gitignore

.gitignore

@@ -191,4 +191,4 @@ docs\deliverables\~$*
 *.synctex.gz
 
 /coverage
-/coverage/*
+/.jhw-cache

.travis.yml

@@ -5,7 +5,7 @@ rvm:
     - 2.0.0
     - ruby-head
 env:
-    - DB=sqlite
+    - DB=sqlite DISPLAY=":99.0"
 matrix:  
   allow_failures:
     - rvm: ruby-head
@@ -30,6 +30,6 @@ script:
 notifications:
     webhooks:
         urls:
-            -http://life.jstfy.com/hook
+            - http://life.jstfy.com/hook
         on_succes: always
         on_failure: never

Gemfile

@@ -14,6 +14,7 @@ gem 'nested_form'
 group :assets do
   gem 'sass-rails',   '~> 3.2.3'
   gem 'coffee-rails', '~> 3.2.1'
+  gem 'coffee-script-source', '1.5.0'
 
   # See https://github.com/sstephenson/execjs#readme for more supported runtimes
   # gem 'therubyracer', :platforms => :ruby
@@ -30,6 +31,7 @@ end
 
 gem 'jquery-rails'
 gem 'wicked_pdf'
+gem 'wkhtmltopdf-binary', '~> 0.9.9', require: false
 
 # To use ActiveModel has_secure_password
 # gem 'bcrypt-ruby', '~> 3.0.0'

Gemfile.lock

@@ -44,23 +44,26 @@ GEM
     coffee-script (2.2.0)
       coffee-script-source
       execjs
-    coffee-script-source (1.6.2)
+    coffee-script-source (1.5.0)
     colorize (0.5.8)
     coveralls (0.6.7)
       colorize
       multi_json (~> 1.3)
       rest-client
       simplecov (>= 0.7)
       thor
-    diff-lcs (1.2.1)
+    diff-lcs (1.2.4)
     erubis (2.7.0)
+    eventmachine (1.0.3)
     eventmachine (1.0.3-x86-mingw32)
     execjs (1.4.0)
       multi_json (~> 1.0)
     faye-websocket (0.4.7)
       eventmachine (>= 0.12.0)
-    ffi (1.5.0-x86-mingw32)
-    hike (1.2.1)
+    ffi (1.8.1)
+    ffi (1.8.1-x86-mingw32)
+    hike (1.2.2)
+    http_parser.rb (0.5.3)
     http_parser.rb (0.5.3-x86-mingw32)
     i18n (0.6.4)
     jasmine (1.3.2)
@@ -78,15 +81,16 @@ GEM
       i18n (>= 0.4.0)
       mime-types (~> 1.16)
       treetop (~> 1.4.8)
-    mime-types (1.21)
-    multi_json (1.7.1)
+    mime-types (1.23)
+    multi_json (1.7.3)
     nested_form (0.3.2)
+    nokogiri (1.5.9)
     nokogiri (1.5.9-x86-mingw32)
     phantomjs (1.8.1.1)
       poltergeist
-    poltergeist (1.2.0)
+    poltergeist (1.3.0)
       capybara (~> 2.1.0)
-      faye-websocket (~> 0.4, >= 0.4.4)
+      faye-websocket (>= 0.4.4, < 0.5.0)
       http_parser.rb (~> 0.5.3)
     polyglot (0.3.3)
     rack (1.4.5)
@@ -111,7 +115,7 @@ GEM
       rake (>= 0.8.7)
       rdoc (~> 3.4)
       thor (>= 0.14.6, < 2.0)
-    rake (10.0.3)
+    rake (10.0.4)
     rdoc (3.12.2)
       json (~> 1.4)
     rest-client (1.6.7)
@@ -123,14 +127,14 @@ GEM
     rspec-core (2.13.1)
     rspec-expectations (2.13.0)
       diff-lcs (>= 1.1.3, < 2.0)
-    rspec-mocks (2.13.0)
+    rspec-mocks (2.13.1)
     rubyzip (0.9.9)
-    sass (3.2.7)
+    sass (3.2.8)
     sass-rails (3.2.6)
       railties (~> 3.2.0)
       sass (>= 3.1.10)
       tilt (~> 1.3)
-    selenium-webdriver (2.31.0)
+    selenium-webdriver (2.32.1)
       childprocess (>= 0.2.5)
       multi_json (~> 1.0)
       rubyzip
@@ -144,17 +148,18 @@ GEM
       multi_json (~> 1.0)
       rack (~> 1.0)
       tilt (~> 1.1, != 1.3.0)
+    sqlite3 (1.3.7)
     sqlite3 (1.3.7-x86-mingw32)
-    teabag (0.7.1)
+    teabag (0.7.2)
       phantomjs (>= 1.8.1.1)
       railties (>= 3.2.5, < 5)
-    thor (0.17.0)
-    tilt (1.3.6)
+    thor (0.18.1)
+    tilt (1.4.1)
     treetop (1.4.12)
       polyglot
       polyglot (>= 0.3.1)
     tzinfo (0.3.37)
-    uglifier (1.3.0)
+    uglifier (2.1.0)
       execjs (>= 0.3.0)
       multi_json (~> 1.0, >= 1.0.2)
     websocket (1.0.7)
@@ -166,10 +171,12 @@ GEM
       nokogiri (~> 1.3)
 
 PLATFORMS
+  ruby
   x86-mingw32
 
 DEPENDENCIES
   coffee-rails (~> 3.2.1)
+  coffee-script-source (= 1.5.0)
   coveralls
   jasmine
   jquery-rails
@@ -182,4 +189,4 @@ DEPENDENCIES
   uglifier (>= 1.0.3)
   wicked_pdf
   will_paginate (~> 3.0)
-  wkhtmltopdf-binary
+  wkhtmltopdf-binary (~> 0.9.9)

README.md

@@ -2,10 +2,45 @@ Programming Life: Gigabase
 ================ 
 Gigabase: Synthetic Biology Cell Modeling Project
 
+## The virtual Cell
+Developing a visual environment for designing and simulating virtual cells.
+
+- Substrate, s.
+- Metabolism converting substrate s into product p.
+- Substrate and product transporter.
+- DNA synthesis.
+- Protein synthesis and degratation.
+- Lipid synthesis.
+
+The lipid membrane separates the inside of the cell from the outside environment, 
+allowing for unequal substrate and product concentrations inside and outside the 
+cell (s#in, p#in and s#ext, p#ext respectively). Each of the components is 
+associated with a cellular process (e.g. molecule synthesis or substrate conversion), 
+which is modeled by one or more differential equations. The proposed model describes
+an av- erage cell in a growing population of cells. Ordinary Differential Equations (ODEs) 
+in this model describe the change of molecule concentrations in time.
+
+## Installation
+Gigabase runs on Rails. You can load this repository onto your hard drive and directly use
+it as a rails app. Just run `bundle install` and `rake db: setup` and you are good to go. 
+For windows users, some gems might not install and display a message such as not native build.
+Download the Ruby Devkit and run the `bundle install` command in `mysys` terminal. All the
+gems will then perfectly build. Don't forget you might need administrator rights.
+
 ## Build Status
 
 ### develop 
 [![develop](https://travis-ci.org/Derkje-J/programming-life.png?branch=develop)](https://travis-ci.org/Derkje-J/programming-life)
 
 ### master
 [![master](https://travis-ci.org/Derkje-J/programming-life.png?branch=master)](https://travis-ci.org/Derkje-J/programming-life)
+
+## Pull Requests
+We are always open to pull requests. After June 2013 the project will no longer be
+fixed in direction, so more freedom on where to go. We do not allow pull requests on master
+or release branches. Fork the repository, create a patch/feature/issue branch and 
+merge to develop.
+
+Your code should be `rdoc` or `codo/coffeedoc` commented, assets should be `/spec/` tested 
+and when applied should have `/test/functional` integration tests. Server side code should
+also be `/test/` unit tested.

app/assets/javascripts/MVC.js.coffee

@@ -1,3 +1,5 @@
 (exports ? this).Model = {}
 (exports ? this).Controller = {}
-(exports ? this).View = {}
+(exports ? this).View = {}
+(exports ? this).Helper = {}
+(exports ? this).Mixin = {}

app/assets/javascripts/application.js

@@ -14,11 +14,14 @@
 //= require jquery_ujs
 //= require jquery_nested_form
 //= require json2
-//= require underscore
+//= require lodash
 //= require big.min
+//= require jquery.svg.js
+//= require jquery.svgdom.patched.js
 //
 //= require MVC
 //
+//= require_tree ./helpers
 //= require_tree ./models
 //= require_tree ./views
 //= require_tree ./controllers
@@ -33,6 +36,8 @@
 //= require g.dot-min
 //= require g.line-min
 //= require raphael-triangle
+//= require raphael-arrow
+//= require raphael-animatevb
 //
 //= require chart
 //= require md5.min

app/assets/javascripts/controllers/main.js.coffee

@@ -6,35 +6,8 @@
 #
 class Controller.Main
 
-	dt: 0.1
-	_tree: new UndoTree()
-
 	# Creates a new instance of Main
-	constructor: ( ) ->
-		@view = new View.Main()
-
-	# Undoes the last move.
-	undo: ( ) ->
-		object = [type, module]
-		@_tree.add( object )
-
-	# Redoes the last move.
-	redo: ( ) ->
-		[type, module] = @_tree.redo()
-		switch type
-			when 'modify' then module.redo()
-
-	# Adds a move to the undotree
 	#
-	# @param [String] type, the type of move. For now, 'modify' is implemented.
-	# @param [Module] module, the module that has done the move.
-	#
-	addMove: ( type, module ) ->
-		object = [type, module]
-		@_tree.add( object )
-
-
-$(document).ready ->
-	(exports ? window).Controller.Main = Controller.Main
-
-
+	# @param container [String, Object] A string with an id or a DOM node to serve as a container for the view
+	constructor: ( container ) ->
+		@_view = new View.Main(container)

app/assets/javascripts/helpers/mixin._.js.coffee

@@ -0,0 +1,43 @@
+#
+#
+class Helper.Mixable
+
+	@ModuleKeyWords : [ 'extended', 'included' ]
+
+	# Extends a class by adding the properties of the mixins to the class
+	#
+	# @param classmixins [Object*] the mixins to add
+	#
+	@extend: ( classmixins... ) ->
+
+		for mixin in classmixins
+			for key, value of mixin when key not in Helper.Mixable.ModuleKeyWords
+				@[ key ] = value
+
+			mixin.extended?.apply( @ )
+		this
+
+	# Includes mixins to a class by adding the properties to the Prototype
+	#
+	# @param  instancemixins [Object*] the mixins to add
+	#
+	@include: ( instancemixins... ) ->
+		for mixin in instancemixins
+			for key, value of mixin when key not in Helper.Mixable.ModuleKeyWords
+				# Assign properties to the prototype
+				@::[ key ] = value
+
+			mixin.included?.apply( @ )
+		return this
+
+	# Concerns automagically include and extend a class
+	#
+	# @param  concerns [Object*] the mixins to add
+	#
+	@concern: ( concerns... ) ->
+
+		for concern in concerns
+			@include concern.InstanceMethods
+			@extend concern.ClassMethods
+
+		return this