GCAT5.0 released

2015-04-10 15:12:45 -05:00
commit 67544a10e6
257 changed files with 61661 additions and 0 deletions
@@ -0,0 +1,5 @@
+.bundle
+db/*.sqlite3
+log/*.log
+tmp/
+.sass-cache/
@@ -0,0 +1,42 @@
+source 'http://rubygems.org'
+
+# gem 'rails', '3.1.0' #no longer supporting security updates
+gem 'rails', '3.2.15'
+
+# Bundle edge Rails instead:
+# gem 'rails',     :git => 'git://github.com/rails/rails.git'
+
+gem 'sqlite3'
+
+
+# Gems used only for assets and not required
+# in production environments by default.
+group :assets do
+  gem 'sass-rails',   '~> 3.2.3'
+  #gem 'coffee-rails', "~> 3.1.0"
+  gem 'uglifier'
+
+  # See https://github.com/sstephenson/execjs#readme for more supported runtimes
+  gem 'therubyracer'
+
+end
+
+gem 'jquery-rails'
+
+# Use unicorn as the web server
+# gem 'unicorn'
+
+# Deploy with Capistrano
+# gem 'capistrano'
+
+# To use debugger
+gem 'debugger'
+
+group :test do
+  # Pretty printed test output
+  gem 'turn', :require => false
+end
+
+gem 'rinruby'
+
+gem 'rubyzip'
@@ -0,0 +1,124 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    actionmailer (3.2.15)
+      actionpack (= 3.2.15)
+      mail (~> 2.5.4)
+    actionpack (3.2.15)
+      activemodel (= 3.2.15)
+      activesupport (= 3.2.15)
+      builder (~> 3.0.0)
+      erubis (~> 2.7.0)
+      journey (~> 1.0.4)
+      rack (~> 1.4.5)
+      rack-cache (~> 1.2)
+      rack-test (~> 0.6.1)
+      sprockets (~> 2.2.1)
+    activemodel (3.2.15)
+      activesupport (= 3.2.15)
+      builder (~> 3.0.0)
+    activerecord (3.2.15)
+      activemodel (= 3.2.15)
+      activesupport (= 3.2.15)
+      arel (~> 3.0.2)
+      tzinfo (~> 0.3.29)
+    activeresource (3.2.15)
+      activemodel (= 3.2.15)
+      activesupport (= 3.2.15)
+    activesupport (3.2.15)
+      i18n (~> 0.6, >= 0.6.4)
+      multi_json (~> 1.0)
+    ansi (1.4.3)
+    arel (3.0.3)
+    builder (3.0.4)
+    columnize (0.3.6)
+    debugger (1.6.6)
+      columnize (>= 0.3.1)
+      debugger-linecache (~> 1.2.0)
+      debugger-ruby_core_source (~> 1.3.2)
+    debugger-linecache (1.2.0)
+    debugger-ruby_core_source (1.3.2)
+    erubis (2.7.0)
+    execjs (2.0.2)
+    hike (1.2.3)
+    i18n (0.6.9)
+    journey (1.0.4)
+    jquery-rails (3.1.0)
+      railties (>= 3.0, < 5.0)
+      thor (>= 0.14, < 2.0)
+    json (1.8.1)
+    libv8 (3.16.14.3)
+    mail (2.5.4)
+      mime-types (~> 1.16)
+      treetop (~> 1.4.8)
+    mime-types (1.25.1)
+    multi_json (1.9.0)
+    polyglot (0.3.4)
+    rack (1.4.5)
+    rack-cache (1.2)
+      rack (>= 0.4)
+    rack-ssl (1.3.3)
+      rack
+    rack-test (0.6.2)
+      rack (>= 1.0)
+    rails (3.2.15)
+      actionmailer (= 3.2.15)
+      actionpack (= 3.2.15)
+      activerecord (= 3.2.15)
+      activeresource (= 3.2.15)
+      activesupport (= 3.2.15)
+      bundler (~> 1.0)
+      railties (= 3.2.15)
+    railties (3.2.15)
+      actionpack (= 3.2.15)
+      activesupport (= 3.2.15)
+      rack-ssl (~> 1.3.2)
+      rake (>= 0.8.7)
+      rdoc (~> 3.4)
+      thor (>= 0.14.6, < 2.0)
+    rake (10.1.1)
+    rdoc (3.12.2)
+      json (~> 1.4)
+    ref (1.0.5)
+    rinruby (2.0.3)
+    rubyzip (1.1.0)
+    sass (3.2.14)
+    sass-rails (3.2.6)
+      railties (~> 3.2.0)
+      sass (>= 3.1.10)
+      tilt (~> 1.3)
+    sprockets (2.2.2)
+      hike (~> 1.2)
+      multi_json (~> 1.0)
+      rack (~> 1.0)
+      tilt (~> 1.1, != 1.3.0)
+    sqlite3 (1.3.9)
+    therubyracer (0.12.1)
+      libv8 (~> 3.16.14.0)
+      ref
+    thor (0.18.1)
+    tilt (1.4.1)
+    treetop (1.4.15)
+      polyglot
+      polyglot (>= 0.3.1)
+    turn (0.9.6)
+      ansi
+    tzinfo (0.3.38)
+    uglifier (2.4.0)
+      execjs (>= 0.3.0)
+      json (>= 1.8.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  debugger
+  jquery-rails
+  rails (= 3.2.15)
+  rinruby
+  rubyzip
+  sass-rails (~> 3.2.3)
+  sqlite3
+  therubyracer
+  turn
+  uglifier
@@ -0,0 +1,18 @@
+Copyright 2012 The Board of Regents of the University of Wisconsin System.
+Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, 
+Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+
+This file is part of GCAT.
+
+GCAT is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+GCAT is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License  
+along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
@@ -0,0 +1,261 @@
+== Welcome to Rails
+
+Rails is a web-application framework that includes everything needed to create
+database-backed web applications according to the Model-View-Control pattern.
+
+This pattern splits the view (also called the presentation) into "dumb"
+templates that are primarily responsible for inserting pre-built data in between
+HTML tags. The model contains the "smart" domain objects (such as Account,
+Product, Person, Post) that holds all the business logic and knows how to
+persist themselves to a database. The controller handles the incoming requests
+(such as Save New Account, Update Product, Show Post) by manipulating the model
+and directing data to the view.
+
+In Rails, the model is handled by what's called an object-relational mapping
+layer entitled Active Record. This layer allows you to present the data from
+database rows as objects and embellish these data objects with business logic
+methods. You can read more about Active Record in
+link:files/vendor/rails/activerecord/README.html.
+
+The controller and view are handled by the Action Pack, which handles both
+layers by its two parts: Action View and Action Controller. These two layers
+are bundled in a single package due to their heavy interdependence. This is
+unlike the relationship between the Active Record and Action Pack that is much
+more separate. Each of these packages can be used independently outside of
+Rails. You can read more about Action Pack in
+link:files/vendor/rails/actionpack/README.html.
+
+
+== Getting Started
+
+1. At the command prompt, create a new Rails application:
+       <tt>rails new myapp</tt> (where <tt>myapp</tt> is the application name)
+
+2. Change directory to <tt>myapp</tt> and start the web server:
+       <tt>cd myapp; rails server</tt> (run with --help for options)
+
+3. Go to http://localhost:3000/ and you'll see:
+       "Welcome aboard: You're riding Ruby on Rails!"
+
+4. Follow the guidelines to start developing your application. You can find
+the following resources handy:
+
+* The Getting Started Guide: http://guides.rubyonrails.org/getting_started.html
+* Ruby on Rails Tutorial Book: http://www.railstutorial.org/
+
+
+== Debugging Rails
+
+Sometimes your application goes wrong. Fortunately there are a lot of tools that
+will help you debug it and get it back on the rails.
+
+First area to check is the application log files. Have "tail -f" commands
+running on the server.log and development.log. Rails will automatically display
+debugging and runtime information to these files. Debugging info will also be
+shown in the browser on requests from 127.0.0.1.
+
+You can also log your own messages directly into the log file from your code
+using the Ruby logger class from inside your controllers. Example:
+
+  class WeblogController < ActionController::Base
+    def destroy
+      @weblog = Weblog.find(params[:id])
+      @weblog.destroy
+      logger.info("#{Time.now} Destroyed Weblog ID ##{@weblog.id}!")
+    end
+  end
+
+The result will be a message in your log file along the lines of:
+
+  Mon Oct 08 14:22:29 +1000 2007 Destroyed Weblog ID #1!
+
+More information on how to use the logger is at http://www.ruby-doc.org/core/
+
+Also, Ruby documentation can be found at http://www.ruby-lang.org/. There are
+several books available online as well:
+
+* Programming Ruby: http://www.ruby-doc.org/docs/ProgrammingRuby/ (Pickaxe)
+* Learn to Program: http://pine.fm/LearnToProgram/ (a beginners guide)
+
+These two books will bring you up to speed on the Ruby language and also on
+programming in general.
+
+
+== Debugger
+
+Debugger support is available through the debugger command when you start your
+Mongrel or WEBrick server with --debugger. This means that you can break out of
+execution at any point in the code, investigate and change the model, and then,
+resume execution! You need to install ruby-debug to run the server in debugging
+mode. With gems, use <tt>sudo gem install ruby-debug</tt>. Example:
+
+  class WeblogController < ActionController::Base
+    def index
+      @posts = Post.all
+      debugger
+    end
+  end
+
+So the controller will accept the action, run the first line, then present you
+with a IRB prompt in the server window. Here you can do things like:
+
+  >> @posts.inspect
+  => "[#<Post:0x14a6be8
+          @attributes={"title"=>nil, "body"=>nil, "id"=>"1"}>,
+       #<Post:0x14a6620
+          @attributes={"title"=>"Rails", "body"=>"Only ten..", "id"=>"2"}>]"
+  >> @posts.first.title = "hello from a debugger"
+  => "hello from a debugger"
+
+...and even better, you can examine how your runtime objects actually work:
+
+  >> f = @posts.first
+  => #<Post:0x13630c4 @attributes={"title"=>nil, "body"=>nil, "id"=>"1"}>
+  >> f.
+  Display all 152 possibilities? (y or n)
+
+Finally, when you're ready to resume execution, you can enter "cont".
+
+
+== Console
+
+The console is a Ruby shell, which allows you to interact with your
+application's domain model. Here you'll have all parts of the application
+configured, just like it is when the application is running. You can inspect
+domain models, change values, and save to the database. Starting the script
+without arguments will launch it in the development environment.
+
+To start the console, run <tt>rails console</tt> from the application
+directory.
+
+Options:
+
+* Passing the <tt>-s, --sandbox</tt> argument will rollback any modifications
+  made to the database.
+* Passing an environment name as an argument will load the corresponding
+  environment. Example: <tt>rails console production</tt>.
+
+To reload your controllers and models after launching the console run
+<tt>reload!</tt>
+
+More information about irb can be found at:
+link:http://www.rubycentral.org/pickaxe/irb.html
+
+
+== dbconsole
+
+You can go to the command line of your database directly through <tt>rails
+dbconsole</tt>. You would be connected to the database with the credentials
+defined in database.yml. Starting the script without arguments will connect you
+to the development database. Passing an argument will connect you to a different
+database, like <tt>rails dbconsole production</tt>. Currently works for MySQL,
+PostgreSQL and SQLite 3.
+
+== Description of Contents
+
+The default directory structure of a generated Ruby on Rails application:
+
+  |-- app
+  |   |-- assets
+  |       |-- images
+  |       |-- javascripts
+  |       `-- stylesheets
+  |   |-- controllers
+  |   |-- helpers
+  |   |-- mailers
+  |   |-- models
+  |   `-- views
+  |       `-- layouts
+  |-- config
+  |   |-- environments
+  |   |-- initializers
+  |   `-- locales
+  |-- db
+  |-- doc
+  |-- lib
+  |   `-- tasks
+  |-- log
+  |-- public
+  |-- script
+  |-- test
+  |   |-- fixtures
+  |   |-- functional
+  |   |-- integration
+  |   |-- performance
+  |   `-- unit
+  |-- tmp
+  |   |-- cache
+  |   |-- pids
+  |   |-- sessions
+  |   `-- sockets
+  `-- vendor
+      |-- assets
+          `-- stylesheets
+      `-- plugins
+
+app
+  Holds all the code that's specific to this particular application.
+
+app/assets
+  Contains subdirectories for images, stylesheets, and JavaScript files.
+
+app/controllers
+  Holds controllers that should be named like weblogs_controller.rb for
+  automated URL mapping. All controllers should descend from
+  ApplicationController which itself descends from ActionController::Base.
+
+app/models
+  Holds models that should be named like post.rb. Models descend from
+  ActiveRecord::Base by default.
+
+app/views
+  Holds the template files for the view that should be named like
+  weblogs/index.html.erb for the WeblogsController#index action. All views use
+  eRuby syntax by default.
+
+app/views/layouts
+  Holds the template files for layouts to be used with views. This models the
+  common header/footer method of wrapping views. In your views, define a layout
+  using the <tt>layout :default</tt> and create a file named default.html.erb.
+  Inside default.html.erb, call <% yield %> to render the view using this
+  layout.
+
+app/helpers
+  Holds view helpers that should be named like weblogs_helper.rb. These are
+  generated for you automatically when using generators for controllers.
+  Helpers can be used to wrap functionality for your views into methods.
+
+config
+  Configuration files for the Rails environment, the routing map, the database,
+  and other dependencies.
+
+db
+  Contains the database schema in schema.rb. db/migrate contains all the
+  sequence of Migrations for your schema.
+
+doc
+  This directory is where your application documentation will be stored when
+  generated using <tt>rake doc:app</tt>
+
+lib
+  Application specific libraries. Basically, any kind of custom code that
+  doesn't belong under controllers, models, or helpers. This directory is in
+  the load path.
+
+public
+  The directory available for the web server. Also contains the dispatchers and the
+  default HTML files. This should be set as the DOCUMENT_ROOT of your web
+  server.
+
+script
+  Helper scripts for automation and generation.
+
+test
+  Unit and functional tests along with fixtures. When using the rails generate
+  command, template test files will be generated for you and placed in this
+  directory.
+
+vendor
+  External libraries that the application depends on. Also includes the plugins
+  subdirectory. If the app has frozen rails, those gems also go here, under
+  vendor/rails/. This directory is in the load path.
@@ -0,0 +1,7 @@
+#!/usr/bin/env rake
+# Add your own tasks in files placed in lib/tasks ending in .rake,
+# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
+
+require File.expand_path('../config/application', __FILE__)
+
+Gcat::Application.load_tasks
@@ -0,0 +1,34 @@
+/*
+ * Copyright 2012 The Board of Regents of the University of Wisconsin System.
+ * Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+ * Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+ *
+ * This file is part of GCAT.
+ *
+ * GCAT is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * GCAT is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+// This is a manifest file that'll be compiled into including all the files listed below.
+// Add new JavaScript/Coffee code in separate files in this directory and they'll automatically
+// be included in the compiled file accessible from http://example.com/assets/application.js
+// It's not advisable to add code directly here, but if you do, it'll appear at the bottom of the
+// the compiled file.
+//
+//= require jquery
+//= require jquery_ujs
+//= require yuiloader-min
+//= require datatable-min
+//= require jquery.loader-min
+//= require_tree .
+//= require bootstrap.min
@@ -0,0 +1,76 @@
+/*
+ * Copyright 2012 The Board of Regents of the University of Wisconsin System.
+ * Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+ * Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+ *
+ * This file is part of GCAT.
+ *
+ * GCAT is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * GCAT is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
+$(document).ready(function(){
+	// Three blocks below for hiding the optional user input fields.
+	$(".user_enter1").on("change", function(){
+  	$(".optional_input1").toggle($(this).hasClass("user_enter1_yes"));
+	});
+
+	$(".user_enter2").on("change", function(){
+  	$(".optional_input2").toggle($(this).hasClass("user_enter2_yes"));
+	});
+
+	$(".user_enter3").on("change", function(){
+  	$(".optional_input3").toggle($(this).hasClass("user_enter3_yes"));
+	});
+
+	// handle error redirect & browser back cases//////////////////////////////////////////
+	/****************************************************
+	 * This function checks the radio box for the
+	 * corresponding optional div with input field.
+	 * If checked show else hide
+	 * @return void
+	****************************************************/
+	function reset_optional_fields(radio, optional_box){
+		if(radio && optional_box){
+			var radio_ckd = radio.prop('checked');
+			if(radio_ckd){
+				optional_box.show();
+			}
+			else {
+				optional_box.hide();
+			}
+		} else{
+			console.error("Error: unknown selector in reset_optional_fields()");
+		}
+	}
+	reset_optional_fields($('#assay_plate_type_m'), $("#time"));
+	reset_optional_fields($("input#assay_blank_value_user"), $("div.optional_input3"));
+	reset_optional_fields($("input#assay_transformation_-1"), $("div.optional_input2"));
+	reset_optional_fields($("input#assay_model_-1"), $("div.optional_input1"));
+	//////////////////////////////////////////////////////////////////////////////////////
+
+	$('#new_assay').submit(function() {
+			$.loader();
+	});
+
+	$("input[name$='assay[plate_type]']").click(function(){
+	  var value = $(this).val();
+	  if(value=='s') {
+	    $("#time").hide();
+	  }
+	  else if(value=='m') {
+	    $("#time").show();
+	   }
+	});        
+});
@@ -0,0 +1,32 @@
+/*
+ * Copyright 2012 The Board of Regents of the University of Wisconsin System.
+ * Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+ * Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+ *
+ * This file is part of GCAT.
+ *
+ * GCAT is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * GCAT is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/*
+ * This is a manifest file that'll automatically include all the stylesheets available in this directory
+ * and any sub-directories. You're free to add application-wide styles to this file and they'll appear at
+ * the top of the compiled file, but it's generally better to create a new file per style scope.
+ *= require_self
+ *= require_tree .
+ *= require bootstrap.min
+*/
+
+//= require datatable
+//= require jquery.loader-min
@@ -0,0 +1,3 @@
+// Place all the styles related to the Assays controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
@@ -0,0 +1,102 @@
+/*
+ * Copyright 2012 The Board of Regents of the University of Wisconsin System.
+ * Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+ * Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+ *
+ * This file is part of GCAT.
+ *
+ * GCAT is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * GCAT is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/*.yui-skin-sam .yui-dt-liner { white-space:nowrap; font-size: 8pt;}
+.twoColLiqLtHdr #mainContent { margin:0;min-height:500px; } //Not used anymore NWD// */
+
+body {
+  background: url("bkg-body.png") repeat-x scroll left top #FFFFFF;
+  background-color: #FFFFFF;
+}
+
+a:visited { color: #428bca !important;}
+
+#nav-bar{
+  background:#B0C5D4;
+  border-bottom:1px solid #B0C5D4;
+  text-align:center;
+  h1{
+    font: 42px impact, sans-serif;
+  }
+}
+
+/*#copyright-stmt {
+  padding: 5px 25px;
+  width: 88%;
+  margin: 20px auto 0;
+  text-align: right;
+}*/
+
+#header h1 {
+  font-size: 32px;
+  color: #4F4F4F;
+}
+
+#results-container {    
+  background-color: #FFFFFF;
+  border: 1px solid black;
+  margin: 20px auto 0;
+  padding: 120px;
+  width: 4000px;        
+}
+
+#form-container {    
+  background-color: #FFFFFF;
+  border: 1px solid black;
+  margin: 20px auto 0;
+  width: 1600px;
+  padding-left: 50px;      
+}
+
+#contents {
+  padding: 5px 25px;
+}
+
+/*#mainContent{
+  margin:0;
+  min-height:500px;
+}*/
+
+/*#header {
+  background: #fffff; 
+  font: 14px arial;
+  color: black; 
+  height:50px;
+  text-align:left;
+  padding: 0px 10px;
+  border-bottom:1px solid #69B03F;
+  width: 1600px;
+}*/
+
+/*#flash_notice, #flash_error, #flash_alert, .notice, .error, .alert {
+  padding: 5px 8px;
+  margin: 10px 0;
+}
+
+#flash_notice, .notice {
+  background-color: #CFC;
+  border: solid 1px #6C6;
+}
+
+#flash_error, #flash_alert, .error, .alert {
+  background-color: #FCC;
+  border: solid 1px #C66;
+}*/
@@ -0,0 +1,56 @@
+body {
+  background-color: #fff;
+  color: #333;
+  font-family: verdana, arial, helvetica, sans-serif;
+  font-size: 13px;
+  line-height: 18px; }
+
+p, ol, ul, td {
+  font-family: verdana, arial, helvetica, sans-serif;
+  font-size: 13px;
+  line-height: 18px; }
+
+pre {
+  background-color: #eee;
+  padding: 10px;
+  font-size: 11px; }
+
+a {
+  color: #000;
+  &:visited {
+    color: #666; }
+  &:hover {
+    color: #fff;
+    background-color: #000; } }
+
+div {
+  &.field, &.actions {
+    margin-bottom: 10px; } }
+
+#notice {
+  color: green; }
+
+.field_with_errors {
+  padding: 2px;
+  background-color: red;
+  display: table; }
+
+#error_explanation {
+  width: 450px;
+  border: 2px solid red;
+  padding: 7px;
+  padding-bottom: 0;
+  margin-bottom: 20px;
+  background-color: #f0f0f0;
+  h2 {
+    text-align: left;
+    font-weight: bold;
+    padding: 5px 5px 5px 15px;
+    font-size: 12px;
+    margin: -7px;
+    margin-bottom: 0px;
+    background-color: #c00;
+    color: #fff; }
+  ul li {
+    font-size: 12px;
+    list-style: square; } }
@@ -0,0 +1,157 @@
+/*
+ * Copyright 2012 The Board of Regents of the University of Wisconsin System.
+ * Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+ * Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+ *
+ * This file is part of GCAT.
+ *
+ * GCAT is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * GCAT is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/*.tooltip:hover:after { content: attr(data-tooltip);
+position: absolute; white-space: nowrap; background: rgba(0, 0, 0, 0.85); padding: 3px 7px; color: #FFF; border-radius: 3px; -moz-border-radius: 3px; -webkit-border-radius: 3px; margin-left: 7px; margin-top: -3px;font-size:10px;}
+*/
+
+
+  /* Make tooltip "links" have a different pointer (as the tooltip uses the "help" cursor by default) */      
+  a[data-tooltip]
+        {
+        cursor:pointer !important;
+        }
+  /* Styles for elements having a data-tooltip attribute - using the star selector is processor intensive
+     so you may wish to change this to list a known, limited set of tags instead */
+  *[data-tooltip]
+        {
+        /* Relativly position the tooltip to enable us to position:absolute 
+           the generated content */
+        position:relative;        
+        /* Links inherit the !important cursor rule from above */
+        cursor:help;
+        /* Moz requires the text-decoration here (as it won't allow the use of
+          text-decoration:none on generated content) which is why I use the bottom 
+          border to display a more accessible underline */
+        text-decoration:none;   
+        border-bottom:1px dotted #aaa; 
+        /* Remove the styles for IE7 and below - could be passed using conditional comments */
+        *text-decoration:inherit;   
+        *border-bottom-width:inherit;
+        *border-bottom-style:inherit;        
+        *cursor:inherit;
+        *position:inherit;            
+        }
+  /* Default :before & :after values */     
+  *[data-tooltip]:after,
+  *[data-tooltip]:before
+        {
+        content:"";
+        /* Don't show tooltip by default */
+        opacity:0;  
+        /* Set a high z-index */
+        z-index:999;
+        
+        /* Animations won't (yet) work on pseudo elements - shame really as this should fade the tooltip in 
+           after one second - but I'll leave the rules for posterity */
+        -moz-transition-property: opacity;
+        -moz-transition-duration: 2s;
+        -moz-transition-delay: 1s;
+        
+        -webkit-transition-property: opacity;
+        -webkit-transition-duration: 2s;
+        -webkit-transition-delay: 1s;
+        
+        -o-transition-property: opacity;
+        -o-transition-duration: 2s;
+        -o-transition-delay: 1s;
+        
+        transition-property: opacity;
+        transition-duration: 2s;
+        transition-delay: 1s;  
+        
+        /* -moz won't understand the text-decoration here but inherits the parent value of "none" successfully */
+        text-decoration:none !important;
+        outline:none;
+        }
+  /* Tooltip arrow - shown on hover or focus */
+  *[data-tooltip]:hover:before,
+  *[data-tooltip]:focus:before
+        {
+        /* Slightly opaque arrow */
+        opacity:0.94;
+        outline:none;
+        content:"";  
+        display:block;        
+        position:absolute;
+        top:20px;
+        left:50%;
+        margin:0 0 0 -5px;
+        width:0;
+        height:0;
+        line-height:0px; 
+        font-size:0px;       
+        /* This sets the tooptip pointer color */
+        border-bottom:5px solid #33acfc;
+        border-left:5px solid transparent;
+        border-right:5px solid transparent;        
+        border-top:transparent;
+        /* Border gradient */        
+        -webkit-border-image:-webkit-gradient(linear, left top, left bottom, from(#33ccff), to(#33acfc));                        
+        }
+  /* Tooltip body - shown on hover or focus */
+  *[data-tooltip]:hover:after,
+  *[data-tooltip]:focus:after
+        {
+        /* Slightly opaque tooltip */
+        opacity:0.94;
+        /* Set display to block (or inline-block) */
+        display:block;
+        /* Use the data-tooltip attribute to set the content*/
+        content:attr(data-tooltip);
+        /* Position the tooltip body under the arrow and in the middle of the text */
+        position:absolute;
+        top:25px;
+        left:50%;
+        margin:0 0 0 -150px;
+        /* Set the width */
+        width:290px;
+        /* Pad */
+        padding:5px;
+        /* Style the tooltip */
+        line-height:18px;
+        /* min-height */
+        min-height:18px; 
+        /* Set font styles */  
+        color:#fcfcfc;
+        font-size:16px;        
+        font-weight:normal;
+        font-family:helvetica neue, calibri, verdana, arial, sans-serif;
+        /* Fallback background color */
+        background:#3198dd; 
+        text-align:center;        
+        outline:none;        
+        /* Moz doesn't recognise the following... */
+        text-decoration:none !important;                  
+        /* Background gradient */        
+        background:-webkit-gradient(linear, left top, left bottom, from(#33acfc), to(#3198dd));
+        background:-moz-linear-gradient(top,#33acfc,#3198dd);         
+        /* Round the corners */
+        -moz-border-radius:10px;
+        -webkit-border-radius:10px;
+        border-radius:10px;        
+        /* Add a drop shadow */
+        -moz-box-shadow:2px 2px 4px #ccc;
+        -webkit-box-shadow:2px 2px 4px #ccc;
+        box-shadow:2px 2px 4px #ccc;        
+        /* Add a Text shadow */
+        text-shadow:#2187c8 0 1px 0px; 
+        }  
@@ -0,0 +1,23 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+class ApplicationController < ActionController::Base
+  protect_from_forgery
+end
@@ -0,0 +1,73 @@
+include ApplicationHelper
+include TableBuilder
+
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+class AssaysController < ApplicationController
+
+  def new
+    @assay= Assay.new
+  end
+
+  def create 
+    #Lazy mass assign from form params
+    @assay = Assay.new(params[:assay])
+
+    if @assay.valid?
+    
+      # Add the calls to methods to parse the form input in @assay and execute R script.
+      # return the results from R into a new instance variable and display results via show template
+      
+      #reassign some parameters. Validate on form input params or after manipulations?
+      @assay = @assay.parse_form_params
+      #debugger
+      
+      #execute R calculation and assign instance variable to display     
+      @result = @assay.r_calculation
+
+      # no need to keep storing old data
+      
+      #temp fix for pdfFiles see ticket #424. string of pdfFiles returned rather than array
+      unless @result[:pdfFiles].nil?
+       @result[:pdfFiles] = @result[:pdfFile].split('pdf')
+       @result[:pdfFiles].collect{|element| element + 'pdf'}
+       end
+      
+      if  ( @result.has_key? :error_message )  #h.has_key?("a") # @result.has_key? :error_message
+        flash.now[:error] = @result[:error_message] #.join("\n")
+        #do not allow bad guys to fill disc space with invalid files
+        FileUtils.rm @result[:path]
+        render :action => 'inputfile_error_message' 
+      else
+        # parse the output text file into a hash in order to create a table in Assays#show
+        @table = output_table(@result, !@result[:layout_file].nil?)
+        remove_old_files(relative_path(@result[:zipfile]))
+        flash.now[:notice] = "Your assay processed!\nPlease click on any of plate diagrams to save your results to a zip archive."  
+        render :action => 'show'
+      end    
+    else
+
+      render :action => 'new'
+    end  
+  end  
+
+
+end
@@ -0,0 +1,51 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+module ApplicationHelper
+
+  def relative_path(fullpath)
+    fullpath.to_s.gsub(Rails.root.to_s + "/public","")
+  end
+
+  #find all directories in generatedFiles/ and remove
+  #any that are more than a day old
+  def remove_old_files(path)
+  	cur_date = extract_date(path)
+  	dirs = Dir.glob(Rails.root + "public/generatedFiles/*") + Dir.glob(Rails.root + "public/uploadedFiles/*")
+  	dirs.compact.each do |dir|
+  		date = extract_date(dir)
+  		if(date != cur_date)
+        puts "Removing: " + dir #log deletions
+  			%x[ rm -rf #{dir} ]
+	    end
+	  end
+  end
+
+  private
+
+    def extract_date(path)
+  	  part = "Files/"
+  	  segment = path.partition(part).last
+  	  date = segment.split(/-[0-9]+/).first
+  	  date.to_i
+    end
+
+
+end
@@ -0,0 +1,29 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+module AssaysHelper
+  
+  def date_time_options
+    
+    [['Y-m-d H:M:S', '%Y-%m-%d %H:%M:%S'],['Y-m-d H:M:S p', '%Y-%m-%d %I:%M:%S %p'],['m/d/y H:M:S','%m/%d/%y %H:%M:%S'],['m/d/y H:M:S p','%m/%d/%y %I:%M:%S %p'],['d/m/y H:M:S','%d/%m/%y %H:%M:%S'],['d/m/y H:M:S p','%d/%m/%y %I:%M:%S %p'],['m/d/Y H:M', '%m/%d/%Y %H:%M']]
+    
+  end
+  
+end
@@ -0,0 +1,64 @@
+module TableBuilder
+
+	# I decided to parse the output file produced by the R library
+	# and build an html table rather than using the YUI JS library
+	# previously implemented.
+	#
+	# This method takes the result hash returned by the R bridge routine and
+	# builds an array of row arrays
+	def output_table result, has_layout
+		# if the user submits a layout file, there will be more columns in the output file
+		offsets = {:pdf => -2, :page => -1}
+		if(has_layout)
+			offsets[:pdf] = -7
+			offsets[:page] = -6
+		end
+		rel_path = result[:txtFile]
+		pdf_path = File.dirname @result[:txtFile] #Rails.root.join("public/"+result[:pdfFile])
+		path = Rails.root.join("public/"+rel_path)
+		raise "File not found" unless File.exists? path
+		file = File.open path
+		output = []
+		file.each_line do |line|
+			if(output.empty?)
+				# the headers seem to be enclosed in quotations
+				# will need to parse a bit differently
+				l_ar = line.split "\"\t\""
+				l_ar.first.delete! "\""
+      	l_ar.last.delete! "\"\n"
+      	l_ar.collect! {|l| l.gsub ".", " "}
+      	output << l_ar
+    	else
+    		l_ar = line.split "\t"
+      	l_ar.last.delete! "\"\n"
+      	break unless l_ar.size > 1
+      	output << format_row(l_ar, pdf_path, offsets)
+    	end
+		end
+		return output
+	end
+
+	# this method: removes quotations from strings, truncates floats to 2 sig. digits,
+	# and creates html links to PDF files
+	# params: 
+	# 	l_ar--An array of the one row of data
+	#   path--directory path where the pdf file is located
+	#   offsets-- a hash containing the negative array offsets for cells needed to build pdf link
+	#
+	# returns: A formatted array of one row from the output.txt data
+	def format_row l_ar, path, offsets
+		result = l_ar.collect! do |entry|
+			if(entry.to_f.zero?)
+				entry.gsub "\"", ""
+			elsif(view_context.number_with_precision(entry.to_f, precision: 2, significant: true).size > 15)
+				"%E" % view_context.number_with_precision(entry.to_f, precision: 2, significant: true)
+			else
+				view_context.number_with_precision(entry.to_f, precision: 2, significant: true)
+			end
+		end
+		result[offsets[:page]] = result[offsets[:page]].to_i  # page number
+		# result[-7] == pdf.name
+		result[0] = "<a href=\"#{path}/#{result[offsets[:pdf]]}?#page=#{result[offsets[:page]]}\" target='_blank'>#{result[0].to_i}</a>".html_safe  # add pdf link to first row
+		return result
+	end
+end
@@ -0,0 +1,393 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+require 'zip'
+# require 'zip/zipfilesystem'
+require 'fileutils'
+include FileUtils
+
+# single-plate timestamp
+SECONDS = "1/3600".to_r.to_f
+MAX_FILE_SIZE = 10000000.0
+
+class Assay
+  
+  include ActiveModel::Validations
+  include ActiveModel::Conversion
+  extend ActiveModel::Naming
+  attr_accessor :input_file, :transformation, :transformation_input, :blank_value, :blank_value_input, :start_index, :remove_points, :remove_jumps, :plate_type,
+  :plate_dimensions_row, :plate_dimensions_column, :timestamp_format, :growth_threshold, :layout_file,:filename,:content_type, :model, :loess_input
+
+  # (1) Validation of input data file
+  validates_presence_of :input_file, :message => '- No input file was specified.'
+  #Either look for .csv as file extension, or in mime type (content_type). No need to validate if there is not filename
+  #validates_format_of :filename, :with => %r{\.(csv|xlsx)$}i, :message => "- You can only upload csv and xlsx files.", :unless => lambda { self.input_file == nil }
+  validates_format_of :filename, :with => %r{\.(csv)$}i, :message => "- You can only upload csv files.", :unless => lambda { self.input_file == nil }
+  
+  def filename
+    unless self.input_file.nil?
+      self.filename = self.input_file.original_filename
+    end
+  end
+  
+  def content_type
+    unless self.input_file.nil?
+      self.content_type = self.input_file.content_type
+    end
+  end
+  
+  # (2)Validation of transformation
+  # if user input is chosen, the user should enter a valid Delta value (A Real Number)
+  validates_presence_of :transformation_input,  :if => :user_input_r_value?, :message => '- Please Enter Your Delta Value.'
+  validates_numericality_of :transformation_input, :if => :user_input_r_value? , :greater_than_or_equal_to => 0 , :message => '- Invalid value for Delta. Please Enter a positive real number.'
+  def user_input_r_value?
+    transformation == "-1"
+  end
+  
+  # (3) Validation of OD blank value
+  # if user input is chosen,, the user should enter a valid OD blank value(A Real Number)
+  #validates_inclusion_of :blank_value, :in => %w( default user  ), :message => '- Invalid blank value. Please choose one of options'
+  validates_presence_of :blank_value_input,  :if => :user_input?, :message => '- Please Enter Your OD Blank Value.'
+  validates_numericality_of :blank_value_input,:if => :user_input?,  :message => '- Invalid OD blank value. Please Enter A Real Number.'
+  def user_input?
+    blank_value == "user"
+  end
+  
+  
+  # (4) Validation of start_index
+  # if user does not enter anything, the system uses the default value start_index = 2
+  validates_format_of :start_index,:with => /^[0-9 \s]*$/i, :unless => :default_value?,:message => '- Invalid value for start index. Please Enter A Positive Integer Number'
+  def default_value?
+    start_index == '' 
+  end
+  
+  
+  # (5) Validation of remove_points
+  # if user does not enter anything, the system uses the default value remove_points = 0, that is an empty list
+  #validates_format_of :remove_points,:with => /^[0-9 \,\s]*$/i, :unless => :remove_points_default_value?, :message => '- Please Enter a comma-separated list of points. Example: 2,3,4,5 (Positive Integer Number)'
+  validates_format_of :remove_points,:with => /^(\d|\d+\s*,\s*)*$/i, :unless => :remove_points_default_value?, :message => '- Please Enter a comma-separated list of points. Example: 2,3,4,5 (Positive Integer Number)'
+  def remove_points_default_value?
+    remove_points == '' 
+  end
+  
+  # (6) Validation of growth threshold
+  validates_numericality_of :growth_threshold, :message => '- Please enter a number.'
+  
+  #validate plate dimensions
+  #v1 not including custom plate dimensions
+  #validates :plate_dimensions_column, :numericality => { :only_integer => true, :greater_than => 0}
+  #validates :plate_dimensions_row, :numericality => { :only_integer => true, :greater_than => 0 }
+  
+  #validate inoculation timepoint
+  validates :start_index, :numericality => { :only_integer => true, :greater_than => 0}
+  
+  
+  def initialize(attributes = {})
+    attributes.each do |name, value|
+      send("#{name}=", value)
+    end
+  end
+
+  def persisted?  #
+    false
+  end
+
+  def parse_form_params
+    
+    # (1) input data file
+    
+    # (2) transformation. N value (A Real Number)
+    if self.transformation == '-1'
+      self.transformation =  Float(self.transformation_input)
+    else
+      self.transformation = self.transformation.to_i
+    end
+
+    # Soothing parameter for growth curve model. Applied for Loess model only.
+    if self.model == '-1' and self.loess_input != ""
+        self.loess_input = Float(self.loess_input)
+    end
+
+    # (3) blank value (A Real Number)
+    if self.blank_value == 'default'
+      self.blank_value = nil
+    else
+      self.blank_value = Float(self.blank_value_input)
+    end
+
+    # (4) start index (A Positive Integer Number)
+    if 
+      start_index == ''
+      self.start_index = 2
+    else  
+      self.start_index.gsub(/\s+/, "")  # remove white spaces
+      self.start_index = self.start_index.to_i
+    end
+    
+    # (5) remove points [a space-separated list of points. Example: 2 3 4 5 (Positive Integer Number)]
+    self.remove_points = self.remove_points.gsub(/\r/,"")  # "Some text with a carriage return \r"
+    self.remove_points = self.remove_points.gsub(/\r\n/,"\n") # "Some text with a carriage return \r\n"
+    self.remove_points = self.remove_points.gsub(/\s+/, "")  # remove white spaces
+
+    ##collect! calls .to_i on each string in the array and replaces the string with the result of the conversion.
+    self.remove_points = self.remove_points.split(',').collect! {|n| n.to_i}
+
+    ## (6) remove jumps (true/false)
+    if self.remove_jumps == 1
+      self.remove_jumps = true
+    else
+      self.remove_jumps = false
+    end
+
+
+############################################################################################
+
+    return self
+
+  end # end of parse_form_params method
+
+  def pad_date(unit)
+    unit.to_i < 10 ? "0" + unit.to_s : unit.to_s
+  end
+    
+  def r_calculation
+
+    # uniqueID = Process.pid.to_s + "-" + Time.now.to_i.to_s
+    #wanted the date to be easier to extract NWD 2/26/14
+    today = Time.now
+    
+    uniqueID = today.year.to_s + pad_date(today.month) + pad_date(today.day) + "-" + today.to_i.to_s
+    # set working directories for uploaded and generated files
+    directoryPath = Rails.root + "public/uploadedFiles/" + uniqueID
+    outDir = Rails.root + "public/generatedFiles/" + uniqueID
+    out_dir_path = outDir.to_s
+    
+    # make directory and set permission 
+    FileUtils.mkdir_p(outDir)
+    FileUtils.chmod 0777, outDir
+    FileUtils.mkdir_p(directoryPath)
+    FileUtils.chmod 0777, directoryPath
+
+    # upload input data file from where it locates into web server via uri/url
+    fromfile = self.input_file
+    inputfile = directoryPath + fromfile.original_filename
+    FileUtils.copy( fromfile.tempfile.path, inputfile )
+ 
+    # upload layout data file from where it locates into web server via uri/url
+    unless self.layout_file.nil?
+      fromfile = self.layout_file
+      layout_file = directoryPath + fromfile.original_filename
+      FileUtils.copy( fromfile.tempfile.path, layout_file )
+    end
+
+    #do not massive files
+    if(File.size(inputfile) > MAX_FILE_SIZE)
+      return {:error_message => "Error: File too big. Maximum file size allowed is #{MAX_FILE_SIZE/(10**6)} MB.", :path => inputfile}
+    end
+ 
+    # use web interface parsed parameters to call R function/library via Rinruby  
+    R.eval ('library(GCAT)')
+    R.assign "out.dir", out_dir_path
+    # That is for Single Plate case. Need modification for multiple plate case
+    #Use one set.constants call only!
+       
+      if self.plate_type == 's'
+        R.assign 'single.plate', 'T'
+        timestamp_format = SECONDS #self.timestamp_format.to_r.to_f
+      elsif self.plate_type == 'm'
+        R.assign 'single.plate', 'F'
+        timestamp_format = ""+self.timestamp_format+""
+      end
+
+    
+    #################for warringer data###########################################
+    # used for custom dims 
+    #R.assign 'plate.nrow', 10
+    #R.assign 'plate.ncol', 20
+    ##############################################################################
+    
+    R.assign 'time.input', timestamp_format
+    #R.eval ("gcat.set.constants(time.format = #{timestamp_format}, plate.nrow = #{self.plate_dimensions_row}, plate.ncol = #{self.plate_dimensions_column})")
+
+    # assign type of file to load.type; ext determines function call by R
+    R.assign "load.type", "csv"
+    ext = "csv" 
+
+
+    # (1) input data file
+    R.assign "file", inputfile.to_s
+
+    first_rows = ["Well positions", "Destination plate name", "Plate ID"]
+    begin
+      file_row = ""
+      File.open(inputfile) {|f| file_row = f.readline.split(",").first}
+      if(first_rows.include?(file_row) == false)
+        return {:error_message => "Error: Unknown file format.", :path => inputfile}
+      end
+    rescue
+      #bad encoding try to validate in R
+      first_rows.collect! {|r| r.gsub(" ", ".")} # convert to R format
+      R.eval("test.out <- read.csv(file)")
+      R.eval("first_entry <- names(test.out)[1]")
+      if(first_rows.include?(R.first_entry) == false)
+        return {:error_message => "Error: Unknown file format.", :path => inputfile}
+      end
+    end
+
+    # (2) transformation. N value (A Real Number)
+    R.assign "add.constant", self.transformation
+    # (3) blank value (A Real Number)
+    if (self.blank_value == nil)
+      R.eval "blank.value <- NULL"
+    else
+      R.assign "blank.value", self.blank_value
+    end
+    # (4) start index (A Positive Integer Number)
+    R.assign "start.index", self.start_index
+    # (5) remove points [a space-separated list of points. Example: 2,3,4,5 (Positive Integer Number)]
+    R.assign "points.to.remove", self.remove_points
+    
+    R.assign  "growth.cutoff", self.growth_threshold
+    
+     if (self.layout_file ==nil)
+      R.eval "layout.file <- NULL"
+    else
+      R.assign "layout.file", layout_file.to_s
+    end
+    
+    #debugger
+    #R.assign "plate.nrow", self.plate_dimensions_row
+    #R.assign "plate.ncol", self.plate_dimensions_column
+    
+    ## (6) remove jumps (true/false)
+    if (self.remove_jumps == true)
+      R.eval "remove.jumps <- T"
+    else
+      R.eval "remove.jumps <- F"
+    end
+    # Using growth curve model. By default if this if block
+    # is not taken then the Sigmund model is used.
+    if (self.model == -1.to_s)
+      R.assign 'use.loess', 'T'
+      if (self.loess_input != "")
+        R.assign 'smooth.param', self.loess_input
+      else
+        R.assign 'smooth.param', 0.1
+      end
+      R.assign 'use.linear.param', 'F'
+    elsif (self.model == 0.to_s)
+      # Currently not in use. May return someday... NWD 9/1
+      #R.assign 'use.linear.param', 'T'
+      R.assign 'use.linear.param', 'F' #must be false
+      R.assign 'use.loess', 'F'
+    else
+      # Initialize values for growth curve models.
+      R.assign 'use.loess', 'F'
+      R.assign 'use.linear.param', 'F'
+      R.assign 'smooth.param', 0.1 # default value
+    end
+    
+    # This block evaluates the files (csv or xlsx, single.plate or multiple.plate)
+    R.eval ('R_file_return_value <- gcat.analysis.main(file, single.plate, layout.file, out.dir=out.dir, graphic.dir = out.dir, add.constant, blank.value, 
+                                    start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param, 
+                                    points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
+                                    multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"), 
+                                    layout.sheet.headers = c("Strain", "Media Definition"), silent = T, verbose = F, return.fit = F, overview.jpgs = T)')
+   
+    # good file returns a list of file path(length is more than 1), bad file returns error message string(array length = 1)
+    print R.R_file_return_value
+    R.eval ('R_array_return_length <- length(R_file_return_value)')
+    unless  R.R_array_return_length == 1
+      puts R.R_file_return_value, "\n"
+      files = R.R_file_return_value  # returns a list of file path
+      status = true
+    else
+      error_message = R.R_file_return_value
+      if(error_message.include? "Error in <remove.points>")
+        num_data_points = error_message.split("data has ").last.gsub("\n\n", "")
+        error_message = "Invalid 'Points to ignore'. Please select a value in the range (1-#{num_data_points})."
+      end
+      return {:error_message => error_message, :path => inputfile}
+    end
+
+    # process generated files
+    raise "no files generated" if files.empty?
+    #search for "_overview.jpg files" from Array of files
+    overviewFiles = ""
+    pdfFile = ""
+    txtFile = ""
+    files_Array_Size = files.size - 1
+
+    for i in 0..files_Array_Size
+      if files[i].include? "_overview.jpg"
+        overviewFiles = overviewFiles + files[i] +  "\n"
+      end
+
+      if files[i].include? "_plots"
+        pdfFile = pdfFile + files[i] +  "\n"
+      end
+
+      if files[i].include? ".txt"
+        txtFile = txtFile + files[i] +  "\n"
+      end
+    end
+ 
+
+    unless pdfFile.empty?
+      #pdfFile = pdfFile.sub!(Rails.root.to_s + '/public/', '') #sub!(pattern, replacement) will return nil if no substitutions were performed
+      pdfFile = pdfFile.gsub(Rails.root.to_s + '/public/', '') #Oct. 04 2011 by Enhai
+      pdfFile = pdfFile.gsub(/\r/,"")  # "Some text with a carriage return \r"
+      pdfFile = pdfFile.gsub(/\r\n/,"\n") # "Some text with a carriage return \r\n"
+      pdfFile = pdfFile.gsub(/\s+/, "")  # remove white spaces
+    end
+
+    unless txtFile.empty?
+      #txtFile = txtFile.sub!(Rails.root.to_s + '/public/', '')#sub!(pattern, replacement) will return nil if no substitutions were performed
+      txtFile = txtFile.gsub(Rails.root.to_s + '/public/', '') #Oct. 04 2011 by Enhai
+      txtFile = txtFile.gsub(/\r/,"")  # "Some text with a carriage return \r"
+      txtFile = txtFile.gsub(/\r\n/,"\n") # "Some text with a carriage return \r\n"
+      txtFile = txtFile.gsub(/\s+/, "")  # remove white spaces
+    end
+
+    # build array named overviewFiles that contains "_overview.jpg files"
+    overviewFiles = overviewFiles.split("\n")
+    raise "no overview files generated" if overviewFiles.empty?
+
+    if self.plate_type == 'm'
+      zipfile = out_dir_path + "/multiplePlateAnalysis.zip"
+    else
+      zipfile = out_dir_path + "/singlePlateAnalysis.zip"
+    end
+    
+    # create Zip files at current directory
+    Zip::File.open(zipfile, Zip::File::CREATE) { |zf|
+      files.each{|file| zf.add(File.basename(file), file)}
+      #files.each{|file| zf.add(file.sub(out_dir_path + "/", ""), file))}
+    }
+
+    #return results unless error
+    #zip files, jpg of overviews, txt file for datagrid, pdf file
+    
+    
+    {:status => status, :overviewFiles => overviewFiles, :zipfile => zipfile, :txtFile => txtFile, :pdfFile => pdfFile, :inputfile => inputfile, :layout_file => layout_file, :model => self.model}
+  end # end of r_calculation method
+
+  
+end # class Assay
@@ -0,0 +1,147 @@
+<%= form_for @assay do |f| %>
+
+  <% if @assay.errors.any? %>
+    <div id="error_explanation">
+      <h2><%= pluralize(@assay.errors.count, "error") %> prohibited this assay from being saved:</h2>
+
+      <ul>
+      <% @assay.errors.full_messages.each do |msg| %>
+        <li><%= msg %></li>
+      <% end %>
+      </ul>
+    </div>
+  <% end %>
+
+
+  <h3>Plate Type</h3>
+  <%= f.radio_button(:plate_type, 's', :checked => true) %>
+  <%= f.label(:plate_type_single, "Single-plate") %><br />
+  <%= f.radio_button(:plate_type, 'm', :checked => false) %>
+  <%= f.label(:plate_type_single, "Multiple-plate") %><br />
+  
+  <h3>Input Data File</h3>
+Please specify a  plate results file to upload for analysis:<br>
+  
+  <div class="field">
+    <%= f.file_field :input_file %>  
+  </div>
+  
+  <h3><span data-tooltip="Optionally upload a companion .csv file containing identifying information for all wells in the experiments(s) to be analyzed, including strain identifiers and growth media (or growth environment) definitions, which are used for graphic output.">Plate Layout File</span></h3>
+Optionally upload a plate layout file:<br>
+    
+  <div class="field">
+    <%= f.file_field :layout_file %>  
+  </div>
+
+ <div class="actions" style="margin-top:30px;">
+        <%= link_to "Single-Plate Example File","/resources/YPDAFEXglucoseTests_2-25-10.csv" %><br>
+        <%= link_to "Single-Plate Layout Example File","/resources/YPDAFEXglucoseTests_2-25-10_Layout.csv" %><br>
+        <%= link_to "Multi-Plate Example File","/resources/test_YYYY_MM_DD_HH_MM_SS.csv" %><br>
+  	<%= link_to "Multi-Plate Layout Example File","/resources/MultiPlateLayout_plateID.csv" %>
+        
+  </div>
+
+ <h3><span data-tooltip="OD value for blank well read. As the default option <NULL>, GCAT will automatically take the first OD reading of each well to be the blank.">Media background</span></h3>
+
+	<%= f.radio_button(:blank_value, "default", {:checked => true, :class => "user_enter3 user_enter3_no"}) %>
+	<%= f.label(:blank_value_blank_value_default, "Take the first OD reading of each well to be the blank") %><br />
+
+	<%= f.radio_button(:blank_value, "user", {:class => "user_enter3 user_enter3_yes"}) %>
+	<%= f.label(:blank_value_user, "User Input.") %>
+
+  	<div class="field optional_input3" style="display:none">
+
+    	<%= f.text_field :blank_value_input, :placeholder => 'Enter your OD blank value here' %>
+  	</div>
+ 
+  <h3><span data-tooltip="GCAT transforms optical density (OD) to log(x+δ). x = OD – Media background. Specify a value for n or choose from the defaults. Note: 0 is not recommended unless all wells contain many repeated measurements for initial density that can be used to accurately estimate the baseline density. See the user manual for more details.">OD Transform</span></h3>
+  
+<%= f.radio_button(:transformation, 1, {:checked => true, :class => "user_enter2 user_enter2_no"}) %>
+<%= f.label(:transformation_one, "log(x + 0.1)") %><br />
+
+<%= f.radio_button(:transformation, 0, {:class => "user_enter2 user_enter2_no"}) %>
+<%= f.label(:transformation_zero, "log(x)") %><br />
+
+<%= f.radio_button(:transformation, -1, {:class => "user_enter2 user_enter2_yes"}) %>
+<%= f.label(:transformation_any, "log(x + δ)") %> 
+
+  <div class="field optional_input2" style="display:none">
+
+    <%= f.text_field :transformation_input, :placeholder => 'Enter your n value here'%>
+  </div>
+
+<h3><span data-tooltip="Choose the preferred growth curve model selection available below.">Growth curve model</span></h3>
+
+
+<%= f.radio_button(:model, 1, {:checked => true, :class => "user_enter1 user_enter1_no"})%>
+<%= f.label(:model_one, "Sigmoid curve") %>
+
+<%#= f.radio_button(:model, 0, {:class => "user_enter1 user_enter1_no"}) %>
+<%#= f.label(:model_zero, "Sigmoid + linear") %>
+
+<%= f.radio_button(:model, -1, {:class => "user_enter1 user_enter1_yes"}) %>
+<%= f.label(:model_any, "LOESS. The default smoothing value is 0.1.") %>
+  
+    <div class="field optional_input1" style="display:none">
+      <%= f.text_field :loess_input, :placeholder => 'Enter the smoothing value here.'%>
+    </div>
+
+<h3><span data-tooltip="Enter the index of the timepoint at which the wells were inoculated with the culture. 
+" >Inoculation timepoint</span></h3>
+
+  <div class="field">
+    <%= f.label :start_index, "Enter the timepoint index (positive integer only).  The default value is 2. "  %><br />
+    <%= f.text_field(:start_index, :type => 'number', :min =>'1', :size => '3', :value => '2') %>
+  </div>
+  
+  <h3><span data-tooltip="Enter a threshold to determine the presence of a growing culture. GCAT rejects curves where the density measurements never reach this value above the specified inoculation timepoint." >Growth Threshold</span></h3>
+
+  <div class="field">
+    <%= f.label :growth_threshold, "Enter the growth threshold. The default value is 0.05. "  %><br />
+    <%= f.text_field(:growth_threshold, :type => 'number', :min =>'0', :size => '3', :value => '0.05', :step => "0.01") %>
+  </div>
+  
+<h3><span data-tooltip="Enter indices (as a comma-separated list) of any erroneous reads that should be removed across the entire experiment. " >Points to ignore</span></h3>  
+  <div class="field">
+    <%= f.label :remove_points,"Enter a comma-separated list of points. Example: 2,3,4,5 (positive integers only). The default is an empty list." %><br />
+    <%= f.text_field :remove_points %>
+  </div>
+
+<!--<h3><span data-tooltip="GCAT automatically detects sudden changes in OD ('jumps'). Check this box if these instances should be removed when possible. If only one or two jumps are present GCAT will attempt to remove only the affected region." >Remove Jumps</span></h3>-->
+<%#= f.check_box(:remove_jumps) %>
+<%#= f.label(:remove_jumps, "Employ the jump detection algorithm to attempt to remove problematic points.") %>
+<%
+=begin %>
+<h3><span data-tooltip="Enter the number of rows (letters) and columns (numbers) of wells on each of the plates of this experiment." >Plate Dimensions</span></h3>
+  <div class="field">
+    <%= f.label 'number of rows' %>
+    <%= f.text_field(:plate_dimensions_row, :type => 'number', :min =>'1', :size => '3', :value => '8') %>
+  </div>
+  <div class="field">
+    <%= f.label 'number of columns' %>
+    <%= f.text_field(:plate_dimensions_column, :type => 'number', :min =>'1', :size => '3', :value => '12') %>
+  </div>
+<%
+=end  %>  
+  <div id="time" class="field">
+    <h3><span data-tooltip="Select a correctly formatted timestamp (see user manual for details). The timestamp will be used to convert the time entries into the number of hours." >Timestamp format</span></h3>
+    <%= f.label :timestamp_format %><br />
+    <%#= f.text_field(:timestamp_format, :value => '1/3600', :id => 'adam') %>
+    <%= f.select  :timestamp_format, options_for_select(date_time_options()) %>
+  </div>
+
+
+  <div class="actions" style="margin-top:30px;">
+    <%= f.submit %>
+  </div>
+  
+  <div class="actions" style="margin-top:30px;">
+  	<%= mail_to "gcat.help@glbrc.wisc.edu","Please Send Any Questions To The GLBRC Help Desk And Be Sure To Include 'GCAT' In Your Subject Title", :subject => "GCAT" %>
+  </div>
+  
+  
+  <div class="actions" style="margin-top:30px;">
+  	<%= link_to "GCAT Users Manual","/resources/GCAT_users_manual.pdf" %>
+  </div>
+  
+<% end %>
@@ -0,0 +1,6 @@
+<div id="form-container">
+	<h1>Error</h1>
+	<p>Please resubmit your file.</p>
+  <%= link_to 'New Assay', new_assay_path%>
+  <br><br><br>
+</div>
@@ -0,0 +1,11 @@
+<div id="form-container">
+	<h1>Growth Curve Analysis Tool</h1>
+
+	<div style="width:25%;">
+	  This tool processes microbial growth curve data collected in a microtiter plate format and 
+	  generates a table of biologically meaningful growth curve characteristics, as well as relevant 
+	  plots. These characteristics can be used to select strains with optimal growth properties.
+	</div>
+
+	<%= render 'form' %>
+</div>
@@ -0,0 +1,42 @@
+<div id="results-container">
+  <% if flash[:notice] %>
+    <div class="alert alert-success alert-dismissible" role="alert" style="width:668px;">
+      <%= flash[:notice] %>
+    </div>
+  <% end %>
+  <% if flash[:alert] %>
+    <div class="alert alert-danger alert-dismissible" role="alert">
+      <%= flash[:alert] %>
+    </div>
+  <% end %>
+  <h1>Analysis Results</h1>
+  <p>
+    Uploaded file: <%=h @result[:inputfile].to_s %>
+    <br>
+    <% if @result[:layout_file] %>
+      Layout file: <%=h @result[:layout_file].to_s %>
+    <% end %>
+  </p>
+  <%= link_to 'New Assay', new_assay_path%>
+  <p>
+    <% @result[:overviewFiles].each do | overview_file | %>
+      <%= link_to image_tag(relative_path(overview_file),
+                  :alt => "Your Submission",
+                  :style => "vertical-align:middle;"),
+                  relative_path(@result[:zipfile])%>
+    <% end %>
+  </p>
+  <br>
+  <h3><i>Analysis Results DataTable</i></h3>
+  <table class="table table-bordered table-striped table-condensed">
+    <% @table.each do |row| %>
+      <% i = 0 %>
+      <tr>
+        <% row.each do |cell| %>
+          <!-- don't round row # -->
+          <td><%= cell %></td>
+        <% end %>
+      </tr>
+    <% end %>
+  </table>
+</div>
@@ -0,0 +1,25 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <title>GCAT</title>
+    <%= favicon_link_tag "/favicon.ico" %>
+    <%= stylesheet_link_tag    "application" %>
+    <%= javascript_include_tag "application" %>
+    <%= csrf_meta_tags %>
+  </head>
+  <body>
+    <nav id="nav-bar" class="navbar navbar-default" role="navigation">
+      <h1>GCAT</h1>
+    </nav>
+    <div>
+      <div id='contents'>
+        <%= yield %>
+      </div>
+      <div id='footer' style='float:right; padding: 5px;'>
+        Copyright &copy; 2012 The Board of Regents of the University of Wisconsin System
+        <%= image_tag 'lgplv.jpg' %>
+        <%= image_tag 'GLBRC_horz_cmyk_small.jpg' %>
+      </div>
+    </div>
+  </body>
+</html>
@@ -0,0 +1,4 @@
+# This file is used by Rack-based servers to start the application.
+
+require ::File.expand_path('../config/environment',  __FILE__)
+run Gcat::Application
@@ -0,0 +1,76 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+require File.expand_path('../boot', __FILE__)
+
+#Not using a database for GCAT
+#require 'rails/all'
+
+require "action_controller/railtie"
+require "action_mailer/railtie"
+require "active_resource/railtie"
+require "rails/test_unit/railtie"
+require "sprockets/railtie"
+
+if defined?(Bundler)
+  # If you precompile assets before deploying to production, use this line
+  #Bundler.require *Rails.groups(:assets => %w(development test))
+  # If you want your assets lazily compiled in production, use this line
+   Bundler.require(:default, :assets, Rails.env)
+end
+
+module Gcat
+  class Application < Rails::Application
+    # Settings in config/environments/* take precedence over those specified here.
+    # Application configuration should go into files in config/initializers
+    # -- all .rb files in that directory are automatically loaded.
+
+    # Custom directories with classes and modules you want to be autoloadable.
+    # config.autoload_paths += %W(#{config.root}/extras)
+
+    # Only load the plugins named here, in the order given (default is alphabetical).
+    # :all can be used as a placeholder for all plugins not explicitly named.
+    # config.plugins = [ :exception_notification, :ssl_requirement, :all ]
+
+    # Activate observers that should always be running.
+    # config.active_record.observers = :cacher, :garbage_collector, :forum_observer
+
+    # Set Time.zone default to the specified zone and make Active Record auto-convert to this zone.
+    # Run "rake -D time" for a list of tasks for finding time zone names. Default is UTC.
+    # config.time_zone = 'Central Time (US & Canada)'
+
+    # The default locale is :en and all translations from config/locales/*.rb,yml are auto loaded.
+    # config.i18n.load_path += Dir[Rails.root.join('my', 'locales', '*.{rb,yml}').to_s]
+    # config.i18n.default_locale = :de
+    config.i18n.enforce_available_locales = false
+
+    # Configure the default encoding used in templates for Ruby 1.9.
+    config.encoding = "utf-8"
+
+    # Configure sensitive parameters which will be filtered from the log file.
+    config.filter_parameters += [:password]
+
+    # Enable the asset pipeline
+    config.assets.enabled = true
+
+    # Version of your assets, change this if you want to expire all your assets
+    config.assets.version = '1.0'
+  end
+end
@@ -0,0 +1,26 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+require 'rubygems'
+
+# Set up gems listed in the Gemfile.
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
+
+require 'bundler/setup' if File.exists?(ENV['BUNDLE_GEMFILE'])
@@ -0,0 +1,25 @@
+# SQLite version 3.x
+#   gem install sqlite3
+#
+#   Ensure the SQLite 3 gem is defined in your Gemfile
+#   gem 'sqlite3'
+development:
+  adapter: sqlite3
+  database: db/development.sqlite3
+  pool: 5
+  timeout: 5000
+
+# Warning: The database defined as "test" will be erased and
+# re-generated from your development database when you run "rake".
+# Do not set this db to the same as development or production.
+test:
+  adapter: sqlite3
+  database: db/test.sqlite3
+  pool: 5
+  timeout: 5000
+
+production:
+  adapter: sqlite3
+  database: db/production.sqlite3
+  pool: 5
+  timeout: 5000
@@ -0,0 +1,25 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Load the rails application
+require File.expand_path('../application', __FILE__)
+
+# Initialize the rails application
+Gcat::Application.initialize!
@@ -0,0 +1,50 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+Gcat::Application.configure do
+  # Settings specified here will take precedence over those in config/application.rb
+
+  # In the development environment your application's code is reloaded on
+  # every request.  This slows down response time but is perfect for development
+  # since you don't have to restart the web server when you make code changes.
+  config.cache_classes = false
+
+  # Log error messages when you accidentally call methods on nil.
+  config.whiny_nils = true
+
+  # Show full error reports and disable caching
+  config.consider_all_requests_local       = true
+  config.action_controller.perform_caching = false
+
+  # Don't care if the mailer can't send
+  config.action_mailer.raise_delivery_errors = false
+
+  # Print deprecation notices to the Rails logger
+  config.active_support.deprecation = :log
+
+  # Only use best-standards-support built into browsers
+  config.action_dispatch.best_standards_support = :builtin
+
+  # Do not compress assets
+  config.assets.compress = false
+
+  # Expands the lines which load the assets
+  config.assets.debug = true
+end
@@ -0,0 +1,80 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+Gcat::Application.configure do
+  # Settings specified here will take precedence over those in config/application.rb
+
+  # Code is not reloaded between requests
+  config.cache_classes = true
+
+  # Full error reports are disabled and caching is turned on
+  config.consider_all_requests_local       = false
+  config.action_controller.perform_caching = true
+
+  # Disable Rails's static asset server (Apache or nginx will already do this)
+  config.serve_static_assets = false
+
+  # Compress JavaScripts and CSS
+  config.assets.compress = true
+
+  # Don't fallback to assets pipeline if a precompiled asset is missed
+  config.assets.compile = true
+
+  # Generate digests for assets URLs
+  config.assets.digest = true
+
+  # Defaults to Rails.root.join("public/assets")
+  # config.assets.manifest = YOUR_PATH
+
+  # Specifies the header that your server uses for sending files
+  # config.action_dispatch.x_sendfile_header = "X-Sendfile" # for apache
+  # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for nginx
+
+  # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
+  # config.force_ssl = true
+
+  # See everything in the log (default is :info)
+  # config.log_level = :debug
+
+  # Use a different logger for distributed setups
+  # config.logger = SyslogLogger.new
+
+  # Use a different cache store in production
+  # config.cache_store = :mem_cache_store
+
+  # Enable serving of images, stylesheets, and JavaScripts from an asset server
+  # config.action_controller.asset_host = "http://assets.example.com"
+
+  # Precompile additional assets (application.js, application.css, and all non-JS/CSS are already added)
+  # config.assets.precompile += %w( search.js )
+
+  # Disable delivery errors, bad email addresses will be ignored
+  # config.action_mailer.raise_delivery_errors = false
+
+  # Enable threaded mode
+  # config.threadsafe!
+
+  # Enable locale fallbacks for I18n (makes lookups for any locale fall back to
+  # the I18n.default_locale when a translation can not be found)
+  config.i18n.fallbacks = true
+
+  # Send deprecation notices to registered listeners
+  config.active_support.deprecation = :notify
+end
@@ -0,0 +1,62 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+Gcat::Application.configure do
+  # Settings specified here will take precedence over those in config/application.rb
+
+  # The test environment is used exclusively to run your application's
+  # test suite.  You never need to work with it otherwise.  Remember that
+  # your test database is "scratch space" for the test suite and is wiped
+  # and recreated between test runs.  Don't rely on the data there!
+  config.cache_classes = true
+
+  # Configure static asset server for tests with Cache-Control for performance
+  config.serve_static_assets = true
+  config.static_cache_control = "public, max-age=3600"
+
+  # Log error messages when you accidentally call methods on nil
+  config.whiny_nils = true
+
+  # Show full error reports and disable caching
+  config.consider_all_requests_local       = true
+  config.action_controller.perform_caching = false
+
+  # Raise exceptions instead of rendering exception templates
+  config.action_dispatch.show_exceptions = false
+
+  # Disable request forgery protection in test environment
+  config.action_controller.allow_forgery_protection    = false
+
+  # Tell Action Mailer not to deliver emails to the real world.
+  # The :test delivery method accumulates sent emails in the
+  # ActionMailer::Base.deliveries array.
+  config.action_mailer.delivery_method = :test
+
+  # Use SQL instead of Active Record's schema dumper when creating the test database.
+  # This is necessary if your schema can't be completely dumped by the schema dumper,
+  # like if you have constraints or database-specific column types
+  # config.active_record.schema_format = :sql
+
+  # Print deprecation notices to the stderr
+  config.active_support.deprecation = :stderr
+
+  # Allow pass debug_assets=true as a query parameter to load pages with unpackaged assets
+  config.assets.allow_debugging = true
+end
@@ -0,0 +1,27 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Be sure to restart your server when you modify this file.
+
+# You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces.
+# Rails.backtrace_cleaner.add_silencer { |line| line =~ /my_noisy_library/ }
+
+# You can also remove all the silencers if you're trying to debug a problem that might stem from framework code.
+# Rails.backtrace_cleaner.remove_silencers!
@@ -0,0 +1,30 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Be sure to restart your server when you modify this file.
+
+# Add new inflection rules using the following format
+# (all these examples are active by default):
+# ActiveSupport::Inflector.inflections do |inflect|
+#   inflect.plural /^(ox)$/i, '\1en'
+#   inflect.singular /^(ox)en/i, '\1'
+#   inflect.irregular 'person', 'people'
+#   inflect.uncountable %w( fish sheep )
+# end
@@ -0,0 +1,25 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Be sure to restart your server when you modify this file.
+
+# Add new mime types for use in respond_to blocks:
+# Mime::Type.register "text/richtext", :rtf
+# Mime::Type.register_alias "text/html", :iphone
@@ -0,0 +1,27 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Be sure to restart your server when you modify this file.
+
+# Your secret key for verifying the integrity of signed cookies.
+# If you change this key, all old signed cookies will become invalid!
+# Make sure the secret is at least 30 characters and all random,
+# no regular words or you'll be exposed to dictionary attacks.
+Gcat::Application.config.secret_token = 'a1ba91ea23f998a7faf1a2c7128510c1e1dbd403d38ef2c7d280401a7e92645a18495e3f8eda0d5e9c67b1613372f0faef0775b4236758cc74650ef5c314d40b'
@@ -0,0 +1,28 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Be sure to restart your server when you modify this file.
+
+Gcat::Application.config.session_store :cookie_store, key: '_gcat_session'
+
+# Use the database for sessions instead of the cookie-based default,
+# which shouldn't be used to store highly confidential information
+# (create the session table with "rails generate session_migration")
+# Gcat::Application.config.session_store :active_record_store
@@ -0,0 +1,34 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Be sure to restart your server when you modify this file.
+#
+# This file contains settings for ActionController::ParamsWrapper which
+# is enabled by default.
+
+# Enable parameter wrapping for JSON. You can disable this by setting :format to an empty array.
+ActiveSupport.on_load(:action_controller) do
+  wrap_parameters format: [:json]
+end
+
+# Disable root element in JSON by default.
+ActiveSupport.on_load(:active_record) do
+  self.include_root_in_json = false
+end
@@ -0,0 +1,5 @@
+# Sample localization file for English. Add more files in this directory for other locales.
+# See https://github.com/svenfuchs/rails-i18n/tree/master/rails%2Flocale for starting points.
+
+en:
+  hello: "Hello world"
@@ -0,0 +1,82 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+Gcat::Application.routes.draw do
+  resources :assays
+  
+  root :to => 'assays#new'
+  
+  # The priority is based upon order of creation:
+  # first created -> highest priority.
+
+  # Sample of regular route:
+  #   match 'products/:id' => 'catalog#view'
+  # Keep in mind you can assign values other than :controller and :action
+
+  # Sample of named route:
+  #   match 'products/:id/purchase' => 'catalog#purchase', :as => :purchase
+  # This route can be invoked with purchase_url(:id => product.id)
+
+  # Sample resource route (maps HTTP verbs to controller actions automatically):
+  #   resources :products
+
+  # Sample resource route with options:
+  #   resources :products do
+  #     member do
+  #       get 'short'
+  #       post 'toggle'
+  #     end
+  #
+  #     collection do
+  #       get 'sold'
+  #     end
+  #   end
+
+  # Sample resource route with sub-resources:
+  #   resources :products do
+  #     resources :comments, :sales
+  #     resource :seller
+  #   end
+
+  # Sample resource route with more complex sub-resources
+  #   resources :products do
+  #     resources :comments
+  #     resources :sales do
+  #       get 'recent', :on => :collection
+  #     end
+  #   end
+
+  # Sample resource route within a namespace:
+  #   namespace :admin do
+  #     # Directs /admin/products/* to Admin::ProductsController
+  #     # (app/controllers/admin/products_controller.rb)
+  #     resources :products
+  #   end
+
+  # You can have the root of your site routed with "root"
+  # just remember to delete public/index.html.
+  # root :to => 'welcome#index'
+
+  # See how all your routes lay out with "rake routes"
+
+  # This is a legacy wild controller route that's not recommended for RESTful applications.
+  # Note: This route will make all actions in every controller accessible via GET requests.
+  # match ':controller(/:action(/:id(.:format)))'
+end
@@ -0,0 +1,36 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+# encoding: UTF-8
+# This file is auto-generated from the current state of the database. Instead
+# of editing this file, please use the migrations feature of Active Record to
+# incrementally modify your database, and then regenerate this schema definition.
+#
+# Note that this schema.rb definition is the authoritative source for your
+# database schema. If you need to create the application database on another
+# system, you should be using db:schema:load, not running all the migrations
+# from scratch. The latter is a flawed and unsustainable approach (the more migrations
+# you'll amass, the slower it'll run and the greater likelihood for issues).
+#
+# It's strongly recommended to check this file into your version control system.
+
+ActiveRecord::Schema.define(:version => 0) do
+
+end
@@ -0,0 +1,27 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+# This file should contain all the record creation needed to seed the database with its default values.
+# The data can then be loaded with the rake db:seed (or created alongside the db with db:setup).
+#
+# Examples:
+#
+#   cities = City.create([{ name: 'Chicago' }, { name: 'Copenhagen' }])
+#   Mayor.create(name: 'Emanuel', city: cities.first)
@@ -0,0 +1,2 @@
+Use this README file to introduce your application and point to useful places in the API for learning more.
+Run "rake doc:app" to generate API documentation for your models, controllers, helpers, and libraries.
@@ -0,0 +1,27 @@
+desc "Configure Subversion for Rails"
+task :configure_for_svn do
+  system "svn remove log/*"
+  system "svn commit -m 'removing all log files from subversion'"
+  system 'svn propset svn:ignore "*.log" log/'
+  system "svn update log/"
+  system "svn commit -m 'Ignoring all files in /log/ ending in .log'"
+  system 'svn propset svn:ignore "*.db" db/'
+  system "svn update db/"
+  system "svn commit -m 'Ignoring all files in /db/ ending in .db'"
+  system "svn move config/database.yml config/database.example"
+  system "svn commit -m 'Moving database.yml to database.example to provide a template for anyone who checks out the code'"
+  system 'svn propset svn:ignore "database.yml" config/'
+  system "svn update config/"
+  system "svn commit -m 'Ignoring database.yml'"
+  system "svn remove tmp/*"
+  system "svn commit -m 'Removing /tmp/ folder'"
+  system 'svn propset svn:ignore "*" tmp/'
+  system "svn update tmp/"
+  system "svn commit -m 'Ignoring all contents of tmp/'"
+end
+desc "Add new files to subversion"
+task :add_new_files do
+   system "svn status | grep '^\?' | sed -e 's/? *//' | sed -e 's/ /\ /g' | xargs svn add"
+end
+desc "shortcut for adding new files"
+task :add => [ :add_new_files ]
@@ -0,0 +1,46 @@
+<!--
+    Copyright 2012 The Board of Regents of the University of Wisconsin System.
+    Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+    Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+
+    This file is part of GCAT.
+
+    GCAT is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    GCAT is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public License
+    along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<!DOCTYPE html>
+<html>
+<head>
+  <title>The page you were looking for doesn't exist (404)</title>
+  <style type="text/css">
+    body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+    div.dialog {
+      width: 25em;
+      padding: 0 4em;
+      margin: 4em auto 0 auto;
+      border: 1px solid #ccc;
+      border-right-color: #999;
+      border-bottom-color: #999;
+    }
+    h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+  </style>
+</head>
+
+<body>
+  <!-- This file lives in public/404.html -->
+  <div class="dialog">
+    <h1>The page you were looking for doesn't exist.</h1>
+    <p>You may have mistyped the address or the page may have moved.</p>
+  </div>
+</body>
+</html>
@@ -0,0 +1,46 @@
+<!--
+    Copyright 2012 The Board of Regents of the University of Wisconsin System.
+    Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+    Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+
+    This file is part of GCAT.
+
+    GCAT is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    GCAT is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public License
+    along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<!DOCTYPE html>
+<html>
+<head>
+  <title>The change you wanted was rejected (422)</title>
+  <style type="text/css">
+    body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+    div.dialog {
+      width: 25em;
+      padding: 0 4em;
+      margin: 4em auto 0 auto;
+      border: 1px solid #ccc;
+      border-right-color: #999;
+      border-bottom-color: #999;
+    }
+    h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+  </style>
+</head>
+
+<body>
+  <!-- This file lives in public/422.html -->
+  <div class="dialog">
+    <h1>The change you wanted was rejected.</h1>
+    <p>Maybe you tried to change something you didn't have access to.</p>
+  </div>
+</body>
+</html>
@@ -0,0 +1,46 @@
+<!--
+    Copyright 2012 The Board of Regents of the University of Wisconsin System.
+    Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+    Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+
+    This file is part of GCAT.
+
+    GCAT is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    GCAT is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public License
+    along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<!DOCTYPE html>
+<html>
+<head>
+  <title>We're sorry, but something went wrong (500)</title>
+  <style type="text/css">
+    body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+    div.dialog {
+      width: 25em;
+      padding: 0 4em;
+      margin: 4em auto 0 auto;
+      border: 1px solid #ccc;
+      border-right-color: #999;
+      border-bottom-color: #999;
+    }
+    h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+  </style>
+</head>
+
+<body>
+  <!-- This file lives in public/500.html -->
+  <div class="dialog">
+    <h1>We're sorry, but something went wrong.</h1>
+    <p>We've been notified about this issue and we'll take a look at it shortly.</p>
+  </div>
+</body>
+</html>
@@ -0,0 +1,141 @@
+"row"	"plate"	"well"	"media"	"strain"	"model"	"lag.time, hrs"	"lag.time.SE, hrs"	"inflection.time, hrs"	"max.spec.growth.rate, log.OD/hr"	"max.spec.growth.rate.SE, log.OD/hr"	"baseline, log.OD"	"baseline.SE, log.OD"	"amplitude, log.OD"	"amplitude.SE, log.OD"	"plateau, log.OD"	"inoc.log.OD"	"max.log.OD"	"projected.growth, log.OD"	"achieved.growth, log.OD"	"baseline.OD"	"amplitude.OD"	"plateau.OD"	"inoc.OD"	"max.OD"	"projected.growth.OD"	"achieved.growth.OD"	"shape.par"	"shape.par.SE"	"R.squared"	"RSS"	"empty"	"asymp.not.reached"	"tank"	"other"	"pdf.file"	"page.no"	"Destination.plate.name"	"Well.ID"	"Plate.source"	"Well.Source"	"Media.Definition"
+1	"YPDAFEXglucoseTests_2-25-10"	"A01"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	2	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+2	"YPDAFEXglucoseTests_2-25-10"	"B01"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	3	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+3	"YPDAFEXglucoseTests_2-25-10"	"C01"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	4	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+4	"YPDAFEXglucoseTests_2-25-10"	"D01"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	5	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+5	"YPDAFEXglucoseTests_2-25-10"	"E01"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	6	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+6	"YPDAFEXglucoseTests_2-25-10"	"F01"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	7	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+7	"YPDAFEXglucoseTests_2-25-10"	"G01"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	8	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+8	"YPDAFEXglucoseTests_2-25-10"	"H01"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	9	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+9	"YPDAFEXglucoseTests_2-25-10"	"A02"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	10	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+10	"YPDAFEXglucoseTests_2-25-10"	"B02"	"YP"	"Lab strain"	"gompertz sigmoid"	0	1.75346931682115	9.008895	0.00387129154161333	0.000169526575673485	0.106012627582768	0.00533332981254499	0.0949774510885174	0.0112054786798504	0.200990078671286	0.112280003029694	0.184252861643961	0.0887100756415918	0.0719728586142672	0.111835916217944	0.0996340592954781	0.222612641821245	0.118826091485523	0.202319805224487	0.103786550335722	0.0834937137389644	NA	NA	0.955970181896242	0.00271004795972447	"I "	"U"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	11	"Control strain plate"	"Sample"	"USDA"	""	"YP"
+11	"YPDAFEXglucoseTests_2-25-10"	"C02"	"YP+0.25% glucose"	"Lab strain"	"richards sigmoid"	2.40987768343735	0.0533048366613944	4.21845083333333	0.0460029603516824	0.000724536080633502	0.0730406465985917	0.00147448206809288	0.20195449827016	0.00148223339842928	0.274995144868751	0.073266311037202	0.274994924460913	0.201728833831549	0.201728613423711	0.0757742625906743	0.22379232217684	0.316524282953919	0.0760170539793741	0.31652399278168	0.240507228974545	0.240506938802306	0.265875936579388	0.100708043886741	0.997917404710374	0.00135388203716233	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	12	"Control strain plate"	"Sample"	"USDA"	""	"YP+0.25% glucose"
+12	"YPDAFEXglucoseTests_2-25-10"	"D02"	"YP+0.5% glucose"	"Lab strain"	"logistic sigmoid."	3.07823403673893	0.0432348209213164	5.3624375	0.0732442091237218	0.00083385044900585	0.0859165104025432	0.00136428289761777	0.336085729465356	0.00149532007847134	0.4220022398679	0.0889960026247708	0.422002205393214	0.333006237243129	0.333006202768443	0.0897153446116215	0.399458994539777	0.525011940504746	0.0930762868815243	0.52501188793044	0.431935653623222	0.431935601048915	NA	NA	0.99892015420286	0.00211931922664724	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	13	"Control strain plate"	"Sample"	"USDA"	""	"YP+0.5% glucose"
+13	"YPDAFEXglucoseTests_2-25-10"	"E02"	"YP+1% glucose"	"Lab strain"	"richards sigmoid"	3.31104934964427	0.0428738829656516	6.24426055555555	0.087498859778052	0.000646229427574331	0.0670789160536515	0.00264084512090784	0.496808437832399	0.00261152544308038	0.56388735388605	0.0759549213884333	0.563886450845895	0.487932432497617	0.487931529457461	0.0693798660836618	0.643467662335959	0.757491228661656	0.0789139371187617	0.75748964157722	0.678577291542894	0.678575704458458	1.22323321021831	0.0913419736269564	0.999523017751576	0.00210815425649153	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	14	"Control strain plate"	"Sample"	"USDA"	""	"YP+1% glucose"
+14	"YPDAFEXglucoseTests_2-25-10"	"F02"	"YP+2% glucose"	"Lab strain"	"richards sigmoid"	3.16160945641398	0.0130132752242264	5.69610027777778	0.0871403267354909	0.000229646786119097	0.08737718548213	0.000697693868328928	0.569725537718312	0.000706582348719082	0.657102723200442	0.0877050574005534	0.656913955188774	0.569397665799888	0.56920889778822	0.0913082277184576	0.767781795419447	0.92919481815215	0.0916660957048965	0.928830682251893	0.837528722447253	0.837164586546997	0.128377244056841	0.0158490082737876	0.999930578411107	0.000418173571721894	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	15	"Control strain plate"	"Sample"	"USDA"	""	"YP+2% glucose"
+15	"YPDAFEXglucoseTests_2-25-10"	"G02"	"YP+5% glucose"	"Lab strain"	"gompertz sigmoid"	1.97362812374979	0.160218470960237	6.10126222222222	0.0637129438472813	0.000882845743042059	0.0636642130548074	0.00677504517335327	0.715651375940815	0.00877835119047133	0.779315588995622	0.0726054464623438	0.769574985282588	0.706710142533278	0.696969538820244	0.0657344789473957	1.0455186500407	1.17997975267831	0.0753061873456158	1.15884851638065	1.10467356533269	1.08354232903504	NA	NA	0.996368548540555	0.0284187363816137	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	16	"Control strain plate"	"Sample"	"USDA"	""	"YP+5% glucose"
+16	"YPDAFEXglucoseTests_2-25-10"	"H02"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	17	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+17	"YPDAFEXglucoseTests_2-25-10"	"A03"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	18	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+18	"YPDAFEXglucoseTests_2-25-10"	"B03"	"YP"	"Wild strain"	"gompertz sigmoid"	0	6.85707287937896	22.1409086111111	0.00240032503165892	0.000622808682835668	0.183471250816661	0.0241038377523601	0.144528358183154	0.243574028025108	0.327999608999814	0.193008393297115	0.240674524494353	0.134991215702699	0.0476661311972385	0.201380426209075	0.155494462222733	0.388188429507373	0.212892973647493	0.27210692827532	0.175295455859879	0.0592139546278265	NA	NA	0.790451631963756	0.00713078905920281	"I "	"U"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	19	"Control strain plate"	"Sample"	"USDA"	""	"YP"
+19	"YPDAFEXglucoseTests_2-25-10"	"C03"	"YP+0.25% glucose"	"Wild strain"	"gompertz sigmoid"	1.9906115468579	0.0691975318131243	3.47962611111111	0.0490374116952237	0.00113344212179788	0.113611335614137	0.00175358527026848	0.199753898562767	0.00189317967250483	0.313365234176905	0.113618321003616	0.313364980275983	0.199746913173288	0.199746659272367	0.120316613087275	0.221102206170602	0.368021087850449	0.120324438962491	0.368020740508678	0.247696648887958	0.247696301546187	NA	NA	0.99399012987845	0.00350258662967115	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	20	"Control strain plate"	"Sample"	"USDA"	""	"YP+0.25% glucose"
+20	"YPDAFEXglucoseTests_2-25-10"	"D03"	"YP+0.5% glucose"	"Wild strain"	"logistic sigmoid."	2.74248926201157	0.0354379553926203	4.43294833333333	0.0945867701955495	0.00125702159577835	0.120482088801679	0.00134117834599991	0.32177887516419	0.00144348747790325	0.442260963965869	0.122204770404787	0.442260963925467	0.320056193561082	0.32005619352068	0.12804053622706	0.379579682895796	0.556221805261732	0.129985465672481	0.556221805198858	0.426236339589251	0.426236339526377	NA	NA	0.998757902847438	0.00205103195615211	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	21	"Control strain plate"	"Sample"	"USDA"	""	"YP+0.5% glucose"
+21	"YPDAFEXglucoseTests_2-25-10"	"E03"	"YP+1% glucose"	"Wild strain"	"richards sigmoid"	3.06558696223571	0.0312092193543957	5.3624375	0.121127558311403	0.000999219504341884	0.0914412547332416	0.00245736106561066	0.492484364444972	0.00245078801862176	0.583925619178214	0.10090202921227	0.583925619102095	0.483023589965944	0.483023589889825	0.0957524045344744	0.636376529891633	0.793063517352536	0.106168264278383	0.79306351721605	0.686895253074153	0.686895252937667	1.80996092627302	0.117497603933281	0.999544726321195	0.00181967924857191	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	22	"Control strain plate"	"Sample"	"USDA"	""	"YP+1% glucose"
+22	"YPDAFEXglucoseTests_2-25-10"	"F03"	"YP+2% glucose"	"Wild strain"	"richards sigmoid"	2.77641833187198	0.0527034516734386	5.62460111111111	0.129882570160111	0.00113584996869085	0.0943645434950579	0.00505890911787811	0.678399507081888	0.00501032007418759	0.772764050576946	0.11484805727615	0.77276399934955	0.657915993300795	0.657915942073399	0.0989602917302299	0.97072108167106	1.16574421483214	0.12170299001548	1.16574410388671	1.04404122481666	1.04404111387123	1.58781592816572	0.131684393376964	0.999371589849352	0.00464022682166854	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	23	"Control strain plate"	"Sample"	"USDA"	""	"YP+2% glucose"
+23	"YPDAFEXglucoseTests_2-25-10"	"G03"	"YP+5% glucose"	"Wild strain"	"richards sigmoid"	2.62155170729439	0.0528519100950448	5.64843416666667	0.120898389355078	0.000856667358787892	0.106939412411106	0.00473823154418831	0.792250602933212	0.00464150376049532	0.899190015344318	0.119165060839678	0.899150109300876	0.78002495450464	0.779985048461198	0.112866826518918	1.20836098124136	1.45761167700228	0.126555853197717	1.45751360540077	1.33105582380456	1.33095775220305	0.651987010079984	0.0715475157170284	0.999508942394936	0.00516491712891745	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	24	"Control strain plate"	"Sample"	"USDA"	""	"YP+5% glucose"
+24	"YPDAFEXglucoseTests_2-25-10"	"H03"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	25	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+25	"YPDAFEXglucoseTests_2-25-10"	"A04"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	26	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+26	"YPDAFEXglucoseTests_2-25-10"	"B04"	"YP"	"Industrial strain"	"gompertz sigmoid"	0	5.0780526120225	14.0138366666667	0.00262196611873332	0.00018437938744914	0.128373333313586	0.0113746241547247	0.0999846427550281	0.0508218894501574	0.228357976068614	0.134971123503685	0.189191289569101	0.0933868525649285	0.0542201660654161	0.136977395010588	0.105153945825447	0.256535054410289	0.144503734616262	0.208272060219704	0.112031319794027	0.0637683256034425	NA	NA	0.855383080839261	0.00575026814686199	"I "	"U"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	27	"Control strain plate"	"Sample"	"Internal source"	""	"YP"
+27	"YPDAFEXglucoseTests_2-25-10"	"C04"	"YP+0.25% glucose"	"Industrial strain"	"gompertz sigmoid"	0.891438154862617	0.0875315924591966	2.31180638888889	0.0535113235044828	0.00124573544664028	0.0881434958395649	0.00304307272545713	0.207061853609148	0.00316468246722843	0.295205349448713	0.0894254262692569	0.295205293059733	0.205779923179456	0.205779866790477	0.0921448290236948	0.230058652994932	0.343402197264266	0.0935457804829503	0.343402121511189	0.249856416781316	0.249856341028238	NA	NA	0.991724253334924	0.00363563892033091	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	28	"Control strain plate"	"Sample"	"Internal source"	""	"YP+0.25% glucose"
+28	"YPDAFEXglucoseTests_2-25-10"	"D04"	"YP+0.5% glucose"	"Industrial strain"	"logistic sigmoid."	1.64713494830746	0.0412877829637357	3.38429388888889	0.0931935829835479	0.00118142556806869	0.0808528949077067	0.00187894210009506	0.326765480130978	0.00196420648303134	0.407618375038685	0.0874704775763749	0.407618375014084	0.32014789746231	0.320147897437709	0.0842113918182088	0.386476282813275	0.503233380311918	0.0914100428976898	0.503233380274936	0.411823337414228	0.411823337377247	NA	NA	0.998561073647885	0.00184537988196709	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	29	"Control strain plate"	"Sample"	"Internal source"	""	"YP+0.5% glucose"
+29	"YPDAFEXglucoseTests_2-25-10"	"E04"	"YP+1% glucose"	"Industrial strain"	"richards sigmoid"	2.00035124383545	0.0281455446975304	4.31378305555555	0.124952394681256	0.000705710849322313	0.066176309959304	0.00266242484922488	0.497003217300128	0.00264805311701161	0.563179527259432	0.0884800685969233	0.563179527257016	0.474699458662509	0.474699458660092	0.0684150727790216	0.643787807270277	0.756247669737942	0.0925124770869246	0.756247669733698	0.663735192651017	0.663735192646773	2.09745464546466	0.104168274133155	0.999771040591133	0.00072098110255013	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	30	"Control strain plate"	"Sample"	"Internal source"	""	"YP+1% glucose"
+30	"YPDAFEXglucoseTests_2-25-10"	"F04"	"YP+2% glucose"	"Industrial strain"	"richards sigmoid"	2.0490071997567	0.0662248504953823	4.76661111111111	0.13306744704186	0.00129515567791922	0.0751622402050358	0.00684502394093866	0.656973009903259	0.00678618652478681	0.732135250108295	0.103854790297524	0.732135243114114	0.628280459810771	0.62828045281659	0.0780590412170139	0.92894459216055	1.07951615758535	0.10943934186153	1.07951614304083	0.970076815723817	0.970076801179305	1.62672197615846	0.161151121349594	0.999229593966034	0.00459582695233057	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	31	"Control strain plate"	"Sample"	"Internal source"	""	"YP+2% glucose"
+31	"YPDAFEXglucoseTests_2-25-10"	"G04"	"YP+5% glucose"	"Industrial strain"	"logistic sigmoid."	1.98629177172554	0.0661342221284037	5.19560611111111	0.122957280170312	0.00117607964263019	0.0764858915144976	0.00452433442917892	0.793858352641992	0.00487921879564307	0.870344244156489	0.106676773149917	0.870336478987225	0.763667471006573	0.763659705837308	0.0794869603035999	1.21191432864705	1.38773267508318	0.112574582376872	1.38771413400679	1.27515809270631	1.27513955162992	NA	NA	0.998885750680602	0.0103824045406066	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	32	"Control strain plate"	"Sample"	"Internal source"	""	"YP+5% glucose"
+32	"YPDAFEXglucoseTests_2-25-10"	"H04"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	33	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+33	"YPDAFEXglucoseTests_2-25-10"	"A05"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	34	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+34	"YPDAFEXglucoseTests_2-25-10"	"B05"	"YP"	"Engineered strain"	"gompertz sigmoid"	0	3.37960900118466	11.4875327777778	0.00260114799703032	0.000171113335294184	0.0996380871643661	0.00702344449132755	0.0812678741827026	0.0218737314876996	0.180905961347069	0.105000794559007	0.157379078978817	0.075905166788062	0.0523782844198106	0.104771014904237	0.084661410443271	0.198302487242874	0.110711492881175	0.17043921871877	0.0875909943616988	0.0597277258375952	NA	NA	0.906033844889994	0.00328284811832938	"I "	"U"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	35	"Control strain plate"	"Sample"	"ATCC"	""	"YP"
+35	"YPDAFEXglucoseTests_2-25-10"	"C05"	"YP+0.25% glucose"	"Engineered strain"	"gompertz sigmoid"	0.983948183597175	0.112859786286644	2.47863777777778	0.0501739409645355	0.00144200881080694	0.0661469359457048	0.00364271202623762	0.205919623922245	0.00380546132645363	0.27206655986795	0.0672650583629558	0.272066410063879	0.204801501504994	0.204801351700923	0.0683836896010714	0.228654445601205	0.312674369836174	0.0695789414490573	0.312674173192226	0.243095428387117	0.243095231743168	NA	NA	0.987488271024703	0.00577672548033825	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	36	"Control strain plate"	"Sample"	"ATCC"	""	"YP+0.25% glucose"
+36	"YPDAFEXglucoseTests_2-25-10"	"D05"	"YP+0.5% glucose"	"Engineered strain"	"richards sigmoid"	1.86398050594022	0.0558531581780885	3.55112527777778	0.0944346403793218	0.00150539518734246	0.0602064687184575	0.00349724664000438	0.368213525552587	0.00348116438514935	0.428419994271045	0.0619674090584591	0.428419978577839	0.366452585212586	0.36645256951938	0.0620558052105851	0.445150582608455	0.534830565662769	0.0639276697585029	0.534830541576357	0.470902895904266	0.470902871817855	0.41241007480043	0.120556305314198	0.997911612798025	0.00385752298874987	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	37	"Control strain plate"	"Sample"	"ATCC"	""	"YP+0.5% glucose"
+37	"YPDAFEXglucoseTests_2-25-10"	"E05"	"YP+1% glucose"	"Engineered strain"	"logistic sigmoid."	1.99006793380884	0.0351079474960275	4.12311861111111	0.121142575431043	0.00106707303416645	0.0644342397186312	0.00208740714872881	0.517632133522502	0.00221049055518603	0.582066373241133	0.0750837822538967	0.582066368203544	0.506982590987236	0.506982585949648	0.0665554389527234	0.678049544482632	0.789732868500092	0.0779744622314236	0.789732859484154	0.711758406268668	0.71175839725273	NA	NA	0.999269039916925	0.00268951955610802	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	38	"Control strain plate"	"Sample"	"ATCC"	""	"YP+1% glucose"
+38	"YPDAFEXglucoseTests_2-25-10"	"F05"	"YP+2% glucose"	"Engineered strain"	"logistic sigmoid."	1.98431414913883	0.0344438902457988	4.48061444444444	0.130673511563394	0.000910297701821604	0.0736708018228489	0.00232986507621017	0.655420765541249	0.00247952515524191	0.729091567364097	0.0914028197402174	0.729091436186734	0.63768874762388	0.637688616446517	0.0764523809998565	0.925952721450692	1.07319639269875	0.0957102901077889	1.07319612074233	0.977486102590961	0.977485830634544	NA	NA	0.999493885845309	0.00307265449990923	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	39	"Control strain plate"	"Sample"	"ATCC"	""	"YP+2% glucose"
+39	"YPDAFEXglucoseTests_2-25-10"	"G05"	"YP+5% glucose"	"Engineered strain"	"logistic sigmoid."	2.10388607358557	0.0485609580954195	5.24327222222222	0.128060724388346	0.000947720103104396	0.0637480626845324	0.00338335491744478	0.806179689301617	0.00365527295985513	0.869927751986149	0.0914242899462062	0.869921741898693	0.778503462039943	0.778497451952487	0.0658238441354071	1.23933666273098	1.38673841018529	0.0957338154859682	1.38672406572182	1.29100459469932	1.29099025023585	NA	NA	0.999357534856407	0.00631075803154068	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	40	"Control strain plate"	"Sample"	"ATCC"	""	"YP+5% glucose"
+40	"YPDAFEXglucoseTests_2-25-10"	"H05"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	41	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+41	"YPDAFEXglucoseTests_2-25-10"	"A06"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	42	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+42	"YPDAFEXglucoseTests_2-25-10"	"B06"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	43	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+43	"YPDAFEXglucoseTests_2-25-10"	"C06"	"Empty"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	44	"Control strain plate"	"Empty"	"Empty"	"Empty"	"Empty"
+44	"YPDAFEXglucoseTests_2-25-10"	"D06"	"Empty"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	45	"Control strain plate"	"Empty"	"Empty"	"Empty"	"Empty"
+45	"YPDAFEXglucoseTests_2-25-10"	"E06"	"Empty"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	46	"Control strain plate"	"Empty"	"Empty"	"Empty"	"Empty"
+46	"YPDAFEXglucoseTests_2-25-10"	"F06"	"Empty"	"Empty"	"logistic sigmoid."	9.73707675795057	0.0985970533305578	14.6811622222222	0.0827678159518767	0.00119202041574655	-0.000880352187845948	0.00297599235664884	0.821196181140969	0.00723578634320824	0.820315828953123	0.00130662738981984	0.80016942429868	0.819009201563303	0.79886279690886	-0.000879964791548726	1.27321739163809	1.27121704036991	0.00130748139930459	1.22591802114689	1.2699095589706	1.22461053974758	NA	NA	0.997343483064722	0.0337108649740508	"E*"	"L"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	47	"Control strain plate"	"Empty"	"Empty"	"Empty"	"Empty"
+47	"YPDAFEXglucoseTests_2-25-10"	"G06"	"Empty"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	48	"Control strain plate"	"Empty"	"Empty"	"Empty"	"Empty"
+48	"YPDAFEXglucoseTests_2-25-10"	"H06"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	49	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+49	"YPDAFEXglucoseTests_2-25-10"	"A07"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	50	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+50	"YPDAFEXglucoseTests_2-25-10"	"B07"	"AFEX"	"Lab strain"	"richards sigmoid"	3.77043529293613	0.0360628422979525	7.69807694444444	0.0922143076373947	0.000396448194603239	0.0415079420521979	0.00249398077489825	0.670137254883342	0.00244318042181785	0.71164519693554	0.0610249599211764	0.711620409573069	0.650620237014363	0.650595449651893	0.0423814404664091	0.954505567660092	1.03734032901714	0.0629254443914062	1.03728982934981	0.974414884625737	0.974364384958405	1.49636190326278	0.0645036016880811	0.999821079386736	0.00149128792010239	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	51	"Control strain plate"	"Sample"	"USDA"	""	"AFEX"
+51	"YPDAFEXglucoseTests_2-25-10"	"C07"	"AFEX+0.25% glucose"	"Lab strain"	"richards sigmoid"	3.81401380371595	0.0414172658123116	7.84107527777778	0.0912912497086539	0.000430847222656137	0.0416798125769253	0.00284816947390064	0.69143284133484	0.00278081561682767	0.733112653911766	0.0607785098125833	0.73305639362929	0.672334144099182	0.672277883816707	0.0425606105081318	0.996574258830031	1.08154967821066	0.0626635185773581	1.08143257293199	1.0188861596333	1.01876905435464	1.38211643616927	0.068441420394402	0.999776277423773	0.00199878407126496	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	52	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+0.25% glucose"
+52	"YPDAFEXglucoseTests_2-25-10"	"D07"	"AFEX+0.5% glucose"	"Lab strain"	"richards sigmoid"	4.10969518183839	0.0412228717219101	8.43690166666667	0.0887040084623295	0.000394405492929288	0.0340862871852733	0.00276975733383969	0.70953425876434	0.00269646137747281	0.743620545949613	0.0553702983243347	0.743521928280257	0.688250247625278	0.688151629955922	0.034673881973359	1.03304416561189	1.10353769905694	0.0569319223405151	1.10333026330024	1.04660577671642	1.04639834095972	1.51337755174144	0.0684110305817092	0.999797902728699	0.00192728932795894	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	53	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+0.5% glucose"
+53	"YPDAFEXglucoseTests_2-25-10"	"E07"	"AFEX+1% glucose"	"Lab strain"	"richards sigmoid"	4.24887937601734	0.0432115785663927	8.81823055555555	0.0859527181410838	0.000375029672246797	0.0356447291331235	0.00283858611378653	0.730548134285546	0.00274599564832944	0.766192863418669	0.0570847529310588	0.765947841016383	0.70910811048761	0.708863088085324	0.0362876182839384	1.07621834228765	1.15155936096669	0.0587455383807147	1.15103224530362	1.09281382258598	1.0922867069229	1.43679372443259	0.0664148620205159	0.999795584571703	0.00207184898977108	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	54	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+1% glucose"
+54	"YPDAFEXglucoseTests_2-25-10"	"F07"	"AFEX+2% glucose"	"Lab strain"	"richards sigmoid"	4.18007396642371	0.0466407733724283	8.81823055555555	0.0839684559025767	0.000369760007946289	0.0335662062693272	0.00302321134929714	0.761208314991861	0.00289043066835203	0.794774521261188	0.0523578984758354	0.794000059559319	0.742416622785352	0.741642161083483	0.0341359077403089	1.14086149330819	1.21394174372853	0.0537528115582857	1.21222779441756	1.16018893217025	1.15847498285928	1.13197498623035	0.0608907037432053	0.999775581271097	0.00245341232352351	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	55	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+2% glucose"
+55	"YPDAFEXglucoseTests_2-25-10"	"G07"	"AFEX+5% glucose"	"Lab strain"	"richards sigmoid"	4.31631141456833	0.0375067738225389	9.10422722222222	0.0746869165814573	0.000251011212616688	0.0449034082917984	0.00217539454600581	0.811374096629365	0.0020199781451565	0.856277504921164	0.0531730581528585	0.847610694845515	0.803104446768305	0.794437636692656	0.0459268271704429	1.25099895262068	1.35438019247854	0.0546121385565925	1.33406339459093	1.29976805392195	1.27945125603434	0.475355275365838	0.0354989182491613	0.99984356158066	0.00187490302158927	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	56	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+5% glucose"
+56	"YPDAFEXglucoseTests_2-25-10"	"H07"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	57	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+57	"YPDAFEXglucoseTests_2-25-10"	"A08"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	58	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+58	"YPDAFEXglucoseTests_2-25-10"	"B08"	"AFEX"	"Wild strain"	"richards sigmoid"	2.71231721101246	0.051377222191618	6.24426055555555	0.114869798087755	0.000679522317637316	0.0686814145642472	0.00460568272264885	0.729956501290573	0.00454362062059059	0.798637915854821	0.10099640348141	0.798636815214796	0.697641512373411	0.697640411733386	0.0710949195446084	1.07499034630887	1.22251161803554	0.10627266302607	1.22250917185165	1.11623895500947	1.11623650882558	1.70292251675116	0.10179548101048	0.999686879664103	0.00266681050440312	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	59	"Control strain plate"	"Sample"	"USDA"	""	"AFEX"
+59	"YPDAFEXglucoseTests_2-25-10"	"C08"	"AFEX+0.25% glucose"	"Wild strain"	"richards sigmoid"	3.01070188606209	0.0455540510180634	6.55409027777778	0.115107998074341	0.000641488536342826	0.0614813761638786	0.00401667627257402	0.743382938801471	0.00395687893333818	0.804864314965349	0.0885306662587629	0.804861736607772	0.716333648706586	0.716331070349009	0.0634106915579287	1.10303794283843	1.23639303316638	0.0925677570623027	1.23638726695289	1.14382527610408	1.14381950989059	1.57881072796814	0.0887320125722592	0.999717695034928	0.00263054987530885	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	60	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+0.25% glucose"
+60	"YPDAFEXglucoseTests_2-25-10"	"D08"	"AFEX+0.5% glucose"	"Wild strain"	"richards sigmoid"	2.97864249972838	0.0440943285573364	6.55409027777778	0.114576828102917	0.000592514268492699	0.0574375614416587	0.0038875686917152	0.760494448227834	0.00382450823238821	0.817932009669493	0.0846335570605372	0.817926981908608	0.733298452608956	0.733293424848071	0.059119138718029	1.13933374880962	1.26580931746965	0.0883181871040035	1.26579792555084	1.17749113036565	1.17747973844683	1.48473851369249	0.0802727796034772	0.999751240782926	0.00242858216652038	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	61	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+0.5% glucose"
+61	"YPDAFEXglucoseTests_2-25-10"	"E08"	"AFEX+1% glucose"	"Wild strain"	"richards sigmoid"	2.92985461453388	0.0457749726886301	6.57792333333333	0.113561152688866	0.000574978160263558	0.060472124586291	0.00402516587449496	0.782067831893148	0.00395231319695858	0.842539956479439	0.0880742344239483	0.842528715447582	0.754465722055491	0.754454481023634	0.0623379840467781	1.18598785054918	1.32225792630317	0.0920691881463056	1.32223182187456	1.23018873815686	1.23016263372825	1.37581261909432	0.0764095517760612	0.999754748600533	0.00252958095458289	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	62	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+1% glucose"
+62	"YPDAFEXglucoseTests_2-25-10"	"F08"	"AFEX+2% glucose"	"Wild strain"	"richards sigmoid"	3.04342230131477	0.0449382687527419	6.81625388888889	0.111344220886614	0.00053211483862603	0.0556626629934722	0.00387136841849492	0.807214512297039	0.00378851478092936	0.862877175290511	0.0817091172313295	0.862843943373837	0.781168058059181	0.781134826142507	0.0572409770684312	1.24165517922426	1.36996971193357	0.0851401153555837	1.36989095460621	1.28482959657798	1.28475083925063	1.25155544499941	0.0687282596513218	0.999773222693453	0.00254586287935126	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	63	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+2% glucose"
+63	"YPDAFEXglucoseTests_2-25-10"	"G08"	"AFEX+5% glucose"	"Wild strain"	"richards sigmoid"	3.40984196234943	0.0273360225985238	7.17374972222222	0.104909950247054	0.000320509638786788	0.0670946887710371	0.00214797629965173	0.835221165477497	0.00207744941670489	0.902315854248534	0.0807525020643599	0.901946971348112	0.821563352184174	0.821194469283752	0.0693967332430874	1.30532384995973	1.46530579421431	0.0841025502173454	1.46439655277464	1.38120324399697	1.38029400255729	0.753286731439822	0.0336141517371988	0.999897955876558	0.00130605700907156	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	64	"Control strain plate"	"Sample"	"USDA"	""	"AFEX+5% glucose"
+64	"YPDAFEXglucoseTests_2-25-10"	"H08"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	65	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+65	"YPDAFEXglucoseTests_2-25-10"	"A09"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	66	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+66	"YPDAFEXglucoseTests_2-25-10"	"B09"	"AFEX"	"Industrial strain"	"richards sigmoid"	2.43102440775711	0.0454605985590097	5.50543583333333	0.126842367574397	0.000788090696060512	0.0539690230506907	0.00446798137137374	0.690558562368951	0.00442509749533481	0.744527585419641	0.0857310638249255	0.74452755483612	0.658796521594716	0.658796491011195	0.0554519069684636	0.994829458783827	1.10544655635026	0.0895132793671187	1.10544649195829	1.01593327698314	1.01593321259117	1.86325174039779	0.111013983680208	0.999682108231503	0.00226178478453787	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	67	"Control strain plate"	"Sample"	"Internal source"	""	"AFEX"
+67	"YPDAFEXglucoseTests_2-25-10"	"C09"	"AFEX+0.25% glucose"	"Industrial strain"	"richards sigmoid"	2.48092971341753	0.0462358408909463	5.62460111111111	0.126022327995321	0.000766265198216623	0.0498912361992905	0.00451231731412719	0.714630509305857	0.00446315308100269	0.764521745505147	0.0803254380277494	0.764521612664574	0.684196307477398	0.684196174636825	0.0511567623538203	1.04343151382482	1.14796685416386	0.0836396678533904	1.14796656882673	1.06432718631047	1.06432690097334	1.6892416239556	0.102428344960951	0.999685472160361	0.00245503448373934	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	68	"Control strain plate"	"Sample"	"Internal source"	""	"AFEX+0.25% glucose"
+68	"YPDAFEXglucoseTests_2-25-10"	"D09"	"AFEX+0.5% glucose"	"Industrial strain"	"richards sigmoid"	2.42408640744135	0.0532786618803828	5.62460111111111	0.124384376977411	0.000823105161949976	0.0492950122622815	0.00516311815303983	0.727641420856731	0.00510226521814267	0.776936433119012	0.0803276492472531	0.776936116027565	0.696608783871759	0.696608466780311	0.0505302243276007	1.07019213302561	1.17479940590863	0.0836420640212081	1.17479871629844	1.09115734188742	1.09115665227723	1.58714593821028	0.108898701673299	0.999619231516236	0.00307919508939737	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	69	"Control strain plate"	"Sample"	"Internal source"	""	"AFEX+0.5% glucose"
+69	"YPDAFEXglucoseTests_2-25-10"	"E09"	"AFEX+1% glucose"	"Industrial strain"	"richards sigmoid"	2.3516083906569	0.0596596631244507	5.69610027777778	0.122918277329311	0.000825310524938601	0.0456238028839663	0.00577234400145717	0.757677923259936	0.00569718881396185	0.803301726143903	0.0794802281473059	0.803300765454603	0.723821497996597	0.723820537307297	0.0466805786671931	1.1333167393977	1.23290119927319	0.0827241518553661	1.23289905414994	1.15017704741783	1.15017490229457	1.50943196721409	0.109906089971898	0.999597425228284	0.00351671862436235	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	70	"Control strain plate"	"Sample"	"Internal source"	""	"AFEX+1% glucose"
+70	"YPDAFEXglucoseTests_2-25-10"	"F09"	"AFEX+2% glucose"	"Industrial strain"	"richards sigmoid"	2.5236010165651	0.0587446480551128	5.93443083333333	0.120073445181908	0.000783304897530514	0.0450247442396835	0.00549978744950499	0.786911440589629	0.00540921373997301	0.831936184829312	0.0732958505454819	0.831929765474958	0.75864033428383	0.758633914929476	0.0460537433930304	1.19660160399639	1.29776333060356	0.0760488394635108	1.29774858049386	1.22171449114005	1.22169974103035	1.2397630247936	0.0944772278955165	0.999601760903923	0.00394547420222901	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	71	"Control strain plate"	"Sample"	"Internal source"	""	"AFEX+2% glucose"
+71	"YPDAFEXglucoseTests_2-25-10"	"G09"	"AFEX+5% glucose"	"Industrial strain"	"richards sigmoid"	2.58690524730753	0.0503605394422555	6.17276138888889	0.109989495010269	0.000552298616707589	0.0475039668950725	0.00430649396880978	0.83068144919568	0.00419058755640174	0.878185416090752	0.0684271066193943	0.878046704871374	0.809758309471358	0.80961959825198	0.0486503609989841	1.2948820530738	1.40652889340594	0.0708225662291506	1.40619510399936	1.33570632717678	1.33537253777021	0.776030021315298	0.0590320987662605	0.999743045862095	0.00295407387389294	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	72	"Control strain plate"	"Sample"	"Internal source"	""	"AFEX+5% glucose"
+72	"YPDAFEXglucoseTests_2-25-10"	"H09"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	73	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+73	"YPDAFEXglucoseTests_2-25-10"	"A10"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	74	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+74	"YPDAFEXglucoseTests_2-25-10"	"B10"	"AFEX"	"Engineered strain"	"richards sigmoid"	2.17498330451382	0.0502798395951241	5.12410694444444	0.122218804779539	0.000784428545413071	0.0435682252869189	0.00476512105024793	0.699692212079932	0.00470444935542924	0.743260437366851	0.0678435113592805	0.743259718765618	0.67541692600757	0.675416207406337	0.0445312553256874	1.01313299408815	1.10278033345246	0.0701978215718182	1.10277882239246	1.03258251188064	1.03258100082064	1.18141837167591	0.0894530619922231	0.999633683586648	0.00265620405353138	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	75	"Control strain plate"	"Sample"	"ATCC"	""	"AFEX"
+75	"YPDAFEXglucoseTests_2-25-10"	"C10"	"AFEX+0.25% glucose"	"Engineered strain"	"richards sigmoid"	2.51277041358427	0.0385075634064252	5.50543583333333	0.124302687102611	0.000662579603795554	0.0363365047244458	0.00363658784524449	0.715682301787501	0.00358889800467861	0.752018806511947	0.0575296223014987	0.75201790943738	0.694489184210448	0.694488287135881	0.0370047447805615	1.04558191041505	1.12127814693769	0.0592166466248745	1.12127624399387	1.06206150031282	1.062059597369	1.22124196187785	0.0728117473772727	0.999746251949321	0.00205128571327075	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	76	"Control strain plate"	"Sample"	"ATCC"	""	"AFEX+0.25% glucose"
+76	"YPDAFEXglucoseTests_2-25-10"	"D10"	"AFEX+0.5% glucose"	"Engineered strain"	"richards sigmoid"	2.53563260737677	0.0376782240880802	5.60076805555555	0.122775490964049	0.000617718940237756	0.0383224027816064	0.00352849516406259	0.723989555808605	0.00348019897003327	0.762311958590212	0.0604113492179259	0.762310653602122	0.701900609372286	0.701899304384196	0.0390661767078291	1.06264585810741	1.14322554568591	0.0622734220263796	1.14322274880392	1.08095212365953	1.08094932677754	1.22916202573701	0.0694532756349596	0.999772141364762	0.00189783824442075	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	77	"Control strain plate"	"Sample"	"ATCC"	""	"AFEX+0.5% glucose"
+77	"YPDAFEXglucoseTests_2-25-10"	"E10"	"AFEX+1% glucose"	"Engineered strain"	"logistic sigmoid."	2.60565520411145	0.0279148207786424	5.67226722222222	0.122180167529517	0.000572646164016784	0.0367511554868138	0.00173132045208087	0.75510174924411	0.00189799830326426	0.791852904730924	0.0552120643649708	0.791846881057418	0.736640840365953	0.736634816692447	0.0374348287497246	1.12782801723342	1.20748289466742	0.0567646930486905	1.20746959755124	1.15071820161873	1.15070490450255	NA	NA	0.999760229166242	0.00222986115644153	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	78	"Control strain plate"	"Sample"	"ATCC"	""	"AFEX+1% glucose"
+78	"YPDAFEXglucoseTests_2-25-10"	"F10"	"AFEX+2% glucose"	"Engineered strain"	"logistic sigmoid."	2.59552092034145	0.0233507552285751	5.7914325	0.12311239814861	0.000459924953718036	0.0376321525320693	0.00147723901592513	0.788206013379693	0.00162316638429969	0.825838165911762	0.0581595525832075	0.82582810286149	0.767678613328555	0.767668550278282	0.0383492084922821	1.19944710612095	1.28379416176132	0.0598840894646306	1.2837711799415	1.22391007229669	1.22388709047687	NA	NA	0.999844012469462	0.00158372380662876	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	79	"Control strain plate"	"Sample"	"ATCC"	""	"AFEX+2% glucose"
+79	"YPDAFEXglucoseTests_2-25-10"	"G10"	"AFEX+5% glucose"	"Engineered strain"	"richards sigmoid"	2.65619332146438	0.0304232772610151	6.00593	0.113927548226674	0.000394015356154558	0.0448535113624544	0.00262903429411648	0.830698452896991	0.00255902360970839	0.875551964259445	0.0596126030160059	0.875406838654098	0.815939361243439	0.815794235638092	0.0458746399354508	1.29492107489454	1.4001997528856	0.0614252739377605	1.39985144771812	1.33877447894784	1.33842617378036	0.630436857242866	0.0359660377290858	0.999878122228538	0.0014247167012055	"I "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	80	"Control strain plate"	"Sample"	"ATCC"	""	"AFEX+5% glucose"
+80	"YPDAFEXglucoseTests_2-25-10"	"H10"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	81	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+81	"YPDAFEXglucoseTests_2-25-10"	"A11"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	82	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+82	"YPDAFEXglucoseTests_2-25-10"	"B11"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	83	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+83	"YPDAFEXglucoseTests_2-25-10"	"C11"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	84	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+84	"YPDAFEXglucoseTests_2-25-10"	"D11"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	85	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+85	"YPDAFEXglucoseTests_2-25-10"	"E11"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	86	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+86	"YPDAFEXglucoseTests_2-25-10"	"F11"	"None"	"Empty"	"richards sigmoid"	14.4916170457847	0.0217082069318843	18.6612825	0.0889624209370597	0.000433181631551599	0.00193467418446847	0.000448535101404725	0.976169168246482	0.0129778271847923	0.97810384243095	0.00193467418448112	0.752023542360525	0.976169168246469	0.750088868176044	0.00193654687405509	1.65426868422052	1.65940879994385	0.00193654687406775	1.12128819301358	1.65747225306978	1.11935164613951	0.07	0.0304918969768742	0.999799864971328	0.00156360720906969	"E*"	"U"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	87	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+87	"YPDAFEXglucoseTests_2-25-10"	"G11"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	88	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+88	"YPDAFEXglucoseTests_2-25-10"	"H11"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	89	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+89	"YPDAFEXglucoseTests_2-25-10"	"A12"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	90	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+90	"YPDAFEXglucoseTests_2-25-10"	"B12"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	91	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+91	"YPDAFEXglucoseTests_2-25-10"	"C12"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	92	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+92	"YPDAFEXglucoseTests_2-25-10"	"D12"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	93	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+93	"YPDAFEXglucoseTests_2-25-10"	"E12"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	94	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+94	"YPDAFEXglucoseTests_2-25-10"	"F12"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	95	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+95	"YPDAFEXglucoseTests_2-25-10"	"G12"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	96	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+96	"YPDAFEXglucoseTests_2-25-10"	"H12"	"None"	"Empty"	"<NA>: skipped"	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	"E "	"-"	"-"	""	"YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf"	97	"Control strain plate"	"Empty"	"Empty"	"Empty"	"None"
+
+# Raw OD values are adjusted and log-transformed before fitting a growth curve as follows: log.OD = log(OD - blank + const) where blank is OD of blank medium and const is specified by the user (1 by default) 
+# Values are reported on the above 'log.OD' scale unless otherwise specified. 
+# .SE columns report standard errors of those values that are estimated directly as parameters of global sigmoid models. 
+# .OD columns report values back-transformed to the linear 'OD - blank' scale. 
+
+# -- Explanation of columns -- 
+#    - model: Name of the model the well was successfully fit with (if any) 
+#    - lag.time: Lag time estimate inferred from the fitted model 
+#    - inflection.time: inflection time point of the growth curve when drawn on the log scale 
+#    - max.spec.growth.rate: maximum specific growth rate estimate inferred from the fitted model.  Estimated as the first derivative of the growth curve at inflection time point 
+#    - baseline: growth curve baseline.  Global sigmoid model: baseline is parameter 'b' of the model.  LOESS: baseline is the same as the lowest predicted log.OD value 
+#    - amplitude: difference between upper plateau and baseline values.  Global sigmoid model: amplitude is parameter 'A' of the model.  LOESS: amplitude = max.log.OD - min.log.OD 
+#    - plateau: upper asymptote value of the fitted model. Global sigmoid model: plateau = b + A.  LOESS: plateau = max.log.OD 
+#    - inoc.log.OD: log.OD value at inoculation.  Estimated value from the fitted model is used, rather than the actual measurement 
+#    - max.log.OD: maximal log.OD value reached during the experiment.  Estimated value from the fitted model is used rather than the actual measurement 
+#    - projected.growth: maximal projected growth over inoculation value.  Global sigmoid model: projected.growth = plateau - inoc.log.OD. LOESS: not reported 
+#    - achieved.growth: maximal growth over inoculation value actually achieved during the experiment.  achieved.growth = max.log.OD - inoc.log.OD 
+#    - shape.par: shape parameter of the Richard equation 
+#    - R.squared: goodness of fit metric.  Also known as coefficient of determination.  R.squared is usually between 0 and 1.  A value close to 1 indicates good fit. 
+#    - RSS: residual sum of squares.  Another goodness of fit metric.  Smaller values indicate better fits. 
+#    - empty: (Well indicator) 
+#              - an 'E' indicates that the well was empty and no growth was detected.  
+#              - an 'I' indicates that the well was inoculated and growth was detected above the threshold.  
+#              - an 'E*' indicates that the well was empty and growth was detected (possible contamination).  
+#              - an '!' indicates that the well was inoculated and no growth was detected.  
+#    - asymp.not.reached: shows “L” if the bottom asymptote (baseline) was not reached and “U” if the upper asymptote (plateau) was not reached. 
+#    - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. 
+#    - other: Additional flag column.  Displays information about whether jumps in OD were detected and what was done about them. 
+#    - pdf.file and page.no: location of the figure for this well in the output .pdf files.
+#
+# -- Source file information-- 
+#  YPDAFEXglucoseTests_2-25-10.csv 
+#  analyzed using GCAT v 5.0 
+#  request sent:  2015-04-07 15:34:27 
+#  completed:  2015-04-07 15:34:33 
+#
+# -- Parameters used in current analysis -- 
+#    - Constant added to log(OD + n) transformation: 1 
+#    - Blank OD value:  First timepoint in well 
+#    - Index of inoculation timepoint 2 
+#    - Minimum growth threshold: 0.05 
+#    - Removed points:  
+#    - Jump detection: FALSE
@@ -0,0 +1,97 @@
+Destination plate name,Row,Column,Well ID,Plate source,Well Source,Strain,Media Definition
+Control strain plate,A,1,Empty,Empty,Empty,Empty,None
+Control strain plate,A,2,Empty,Empty,Empty,Empty,None
+Control strain plate,A,3,Empty,Empty,Empty,Empty,None
+Control strain plate,A,4,Empty,Empty,Empty,Empty,None
+Control strain plate,A,5,Empty,Empty,Empty,Empty,None
+Control strain plate,A,6,Empty,Empty,Empty,Empty,None
+Control strain plate,A,7,Empty,Empty,Empty,Empty,None
+Control strain plate,A,8,Empty,Empty,Empty,Empty,None
+Control strain plate,A,9,Empty,Empty,Empty,Empty,None
+Control strain plate,A,10,Empty,Empty,Empty,Empty,None
+Control strain plate,A,11,Empty,Empty,Empty,Empty,None
+Control strain plate,A,12,Empty,Empty,Empty,Empty,None
+Control strain plate,B,1,Empty,Empty,Empty,Empty,None
+Control strain plate,B,2,Sample,USDA,,Lab strain,YP
+Control strain plate,B,3,Sample,USDA,,Wild strain,YP
+Control strain plate,B,4,Sample,Internal source,,Industrial strain,YP
+Control strain plate,B,5,Sample,ATCC,,Engineered strain,YP
+Control strain plate,B,6,Empty,Empty,Empty,Empty,None
+Control strain plate,B,7,Sample,USDA,,Lab strain,AFEX
+Control strain plate,B,8,Sample,USDA,,Wild strain,AFEX
+Control strain plate,B,9,Sample,Internal source,,Industrial strain,AFEX
+Control strain plate,B,10,Sample,ATCC,,Engineered strain,AFEX
+Control strain plate,B,11,Empty,Empty,Empty,Empty,None
+Control strain plate,B,12,Empty,Empty,Empty,Empty,None
+Control strain plate,C,1,Empty,Empty,Empty,Empty,None
+Control strain plate,C,2,Sample,USDA,,Lab strain,YP+0.25% glucose
+Control strain plate,C,3,Sample,USDA,,Wild strain,YP+0.25% glucose
+Control strain plate,C,4,Sample,Internal source,,Industrial strain,YP+0.25% glucose
+Control strain plate,C,5,Sample,ATCC,,Engineered strain,YP+0.25% glucose
+Control strain plate,C,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,C,7,Sample,USDA,,Lab strain,AFEX+0.25% glucose
+Control strain plate,C,8,Sample,USDA,,Wild strain,AFEX+0.25% glucose
+Control strain plate,C,9,Sample,Internal source,,Industrial strain,AFEX+0.25% glucose
+Control strain plate,C,10,Sample,ATCC,,Engineered strain,AFEX+0.25% glucose
+Control strain plate,C,11,Empty,Empty,Empty,Empty,None
+Control strain plate,C,12,Empty,Empty,Empty,Empty,None
+Control strain plate,D,1,Empty,Empty,Empty,Empty,None
+Control strain plate,D,2,Sample,USDA,,Lab strain,YP+0.5% glucose
+Control strain plate,D,3,Sample,USDA,,Wild strain,YP+0.5% glucose
+Control strain plate,D,4,Sample,Internal source,,Industrial strain,YP+0.5% glucose
+Control strain plate,D,5,Sample,ATCC,,Engineered strain,YP+0.5% glucose
+Control strain plate,D,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,D,7,Sample,USDA,,Lab strain,AFEX+0.5% glucose
+Control strain plate,D,8,Sample,USDA,,Wild strain,AFEX+0.5% glucose
+Control strain plate,D,9,Sample,Internal source,,Industrial strain,AFEX+0.5% glucose
+Control strain plate,D,10,Sample,ATCC,,Engineered strain,AFEX+0.5% glucose
+Control strain plate,D,11,Empty,Empty,Empty,Empty,None
+Control strain plate,D,12,Empty,Empty,Empty,Empty,None
+Control strain plate,E,1,Empty,Empty,Empty,Empty,None
+Control strain plate,E,2,Sample,USDA,,Lab strain,YP+1% glucose
+Control strain plate,E,3,Sample,USDA,,Wild strain,YP+1% glucose
+Control strain plate,E,4,Sample,Internal source,,Industrial strain,YP+1% glucose
+Control strain plate,E,5,Sample,ATCC,,Engineered strain,YP+1% glucose
+Control strain plate,E,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,E,7,Sample,USDA,,Lab strain,AFEX+1% glucose
+Control strain plate,E,8,Sample,USDA,,Wild strain,AFEX+1% glucose
+Control strain plate,E,9,Sample,Internal source,,Industrial strain,AFEX+1% glucose
+Control strain plate,E,10,Sample,ATCC,,Engineered strain,AFEX+1% glucose
+Control strain plate,E,11,Empty,Empty,Empty,Empty,None
+Control strain plate,E,12,Empty,Empty,Empty,Empty,None
+Control strain plate,F,1,Empty,Empty,Empty,Empty,None
+Control strain plate,F,2,Sample,USDA,,Lab strain,YP+2% glucose
+Control strain plate,F,3,Sample,USDA,,Wild strain,YP+2% glucose
+Control strain plate,F,4,Sample,Internal source,,Industrial strain,YP+2% glucose
+Control strain plate,F,5,Sample,ATCC,,Engineered strain,YP+2% glucose
+Control strain plate,F,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,F,7,Sample,USDA,,Lab strain,AFEX+2% glucose
+Control strain plate,F,8,Sample,USDA,,Wild strain,AFEX+2% glucose
+Control strain plate,F,9,Sample,Internal source,,Industrial strain,AFEX+2% glucose
+Control strain plate,F,10,Sample,ATCC,,Engineered strain,AFEX+2% glucose
+Control strain plate,F,11,Empty,Empty,Empty,Empty,None
+Control strain plate,F,12,Empty,Empty,Empty,Empty,None
+Control strain plate,G,1,Empty,Empty,Empty,Empty,None
+Control strain plate,G,2,Sample,USDA,,Lab strain,YP+5% glucose
+Control strain plate,G,3,Sample,USDA,,Wild strain,YP+5% glucose
+Control strain plate,G,4,Sample,Internal source,,Industrial strain,YP+5% glucose
+Control strain plate,G,5,Sample,ATCC,,Engineered strain,YP+5% glucose
+Control strain plate,G,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,G,7,Sample,USDA,,Lab strain,AFEX+5% glucose
+Control strain plate,G,8,Sample,USDA,,Wild strain,AFEX+5% glucose
+Control strain plate,G,9,Sample,Internal source,,Industrial strain,AFEX+5% glucose
+Control strain plate,G,10,Sample,ATCC,,Engineered strain,AFEX+5% glucose
+Control strain plate,G,11,Empty,Empty,Empty,Empty,None
+Control strain plate,G,12,Empty,Empty,Empty,Empty,None
+Control strain plate,H,1,Empty,Empty,Empty,Empty,None
+Control strain plate,H,2,Empty,Empty,Empty,Empty,None
+Control strain plate,H,3,Empty,Empty,Empty,Empty,None
+Control strain plate,H,4,Empty,Empty,Empty,Empty,None
+Control strain plate,H,5,Empty,Empty,Empty,Empty,None
+Control strain plate,H,6,Empty,Empty,Empty,Empty,None
+Control strain plate,H,7,Empty,Empty,Empty,Empty,None
+Control strain plate,H,8,Empty,Empty,Empty,Empty,None
+Control strain plate,H,9,Empty,Empty,Empty,Empty,None
+Control strain plate,H,10,Empty,Empty,Empty,Empty,None
+Control strain plate,H,11,Empty,Empty,Empty,Empty,None
+Control strain plate,H,12,Empty,Empty,Empty,Empty,None
@@ -0,0 +1,97 @@
+Destination plate name,Row,Column,Well ID,Plate source,Well Source,Strain,Media Definition
+Control strain plate,A,1,Empty,Empty,Empty,Empty,None
+Control strain plate,A,2,Empty,Empty,Empty,Empty,None
+Control strain plate,A,3,Empty,Empty,Empty,Empty,None
+Control strain plate,A,4,Empty,Empty,Empty,Empty,None
+Control strain plate,A,5,Empty,Empty,Empty,Empty,None
+Control strain plate,A,6,Empty,Empty,Empty,Empty,None
+Control strain plate,A,7,Empty,Empty,Empty,Empty,None
+Control strain plate,A,8,Empty,Empty,Empty,Empty,None
+Control strain plate,A,9,Empty,Empty,Empty,Empty,None
+Control strain plate,A,10,Empty,Empty,Empty,Empty,None
+Control strain plate,A,11,Empty,Empty,Empty,Empty,None
+Control strain plate,A,12,Empty,Empty,Empty,Empty,None
+Control strain plate,B,1,Empty,Empty,Empty,Empty,None
+Control strain plate,B,2,Sample,USDA,,Lab strain,YP
+Control strain plate,B,3,Sample,USDA,,Wild strain,YP
+Control strain plate,B,4,Sample,Internal source,,Industrial strain,YP
+Control strain plate,B,5,Sample,ATCC,,Engineered strain,YP
+Control strain plate,B,6,Empty,Empty,Empty,Empty,None
+Control strain plate,B,7,Sample,USDA,,Lab strain,AFEX
+Control strain plate,B,8,Sample,USDA,,Wild strain,AFEX
+Control strain plate,B,9,Sample,Internal source,,Industrial strain,AFEX
+Control strain plate,B,10,Sample,ATCC,,Engineered strain,AFEX
+Control strain plate,B,11,Empty,Empty,Empty,Empty,None
+Control strain plate,B,12,Empty,Empty,Empty,Empty,None
+Control strain plate,C,1,Empty,Empty,Empty,Empty,None
+Control strain plate,C,2,Sample,USDA,,Lab strain,YP+0.25% glucose
+Control strain plate,C,3,Sample,USDA,,Wild strain,YP+0.25% glucose
+Control strain plate,C,4,Sample,Internal source,,Industrial strain,YP+0.25% glucose
+Control strain plate,C,5,Sample,ATCC,,Engineered strain,YP+0.25% glucose
+Control strain plate,C,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,C,7,Sample,USDA,,Lab strain,AFEX+0.25% glucose
+Control strain plate,C,8,Sample,USDA,,Wild strain,AFEX+0.25% glucose
+Control strain plate,C,9,Sample,Internal source,,Industrial strain,AFEX+0.25% glucose
+Control strain plate,C,10,Sample,ATCC,,Engineered strain,AFEX+0.25% glucose
+Control strain plate,C,11,Empty,Empty,Empty,Empty,None
+Control strain plate,C,12,Empty,Empty,Empty,Empty,None
+Control strain plate,D,1,Empty,Empty,Empty,Empty,None
+Control strain plate,D,2,Sample,USDA,,Lab strain,YP+0.5% glucose
+Control strain plate,D,3,Sample,USDA,,Wild strain,YP+0.5% glucose
+Control strain plate,D,4,Sample,Internal source,,Industrial strain,YP+0.5% glucose
+Control strain plate,D,5,Sample,ATCC,,Engineered strain,YP+0.5% glucose
+Control strain plate,D,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,D,7,Sample,USDA,,Lab strain,AFEX+0.5% glucose
+Control strain plate,D,8,Sample,USDA,,Wild strain,AFEX+0.5% glucose
+Control strain plate,D,9,Sample,Internal source,,Industrial strain,AFEX+0.5% glucose
+Control strain plate,D,10,Sample,ATCC,,Engineered strain,AFEX+0.5% glucose
+Control strain plate,D,11,Empty,Empty,Empty,Empty,None
+Control strain plate,D,12,Empty,Empty,Empty,Empty,None
+Control strain plate,E,1,Empty,Empty,Empty,Empty,None
+Control strain plate,E,2,Sample,USDA,,Lab strain,YP+1% glucose
+Control strain plate,E,3,Sample,USDA,,Wild strain,YP+1% glucose
+Control strain plate,E,4,Sample,Internal source,,Industrial strain,YP+1% glucose
+Control strain plate,E,5,Sample,ATCC,,Engineered strain,YP+1% glucose
+Control strain plate,E,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,E,7,Sample,USDA,,Lab strain,AFEX+1% glucose
+Control strain plate,E,8,Sample,USDA,,Wild strain,AFEX+1% glucose
+Control strain plate,E,9,Sample,Internal source,,Industrial strain,AFEX+1% glucose
+Control strain plate,E,10,Sample,ATCC,,Engineered strain,AFEX+1% glucose
+Control strain plate,E,11,Empty,Empty,Empty,Empty,None
+Control strain plate,E,12,Empty,Empty,Empty,Empty,None
+Control strain plate,F,1,Empty,Empty,Empty,Empty,None
+Control strain plate,F,2,Sample,USDA,,Lab strain,YP+2% glucose
+Control strain plate,F,3,Sample,USDA,,Wild strain,YP+2% glucose
+Control strain plate,F,4,Sample,Internal source,,Industrial strain,YP+2% glucose
+Control strain plate,F,5,Sample,ATCC,,Engineered strain,YP+2% glucose
+Control strain plate,F,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,F,7,Sample,USDA,,Lab strain,AFEX+2% glucose
+Control strain plate,F,8,Sample,USDA,,Wild strain,AFEX+2% glucose
+Control strain plate,F,9,Sample,Internal source,,Industrial strain,AFEX+2% glucose
+Control strain plate,F,10,Sample,ATCC,,Engineered strain,AFEX+2% glucose
+Control strain plate,F,11,Empty,Empty,Empty,Empty,None
+Control strain plate,F,12,Empty,Empty,Empty,Empty,None
+Control strain plate,G,1,Empty,Empty,Empty,Empty,None
+Control strain plate,G,2,Sample,USDA,,Lab strain,YP+5% glucose
+Control strain plate,G,3,Sample,USDA,,Wild strain,YP+5% glucose
+Control strain plate,G,4,Sample,Internal source,,Industrial strain,YP+5% glucose
+Control strain plate,G,5,Sample,ATCC,,Engineered strain,YP+5% glucose
+Control strain plate,G,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,G,7,Sample,USDA,,Lab strain,AFEX+5% glucose
+Control strain plate,G,8,Sample,USDA,,Wild strain,AFEX+5% glucose
+Control strain plate,G,9,Sample,Internal source,,Industrial strain,AFEX+5% glucose
+Control strain plate,G,10,Sample,ATCC,,Engineered strain,AFEX+5% glucose
+Control strain plate,G,11,Empty,Empty,Empty,Empty,None
+Control strain plate,G,12,Empty,Empty,Empty,Empty,None
+Control strain plate,H,1,Empty,Empty,Empty,Empty,None
+Control strain plate,H,2,Empty,Empty,Empty,Empty,None
+Control strain plate,H,3,Empty,Empty,Empty,Empty,None
+Control strain plate,H,4,Empty,Empty,Empty,Empty,None
+Control strain plate,H,5,Empty,Empty,Empty,Empty,None
+Control strain plate,H,6,Empty,Empty,Empty,Empty,None
+Control strain plate,H,7,Empty,Empty,Empty,Empty,None
+Control strain plate,H,8,Empty,Empty,Empty,Empty,None
+Control strain plate,H,9,Empty,Empty,Empty,Empty,None
+Control strain plate,H,10,Empty,Empty,Empty,Empty,None
+Control strain plate,H,11,Empty,Empty,Empty,Empty,None
+Control strain plate,H,12,Empty,Empty,Empty,Empty,None
@@ -0,0 +1,5 @@
+# See http://www.robotstxt.org/wc/norobots.html for documentation on how to use the robots.txt file
+#
+# To ban all spiders from the entire site uncomment the next two lines:
+# User-Agent: *
+# Disallow: /
@@ -0,0 +1,97 @@
+Destination plate name,Row,Column,Well ID,Plate source,Well Source,Strain,Media Definition
+Control strain plate,A,1,Empty,Empty,Empty,Empty,None
+Control strain plate,A,2,Empty,Empty,Empty,Empty,None
+Control strain plate,A,3,Empty,Empty,Empty,Empty,None
+Control strain plate,A,4,Empty,Empty,Empty,Empty,None
+Control strain plate,A,5,Empty,Empty,Empty,Empty,None
+Control strain plate,A,6,Empty,Empty,Empty,Empty,None
+Control strain plate,A,7,Empty,Empty,Empty,Empty,None
+Control strain plate,A,8,Empty,Empty,Empty,Empty,None
+Control strain plate,A,9,Empty,Empty,Empty,Empty,None
+Control strain plate,A,10,Empty,Empty,Empty,Empty,None
+Control strain plate,A,11,Empty,Empty,Empty,Empty,None
+Control strain plate,A,12,Empty,Empty,Empty,Empty,None
+Control strain plate,B,1,Empty,Empty,Empty,Empty,None
+Control strain plate,B,2,Sample,USDA,,Lab strain,YP
+Control strain plate,B,3,Sample,USDA,,Wild strain,YP
+Control strain plate,B,4,Sample,Internal source,,Industrial strain,YP
+Control strain plate,B,5,Sample,ATCC,,Engineered strain,YP
+Control strain plate,B,6,Empty,Empty,Empty,Empty,None
+Control strain plate,B,7,Sample,USDA,,Lab strain,AFEX
+Control strain plate,B,8,Sample,USDA,,Wild strain,AFEX
+Control strain plate,B,9,Sample,Internal source,,Industrial strain,AFEX
+Control strain plate,B,10,Sample,ATCC,,Engineered strain,AFEX
+Control strain plate,B,11,Empty,Empty,Empty,Empty,None
+Control strain plate,B,12,Empty,Empty,Empty,Empty,None
+Control strain plate,C,1,Empty,Empty,Empty,Empty,None
+Control strain plate,C,2,Sample,USDA,,Lab strain,YP+0.25% glucose
+Control strain plate,C,3,Sample,USDA,,Wild strain,YP+0.25% glucose
+Control strain plate,C,4,Sample,Internal source,,Industrial strain,YP+0.25% glucose
+Control strain plate,C,5,Sample,ATCC,,Engineered strain,YP+0.25% glucose
+Control strain plate,C,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,C,7,Sample,USDA,,Lab strain,AFEX+0.25% glucose
+Control strain plate,C,8,Sample,USDA,,Wild strain,AFEX+0.25% glucose
+Control strain plate,C,9,Sample,Internal source,,Industrial strain,AFEX+0.25% glucose
+Control strain plate,C,10,Sample,ATCC,,Engineered strain,AFEX+0.25% glucose
+Control strain plate,C,11,Empty,Empty,Empty,Empty,None
+Control strain plate,C,12,Empty,Empty,Empty,Empty,None
+Control strain plate,D,1,Empty,Empty,Empty,Empty,None
+Control strain plate,D,2,Sample,USDA,,Lab strain,YP+0.5% glucose
+Control strain plate,D,3,Sample,USDA,,Wild strain,YP+0.5% glucose
+Control strain plate,D,4,Sample,Internal source,,Industrial strain,YP+0.5% glucose
+Control strain plate,D,5,Sample,ATCC,,Engineered strain,YP+0.5% glucose
+Control strain plate,D,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,D,7,Sample,USDA,,Lab strain,AFEX+0.5% glucose
+Control strain plate,D,8,Sample,USDA,,Wild strain,AFEX+0.5% glucose
+Control strain plate,D,9,Sample,Internal source,,Industrial strain,AFEX+0.5% glucose
+Control strain plate,D,10,Sample,ATCC,,Engineered strain,AFEX+0.5% glucose
+Control strain plate,D,11,Empty,Empty,Empty,Empty,None
+Control strain plate,D,12,Empty,Empty,Empty,Empty,None
+Control strain plate,E,1,Empty,Empty,Empty,Empty,None
+Control strain plate,E,2,Sample,USDA,,Lab strain,YP+1% glucose
+Control strain plate,E,3,Sample,USDA,,Wild strain,YP+1% glucose
+Control strain plate,E,4,Sample,Internal source,,Industrial strain,YP+1% glucose
+Control strain plate,E,5,Sample,ATCC,,Engineered strain,YP+1% glucose
+Control strain plate,E,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,E,7,Sample,USDA,,Lab strain,AFEX+1% glucose
+Control strain plate,E,8,Sample,USDA,,Wild strain,AFEX+1% glucose
+Control strain plate,E,9,Sample,Internal source,,Industrial strain,AFEX+1% glucose
+Control strain plate,E,10,Sample,ATCC,,Engineered strain,AFEX+1% glucose
+Control strain plate,E,11,Empty,Empty,Empty,Empty,None
+Control strain plate,E,12,Empty,Empty,Empty,Empty,None
+Control strain plate,F,1,Empty,Empty,Empty,Empty,None
+Control strain plate,F,2,Sample,USDA,,Lab strain,YP+2% glucose
+Control strain plate,F,3,Sample,USDA,,Wild strain,YP+2% glucose
+Control strain plate,F,4,Sample,Internal source,,Industrial strain,YP+2% glucose
+Control strain plate,F,5,Sample,ATCC,,Engineered strain,YP+2% glucose
+Control strain plate,F,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,F,7,Sample,USDA,,Lab strain,AFEX+2% glucose
+Control strain plate,F,8,Sample,USDA,,Wild strain,AFEX+2% glucose
+Control strain plate,F,9,Sample,Internal source,,Industrial strain,AFEX+2% glucose
+Control strain plate,F,10,Sample,ATCC,,Engineered strain,AFEX+2% glucose
+Control strain plate,F,11,Empty,Empty,Empty,Empty,None
+Control strain plate,F,12,Empty,Empty,Empty,Empty,None
+Control strain plate,G,1,Empty,Empty,Empty,Empty,None
+Control strain plate,G,2,Sample,USDA,,Lab strain,YP+5% glucose
+Control strain plate,G,3,Sample,USDA,,Wild strain,YP+5% glucose
+Control strain plate,G,4,Sample,Internal source,,Industrial strain,YP+5% glucose
+Control strain plate,G,5,Sample,ATCC,,Engineered strain,YP+5% glucose
+Control strain plate,G,6,Empty,Empty,Empty,Empty,Empty
+Control strain plate,G,7,Sample,USDA,,Lab strain,AFEX+5% glucose
+Control strain plate,G,8,Sample,USDA,,Wild strain,AFEX+5% glucose
+Control strain plate,G,9,Sample,Internal source,,Industrial strain,AFEX+5% glucose
+Control strain plate,G,10,Sample,ATCC,,Engineered strain,AFEX+5% glucose
+Control strain plate,G,11,Empty,Empty,Empty,Empty,None
+Control strain plate,G,12,Empty,Empty,Empty,Empty,None
+Control strain plate,H,1,Empty,Empty,Empty,Empty,None
+Control strain plate,H,2,Empty,Empty,Empty,Empty,None
+Control strain plate,H,3,Empty,Empty,Empty,Empty,None
+Control strain plate,H,4,Empty,Empty,Empty,Empty,None
+Control strain plate,H,5,Empty,Empty,Empty,Empty,None
+Control strain plate,H,6,Empty,Empty,Empty,Empty,None
+Control strain plate,H,7,Empty,Empty,Empty,Empty,None
+Control strain plate,H,8,Empty,Empty,Empty,Empty,None
+Control strain plate,H,9,Empty,Empty,Empty,Empty,None
+Control strain plate,H,10,Empty,Empty,Empty,Empty,None
+Control strain plate,H,11,Empty,Empty,Empty,Empty,None
+Control strain plate,H,12,Empty,Empty,Empty,Empty,None
@@ -0,0 +1,6 @@
+#!/usr/bin/env ruby
+# This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
+
+APP_PATH = File.expand_path('../../config/application',  __FILE__)
+require File.expand_path('../../config/boot',  __FILE__)
+require 'rails/commands'
@@ -0,0 +1,27 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+require 'test_helper'
+
+class AssaysControllerTest < ActionController::TestCase
+  # test "the truth" do
+  #   assert true
+  # end
+end
@@ -0,0 +1,32 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+require 'test_helper'
+require 'rails/performance_test_help'
+
+class BrowsingTest < ActionDispatch::PerformanceTest
+  # Refer to the documentation for all available options
+  # self.profile_options = { :runs => 5, :metrics => [:wall_time, :memory]
+  #                          :output => 'tmp/performance', :formats => [:flat] }
+
+  def test_homepage
+    get '/'
+  end
+end
@@ -0,0 +1,33 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+ENV["RAILS_ENV"] = "test"
+require File.expand_path('../../config/environment', __FILE__)
+require 'rails/test_help'
+
+class ActiveSupport::TestCase
+  # Setup all fixtures in test/fixtures/*.(yml|csv) for all tests in alphabetical order.
+  #
+  # Note: You'll currently still have to declare fixtures explicitly in integration tests
+  # -- they do not yet inherit this setting
+  fixtures :all
+
+  # Add more helper methods to be used by all tests here...
+end
@@ -0,0 +1,24 @@
+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+require 'test_helper'
+
+class AssaysHelperTest < ActionView::TestCase
+end
@@ -0,0 +1,50 @@
+/*
+ * Copyright 2012 The Board of Regents of the University of Wisconsin System.
+ * Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+ * Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+ *
+ * This file is part of GCAT.
+ *
+ * GCAT is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * GCAT is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+var jQueryLoaderOptions=null;
+(function(a){a.loader=function(d){switch(d){case"close":if(jQueryLoaderOptions){if(a("#"+jQueryLoaderOptions.id)){a("#"+jQueryLoaderOptions.id+", #"+jQueryLoaderOptions.background.id).remove()
+}}return;
+break;
+case"setContent":if(jQueryLoaderOptions){if(a("#"+jQueryLoaderOptions.id)){if(a.loader.arguments.length==2){a("#"+jQueryLoaderOptions.id).html(a.loader.arguments[1])
+}else{if(console){console.error("setContent method must have 2 arguments $.loader('setContent', 'new content');")
+}else{alert("setContent method must have 2 arguments $.loader('setContent', 'new content');")
+}}}}return;
+break;
+default:var b=a.extend({content:"<div>Loading ...</div>",className:"loader",id:"jquery-loader",height:100,width:200,zIndex:30000,background:{opacity:0.4,id:"jquery-loader-background"}},d)
+}jQueryLoaderOptions=b;
+var c=a(document).height();
+var e=a(window).width();
+var g=a('<div id="'+b.background.id+'"/>');
+g.css({zIndex:b.zIndex,position:"absolute",top:"0px",left:"0px",width:e,height:c,opacity:b.background.opacity});
+g.appendTo("body");
+if(jQuery.bgiframe){g.bgiframe()
+}var f=a('<div id="'+b.id+'" class="'+b.className+'"></div>');
+f.css({zIndex:b.zIndex+1,width:b.width,height:b.height});
+f.appendTo("body");
+f.center();
+a(b.content).appendTo(f)
+};
+a.fn.center=function(){this.css("position","absolute");
+this.css("top",(a(window).height()-this.outerHeight())/2+a(window).scrollTop()+"px");
+this.css("left",(a(window).width()-this.outerWidth())/2+a(window).scrollLeft()+"px");
+return this
+}
+})(jQuery);
@@ -0,0 +1,26 @@
+/*
+ * Copyright 2012 The Board of Regents of the University of Wisconsin System.
+ * Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+ * Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+ *
+ * This file is part of GCAT.
+ *
+ * GCAT is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * GCAT is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+@CHARSET "UTF-8";
+#jquery-loader{border:1px grey solid;padding-top:10px;background-color:white;text-align:center;background-image:url(ajax-loader.gif);background-position:center center;background-repeat:no-repeat;}
+#jquery-loader-background{background-color:silver;}
+#jquery-loader.blue-with-image{border:2px #008587 solid;padding-top:10px;background-color:white;text-align:center;background-image:url(ajax-loader.gif);background-position:center center;background-repeat:no-repeat;}
+#jquery-loader.blue-with-image-2{border:none;padding-top:10px;background-color:transparent;text-align:center;background-image:url(ajax-loader.gif);background-position:center center;background-repeat:no-repeat;}