here
+This one
 
 ## Contributing
 

data/lib/cell_cycle/version.rb

@@ -1,3 +1,3 @@
 module CellCycle
-  VERSION = "0.0.2"
+  VERSION = "0.0.3"
 end

data/lib/cell_cycle/virginia_tech.rb

@@ -22,9 +22,6 @@ end
 
 def fod &nullary_block; FirstOrderDegradation.new &nullary_block end
 
-
-
-
 # ==============================================================================
 # THE MODEL ITSELF
 # ==============================================================================
@@ -45,10 +42,20 @@ CASE = 1; G2_MODULE = true
 # cell_cycle/virginia/mammalian_constants.rb
 # ==============================================================================
 
-begin; require_relative './virginia_tech/mammalian_constants'; rescue LoadError
+begin; require_relative 'virginia_tech/mammalian_constants'; rescue LoadError
   require './virginia_tech/mammalian_constants'
 end
 
+# begin
+#   require_relative 'mammalian_constants'
+# rescue LoadError
+#   begin
+#     require './mammalian_constants'
+#   rescue LoadError
+#     require 'cell_cycle/mammalian_constants.rb'
+#   end
+# end
+
 # == PLACES =====================================================================
 
 # Cell mass

data/lib/cell_cycle/virginia_tech/mammalian_constants.rb

@@ -5,6 +5,7 @@
 # PUBLICATION ID: Csikasznagy2006agm
 # ==============================================================================
 
+
 require 'sy'; require 'y_nelson' and include YNelson
 
 # Golbeter-Koshland function used in Csikasznagy2006agm.

data/test/virginia_test.rb

@@ -1,42 +1,17 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
+
 require 'minitest/autorun'
 require 'sy'
 require 'y_nelson' and include YNelson
 
-bp = './../../lib/'
-  .tap { |s| s.singleton_class.class_exec do attr_accessor :loaded end }
-  .tap { |s| s.loaded = {} }
-
-require_once = -> path do
-  bp.loaded[ path ] or
-    require( bp + path ) && bp.loaded.update( path => true )
-end
-
-describe :mammalian_cell_cycle do
+describe "virginia tech cell cycle" do
   before do
-    require_once.( 'ttp_pathway/version' )
-    require_once.( 'michaelis_menten' )
-    require_once.( 'general_assumptions' )
-    require_once.( 'cell_cycle/virginia' )
+    require './../lib/cell_cycle/virginia_tech'
   end
 
-  describe "sanity of this test itself" do
-    it "should have version loaded" do
-      TtpPathway::VERSION.must_be_kind_of String
-    end
-
-    it "should have michaelis_menten loaded" do
-      [ Vmax, Km_reduced, Occupancy, MMi ].all? &[ :kind_of?, Proc ]
-    end
-
-    it "should have general_assumptions loaded" do
-      assert defined? Cell_diameter
-      assert defined? Cytoplasm_volume
-      assert defined? Pieces_per_µM
-    end
-  end
+  # TODO: This is how far I came.
 
   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: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-14 00:00:00.000000000 Z
+date: 2014-10-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler