diff --git a/.gitignore b/.gitignore
index 56172aaff..c834d231d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,5 +18,8 @@ orig.public
 public/maps/*
 config/initializers/site_keys.rb
 .Rproj.user
+public/assets
+script/load.bety.sh
 
-
+# Ignore encrypted secrets key file.
+config/secrets.yml.key
diff --git a/.ruby-gemset b/.ruby-gemset
index b37d060df..1d2770e17 100644
--- a/.ruby-gemset
+++ b/.ruby-gemset
@@ -1 +1 @@
-betydb_rails3
+betydb_rails5
diff --git a/.ruby-version b/.ruby-version
index d427c89b6..a831048a2 100644
--- a/.ruby-version
+++ b/.ruby-version
@@ -1 +1 @@
-ruby-2.1.5
+ruby-2.3.0
diff --git a/.travis.yml b/.travis.yml
index baaad9d05..1b206e858 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,8 +7,6 @@ sudo: false
 # versions of ruby to use
 # see the list at http://rubies.travis-ci.org/
 rvm:
-  - 2.1.5
-  - 2.1.8
   - 2.2.4
   - 2.3.0
 
diff --git a/Dockerfile b/Dockerfile
index e2fa2de5b..48c079548 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ruby:2.1
+FROM ruby:2.3
 MAINTAINER Max Burnette <mburnet2@illinois.edu>
 
 # Install dependencies
@@ -6,7 +6,9 @@ RUN apt-get update \
     && apt-get install --no-install-recommends -y \
         curl \
         git \
+        libgeos-dev \
         netcat \
+        nodejs \
         postgresql-client \
     && rm -rf /var/lib/apt/lists/*
 
@@ -15,15 +17,17 @@ WORKDIR /home/bety
 
 # install gems (allowing for caching)
 COPY /Gemfile* /home/bety/
-RUN gem install bundler && \
-    bundle install --without javascript_testing --path vendor/bundle
+RUN gem install bundler \
+    && bundle install --with docker --without "test development production debug javascript_testing"
+
 
 # port that is exposed (standard ruby port)
-EXPOSE 3000
+EXPOSE 8000
 
 # copy rest of the files
 COPY / /home/bety
 COPY /docker/database.yml /home/bety/config/database.yml
+COPY /docker/config.ru /home/bety/config.ru
 
 # download dump.bety and load.bety scripts and configure app
 RUN curl -LOs https://raw.githubusercontent.com/PecanProject/pecan/master/scripts/load.bety.sh \
@@ -41,11 +45,18 @@ ARG BETY_GIT_DATE="unknown"
 ENV LOCAL_SERVER=99 \
     REMOTE_SERVERS="0 1 2 5" \
     RAILS_ENV="production" \
+    RAILS_RELATIVE_URL_ROOT="" \
+    SECRET_KEY_BASE="ThisIsNotReallySuchAGreatSecret" \
+    UNICORN_WORKER_PROCESSES="3" \
+    UNICORN_PORT="8000" \
     BETY_GIT_TAGS=${BETY_GIT_TAGS} \
     BETY_GIT_BRANCH=${BETY_GIT_BRANCH} \
     BETY_GIT_CHECKSUM=${BETY_GIT_CHECKSUM} \
     BETY_GIT_DATE=${BETY_GIT_DATE}
 
+# expose public files
+VOLUME ["/home/bety/public"]
+
 # default command to run bety web-app
 ENTRYPOINT ["/home/bety/docker/entrypoint.sh"]
-CMD ["server"]
+CMD ["unicorn"]
diff --git a/Gemfile b/Gemfile
index a7577b585..2d9206e10 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,16 +1,15 @@
 source "http://rubygems.org"
 
-gem "rails", "4.2.10"
+gem "rails", "5.1.5"
 # needed for rails 3.1 and above until we phase out prototype:
-gem 'prototype-rails', github: 'rails/prototype-rails', branch: '4.2' # see https://github.com/rails/prototype-rails/issues/37
-gem "query_reviewer", "0.1.6"
+## gem 'prototype-rails', github: 'rails/prototype-rails', branch: '4.2' # see https://github.com/rails/prototype-rails/issues/37
 gem "nokogiri"
 gem "narray", "0.6.0.4"
 gem "choice", "0.1.6"
 gem "comma", "3.0.4"
 gem "json"
 gem "rgeo", "~> 0.5.0"
-gem "multi_json", "1.3.6"
+gem "multi_json"
 gem "railroad", "0.5.0"
 gem "recaptcha", "4.8.0", :require => "recaptcha/rails"
 gem "ruby-graphviz", "1.0.8"
@@ -25,10 +24,13 @@ gem 'rabl'
 gem 'yajl-ruby', '~> 1.3.1'
 gem 'rubyzip', '~> 1.2.1'
 gem 'activerecord-session_store' # no longer part of Rails proper
-gem 'protected_attributes' # Use this until and unless we start using Strong Parameters.
+gem 'protected_attributes_continued' # Use this until and unless we start using Strong Parameters.
+gem 'sass-rails'
+gem 'coffee-rails'
+gem 'uglifier'
 
-# to-do: remove prototype dependencies so we no longer need this gem
-gem 'prototype_legacy_helper', '0.0.0', :git => 'git://github.com/rails/prototype_legacy_helper.git'
+gem 'jquery-rails'
+gem 'jquery-ui-rails'
 
 gem 'memoist'
 
@@ -53,13 +55,17 @@ group :development, :test do
   gem "yard"
 end
 
-
+group :development, :test do
+  gem "pry-rails"
+  gem "pry-byebug"
+end
 
 group :test do
   # phasing out webrat:    
   # gem "webrat", "0.7.1"
-  gem "capybara"
+  gem "capybara", "~> 2.8"
   gem "database_cleaner"
+  gem "rails-controller-testing" # TO-DO: rewrite the specs that rely on this
 end
 
 # If you have difficulty installing or don't wish to install capybara-webkit,
@@ -68,7 +74,7 @@ end
 #     bundle install --without javascript_testing
 #
 group :javascript_testing do
-  gem "capybara-webkit", "1.7.1"
+  gem "capybara-webkit", "~>1.7"
 end
 
 # This group is used by RSpec if the environment variable RAILS_DEBUG is set to
@@ -78,19 +84,20 @@ group :debug do
   gem "pry"
 end
 
-# Comment this out if you can't or don't wish to install capybara-webkit:
-
 group :production do
-  #  gem "rmagick", "2.13.1"
   gem "passenger"
 end
 
+group :docker do
+  gem 'unicorn'
+end
+
 # API-related Gems:
 
 gem "rspec_api_documentation"
 gem "json-schema" # needed by rspec_api_documentation
 
-gem "apipie-rails"
+gem "apipie-rails", "0.5.6"
 
 # Although it was previously noted that test-unit seems to be needed by
 # apipie-rails and prototype-rails, it interferes with routing specs, so we are
diff --git a/Gemfile.lock b/Gemfile.lock
index 83f34285e..0a77f2f08 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,164 +1,180 @@
-GIT
-  remote: git://github.com/rails/prototype-rails.git
-  revision: 0fed929ff48c10c3b978edd3baa983a81f404dbf
-  branch: 4.2
-  specs:
-    prototype-rails (4.0.0)
-      rails (~> 4.0)
-
-GIT
-  remote: git://github.com/rails/prototype_legacy_helper.git
-  revision: a2cd95c3e3c1a4f7a9566efdab5ce59c886cb05f
-  specs:
-    prototype_legacy_helper (0.0.0)
-
 GEM
   remote: http://rubygems.org/
   specs:
-    actionmailer (4.2.10)
-      actionpack (= 4.2.10)
-      actionview (= 4.2.10)
-      activejob (= 4.2.10)
+    actioncable (5.1.5)
+      actionpack (= 5.1.5)
+      nio4r (~> 2.0)
+      websocket-driver (~> 0.6.1)
+    actionmailer (5.1.5)
+      actionpack (= 5.1.5)
+      actionview (= 5.1.5)
+      activejob (= 5.1.5)
       mail (~> 2.5, >= 2.5.4)
-      rails-dom-testing (~> 1.0, >= 1.0.5)
-    actionpack (4.2.10)
-      actionview (= 4.2.10)
-      activesupport (= 4.2.10)
-      rack (~> 1.6)
-      rack-test (~> 0.6.2)
-      rails-dom-testing (~> 1.0, >= 1.0.5)
+      rails-dom-testing (~> 2.0)
+    actionpack (5.1.5)
+      actionview (= 5.1.5)
+      activesupport (= 5.1.5)
+      rack (~> 2.0)
+      rack-test (>= 0.6.3)
+      rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.2)
-    actionview (4.2.10)
-      activesupport (= 4.2.10)
+    actionview (5.1.5)
+      activesupport (= 5.1.5)
       builder (~> 3.1)
-      erubis (~> 2.7.0)
-      rails-dom-testing (~> 1.0, >= 1.0.5)
+      erubi (~> 1.4)
+      rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.3)
-    activejob (4.2.10)
-      activesupport (= 4.2.10)
-      globalid (>= 0.3.0)
-    activemodel (4.2.10)
-      activesupport (= 4.2.10)
-      builder (~> 3.1)
-    activerecord (4.2.10)
-      activemodel (= 4.2.10)
-      activesupport (= 4.2.10)
-      arel (~> 6.0)
-    activerecord-postgis-adapter (3.1.5)
-      activerecord (~> 4.2)
-      rgeo-activerecord (>= 4.0.4)
-    activerecord-session_store (0.1.2)
-      actionpack (>= 4.0.0, < 5)
-      activerecord (>= 4.0.0, < 5)
-      railties (>= 4.0.0, < 5)
-    activesupport (4.2.10)
+    activejob (5.1.5)
+      activesupport (= 5.1.5)
+      globalid (>= 0.3.6)
+    activemodel (5.1.5)
+      activesupport (= 5.1.5)
+    activerecord (5.1.5)
+      activemodel (= 5.1.5)
+      activesupport (= 5.1.5)
+      arel (~> 8.0)
+    activerecord-postgis-adapter (5.0.3)
+      activerecord (~> 5.1)
+      rgeo-activerecord (~> 5.1)
+    activerecord-session_store (1.1.1)
+      actionpack (>= 4.0)
+      activerecord (>= 4.0)
+      multi_json (~> 1.11, >= 1.11.2)
+      rack (>= 1.5.2, < 3)
+      railties (>= 4.0)
+    activesupport (5.1.5)
+      concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (~> 0.7)
       minitest (~> 5.1)
-      thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
     addressable (2.5.2)
       public_suffix (>= 2.0.2, < 4.0)
-    apipie-rails (0.4.0)
-      json
-      rails (>= 4.0)
-    arel (6.0.4)
+    apipie-rails (0.5.6)
+      rails (>= 4.1)
+    arel (8.0.0)
     bootstrap-will_paginate (1.0.0)
       will_paginate
     builder (3.2.3)
-    capybara (2.5.0)
-      mime-types (>= 1.16)
+    byebug (10.0.2)
+    capybara (2.18.0)
+      addressable
+      mini_mime (>= 0.1.3)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
-      xpath (~> 2.0)
-    capybara-webkit (1.7.1)
-      capybara (>= 2.3.0, < 2.6.0)
+      xpath (>= 2.0, < 4.0)
+    capybara-webkit (1.15.0)
+      capybara (>= 2.3, < 4.0)
       json
-    childprocess (0.8.0)
+    childprocess (0.9.0)
       ffi (~> 1.0, >= 1.0.11)
     choice (0.1.6)
     coderay (1.1.2)
+    coffee-rails (4.2.2)
+      coffee-script (>= 2.2.0)
+      railties (>= 4.0.0)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.12.2)
     comma (3.0.4)
     concurrent-ruby (1.0.5)
-    crass (1.0.3)
-    database_cleaner (1.6.2)
+    crass (1.0.4)
+    database_cleaner (1.7.0)
     diff-lcs (1.3)
     dynamic_form (1.1.4)
-    erubis (2.7.0)
-    ffi (1.9.18)
+    erubi (1.7.1)
+    execjs (2.7.0)
+    ffi (1.9.23)
     globalid (0.4.1)
       activesupport (>= 4.2.0)
-    i18n (0.9.3)
+    i18n (0.9.5)
       concurrent-ruby (~> 1.0)
+    jquery-rails (4.3.3)
+      rails-dom-testing (>= 1, < 3)
+      railties (>= 4.2.0)
+      thor (>= 0.14, < 2.0)
+    jquery-ui-rails (6.0.1)
+      railties (>= 3.2.16)
     json (2.1.0)
     json-schema (2.8.0)
       addressable (>= 2.4)
-    loofah (2.1.1)
+    kgio (2.11.2)
+    loofah (2.2.2)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     mail (2.7.0)
       mini_mime (>= 0.1.1)
     memoist (0.16.0)
     method_source (0.9.0)
-    mime-types (3.1)
-      mime-types-data (~> 3.2015)
-    mime-types-data (3.2016.0521)
     mini_mime (1.0.0)
     mini_portile2 (2.3.0)
     minitest (5.11.3)
-    multi_json (1.3.6)
+    multi_json (1.13.1)
     mustache (1.0.5)
     narray (0.6.0.4)
-    nokogiri (1.8.1)
+    nio4r (2.3.0)
+    nokogiri (1.8.2)
       mini_portile2 (~> 2.3.0)
-    passenger (5.1.12)
+    passenger (5.3.4)
       rack
       rake (>= 0.8.1)
-    pg (0.21.0)
-    protected_attributes (1.1.4)
-      activemodel (>= 4.0.1, < 5.0)
+    pg (1.0.0)
+    protected_attributes_continued (1.3.0)
+      activemodel (~> 5.0)
     pry (0.11.3)
       coderay (~> 1.1.0)
       method_source (~> 0.9.0)
-    public_suffix (3.0.1)
-    query_reviewer (0.1.6)
+    pry-byebug (3.6.0)
+      byebug (~> 10.0)
+      pry (~> 0.10)
+    pry-rails (0.3.6)
+      pry (>= 0.10.4)
+    public_suffix (3.0.2)
     rabl (0.13.1)
       activesupport (>= 2.3.14)
-    rack (1.6.8)
-    rack-test (0.6.3)
-      rack (>= 1.0)
+    rack (2.0.5)
+    rack-test (1.0.0)
+      rack (>= 1.0, < 3)
     railroad (0.5.0)
-    rails (4.2.10)
-      actionmailer (= 4.2.10)
-      actionpack (= 4.2.10)
-      actionview (= 4.2.10)
-      activejob (= 4.2.10)
-      activemodel (= 4.2.10)
-      activerecord (= 4.2.10)
-      activesupport (= 4.2.10)
-      bundler (>= 1.3.0, < 2.0)
-      railties (= 4.2.10)
-      sprockets-rails
-    rails-deprecated_sanitizer (1.0.3)
-      activesupport (>= 4.2.0.alpha)
-    rails-dom-testing (1.0.9)
-      activesupport (>= 4.2.0, < 5.0)
-      nokogiri (~> 1.6)
-      rails-deprecated_sanitizer (>= 1.0.1)
-    rails-html-sanitizer (1.0.3)
-      loofah (~> 2.0)
+    rails (5.1.5)
+      actioncable (= 5.1.5)
+      actionmailer (= 5.1.5)
+      actionpack (= 5.1.5)
+      actionview (= 5.1.5)
+      activejob (= 5.1.5)
+      activemodel (= 5.1.5)
+      activerecord (= 5.1.5)
+      activesupport (= 5.1.5)
+      bundler (>= 1.3.0)
+      railties (= 5.1.5)
+      sprockets-rails (>= 2.0.0)
+    rails-controller-testing (1.0.2)
+      actionpack (~> 5.x, >= 5.0.1)
+      actionview (~> 5.x, >= 5.0.1)
+      activesupport (~> 5.x)
+    rails-dom-testing (2.0.3)
+      activesupport (>= 4.2.0)
+      nokogiri (>= 1.6)
+    rails-html-sanitizer (1.0.4)
+      loofah (~> 2.2, >= 2.2.2)
     rails3-restful-authentication (3.0.1)
-    railties (4.2.10)
-      actionpack (= 4.2.10)
-      activesupport (= 4.2.10)
+    railties (5.1.5)
+      actionpack (= 5.1.5)
+      activesupport (= 5.1.5)
+      method_source
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
-    rake (12.3.0)
+    raindrops (0.19.0)
+    rake (12.3.1)
+    rb-fsevent (0.10.3)
+    rb-inotify (0.9.10)
+      ffi (>= 0.5.0, < 2)
     recaptcha (4.8.0)
       json
     rgeo (0.5.3)
-    rgeo-activerecord (4.0.5)
-      activerecord (~> 4.2)
+    rgeo-activerecord (5.1.1)
+      activerecord (~> 5.0)
       rgeo (~> 0.3)
     rspec (3.7.0)
       rspec-core (~> 3.7.0)
@@ -180,7 +196,7 @@ GEM
       rspec-expectations (~> 3.7.0)
       rspec-mocks (~> 3.7.0)
       rspec-support (~> 3.7.0)
-    rspec-support (3.7.0)
+    rspec-support (3.7.1)
     rspec_api_documentation (5.1.0)
       activesupport (>= 3.0.0)
       mustache (~> 1.0, >= 0.99.4)
@@ -189,10 +205,21 @@ GEM
     rubyzip (1.2.1)
     safe_attributes (1.0.10)
       activerecord (>= 3.0.0)
+    sass (3.5.6)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    sass-rails (5.0.7)
+      railties (>= 4.0.0, < 6)
+      sass (~> 3.1)
+      sprockets (>= 2.8, < 4.0)
+      sprockets-rails (>= 2.0, < 4.0)
+      tilt (>= 1.1, < 3)
     seer (0.10.0)
-    selenium-webdriver (3.8.0)
+    selenium-webdriver (3.11.0)
       childprocess (~> 0.5)
-      rubyzip (~> 1.0)
+      rubyzip (~> 1.2)
     sprockets (3.7.1)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
@@ -202,12 +229,21 @@ GEM
       sprockets (>= 3.0.0)
     thor (0.20.0)
     thread_safe (0.3.6)
+    tilt (2.0.8)
     trollop (2.1.2)
-    tzinfo (1.2.4)
+    tzinfo (1.2.5)
       thread_safe (~> 0.1)
+    uglifier (4.1.9)
+      execjs (>= 0.3.0, < 3)
+    unicorn (5.4.0)
+      kgio (~> 2.6)
+      raindrops (~> 0.7)
+    websocket-driver (0.6.5)
+      websocket-extensions (>= 0.1.0)
+    websocket-extensions (0.1.3)
     will_paginate (3.1.6)
-    xpath (2.1.0)
-      nokogiri (~> 1.3)
+    xpath (3.0.0)
+      nokogiri (~> 1.8)
     yajl-ruby (1.3.1)
     yard (0.9.12)
 
@@ -217,30 +253,33 @@ PLATFORMS
 DEPENDENCIES
   activerecord-postgis-adapter
   activerecord-session_store
-  apipie-rails
+  apipie-rails (= 0.5.6)
   bootstrap-will_paginate
-  capybara
-  capybara-webkit (= 1.7.1)
+  capybara (~> 2.8)
+  capybara-webkit (~> 1.7)
   choice (= 0.1.6)
+  coffee-rails
   comma (= 3.0.4)
   database_cleaner
   dynamic_form
+  jquery-rails
+  jquery-ui-rails
   json
   json-schema
   memoist
-  multi_json (= 1.3.6)
+  multi_json
   narray (= 0.6.0.4)
   nokogiri
   passenger
   pg
-  protected_attributes
-  prototype-rails!
-  prototype_legacy_helper (= 0.0.0)!
+  protected_attributes_continued
   pry
-  query_reviewer (= 0.1.6)
+  pry-byebug
+  pry-rails
   rabl
   railroad (= 0.5.0)
-  rails (= 4.2.10)
+  rails (= 5.1.5)
+  rails-controller-testing
   rails3-restful-authentication (~> 3.0.1)
   recaptcha (= 4.8.0)
   rgeo (~> 0.5.0)
@@ -249,10 +288,13 @@ DEPENDENCIES
   ruby-graphviz (= 1.0.8)
   rubyzip (~> 1.2.1)
   safe_attributes
+  sass-rails
   seer (= 0.10.0)
   selenium-webdriver
   trollop
   tzinfo
+  uglifier
+  unicorn
   will_paginate
   yajl-ruby (~> 1.3.1)
   yard
diff --git a/README.md b/README.md
index 69eab408a..00485bd36 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,27 @@ This is the source code for the [Biofuel Ecophysiological Traits and Yields data
 The website is primarily written in Ruby-on-Rails, and has a PostgreSQL backend.
 BETYdb provides an interface for contributing and accessing data, and is the informatics backend for the [Predictive Ecosystem Analyzer (PEcAn)](http://www.pecanproject.org).
 
+## Running BETY using Docker
+
+To get started with BETY you can use the docker-compose.yml file included. This will start the database (postgresql with postgis version 9.5) as well as the BETY container. If this is the first time you start it you will need to initialize the database, this can be done using the following commands:
+
+```
+docker-compose -p bety up -d postgres
+docker run --rm --network bety_bety pecan/bety initialize
+```
+
+Once bety finishes inializing the database, or to restart BETY, you can bring up the all the containers using:
+
+```
+docker-compose -p bety up -d
+```
+
+To change the path BETY runs under you can change the path using the environment variable RAILS_RELATIVE_URL_ROOT, for example to just run bety you can use the following command. This will precompile any of the static assets and run BETY.
+
+```
+docker run -e RAILS_RELATIVE_URL_ROOT="/bety" pecan/bety
+```
+
 ## Documentation.
 
 * Technical Documentation: https://pecan.gitbooks.io/betydb-documentation/content/
diff --git a/Rakefile b/Rakefile
index f01e21ae9..8309d623a 100644
--- a/Rakefile
+++ b/Rakefile
@@ -4,4 +4,4 @@
 require File.expand_path('../config/application', __FILE__)
 require 'rake'
 
-BetyRails3::Application.load_tasks
+BetyRails5::Application.load_tasks
diff --git a/public/images/.gitignore b/app/assets/images/.gitignore
similarity index 100%
rename from public/images/.gitignore
rename to app/assets/images/.gitignore
diff --git a/public/images/4.jpg b/app/assets/images/4.jpg
similarity index 100%
rename from public/images/4.jpg
rename to app/assets/images/4.jpg
diff --git a/public/images/EBI-Logo.jpg b/app/assets/images/EBI-Logo.jpg
similarity index 100%
rename from public/images/EBI-Logo.jpg
rename to app/assets/images/EBI-Logo.jpg
diff --git a/public/images/Sorting icons.psd b/app/assets/images/Sorting icons.psd
similarity index 100%
rename from public/images/Sorting icons.psd
rename to app/assets/images/Sorting icons.psd
diff --git a/public/images/arrow-gr.png b/app/assets/images/arrow-gr.png
similarity index 100%
rename from public/images/arrow-gr.png
rename to app/assets/images/arrow-gr.png
diff --git a/public/images/back_disabled.png b/app/assets/images/back_disabled.png
similarity index 100%
rename from public/images/back_disabled.png
rename to app/assets/images/back_disabled.png
diff --git a/public/images/back_enabled.png b/app/assets/images/back_enabled.png
similarity index 100%
rename from public/images/back_enabled.png
rename to app/assets/images/back_enabled.png
diff --git a/public/images/back_enabled_hover.png b/app/assets/images/back_enabled_hover.png
similarity index 100%
rename from public/images/back_enabled_hover.png
rename to app/assets/images/back_enabled_hover.png
diff --git a/public/images/bety-db.png b/app/assets/images/bety-db.png
similarity index 100%
rename from public/images/bety-db.png
rename to app/assets/images/bety-db.png
diff --git a/public/images/bg-grain-grey.jpg b/app/assets/images/bg-grain-grey.jpg
similarity index 100%
rename from public/images/bg-grain-grey.jpg
rename to app/assets/images/bg-grain-grey.jpg
diff --git a/public/images/bg-nav-item.png b/app/assets/images/bg-nav-item.png
similarity index 100%
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rename to app/assets/images/bg-nav-item.png
diff --git a/public/images/bg-nav.jpg b/app/assets/images/bg-nav.jpg
similarity index 100%
rename from public/images/bg-nav.jpg
rename to app/assets/images/bg-nav.jpg
diff --git a/public/images/blu-circle_maps.png b/app/assets/images/blu-circle_maps.png
similarity index 100%
rename from public/images/blu-circle_maps.png
rename to app/assets/images/blu-circle_maps.png
diff --git a/public/images/blueball.gif b/app/assets/images/blueball.gif
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diff --git a/public/images/blueball.png b/app/assets/images/blueball.png
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diff --git a/public/images/ch_beg_r.gif b/app/assets/images/ch_beg_r.gif
similarity index 100%
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diff --git a/public/images/ch_beg_r.png b/app/assets/images/ch_beg_r.png
similarity index 100%
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similarity index 100%
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rename to app/assets/images/ch_begin.gif
diff --git a/public/images/ch_begin.png b/app/assets/images/ch_begin.png
similarity index 100%
rename from public/images/ch_begin.png
rename to app/assets/images/ch_begin.png
diff --git a/public/images/ch_del_r.gif b/app/assets/images/ch_del_r.gif
similarity index 100%
rename from public/images/ch_del_r.gif
rename to app/assets/images/ch_del_r.gif
diff --git a/public/images/ch_del_r.png b/app/assets/images/ch_del_r.png
similarity index 100%
rename from public/images/ch_del_r.png
rename to app/assets/images/ch_del_r.png
diff --git a/public/images/ch_delet.gif b/app/assets/images/ch_delet.gif
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rename to app/assets/images/check.gif
diff --git a/public/images/citations_new.png b/app/assets/images/citations_new.png
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rename to app/assets/images/citations_new.png
diff --git a/public/images/contents.gif b/app/assets/images/contents.gif
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rename to app/assets/images/eye.png
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diff --git a/public/images/feedback-tab.png b/app/assets/images/feedback-tab.png
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diff --git a/public/images/h/Thumbs.db b/app/assets/images/h/Thumbs.db
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diff --git a/public/images/h/apple-touch-icon.png b/app/assets/images/h/apple-touch-icon.png
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diff --git a/public/images/h/splash.png b/app/assets/images/h/splash.png
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diff --git a/public/images/igb-copy.png b/app/assets/images/igb-copy.png
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diff --git a/public/images/nx_grp_g.gif b/app/assets/images/nx_grp_g.gif
similarity index 100%
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similarity index 100%
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diff --git a/public/images/orangeball.gif b/app/assets/images/orangeball.gif
similarity index 100%
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diff --git a/public/images/orangeball.png b/app/assets/images/orangeball.png
similarity index 100%
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diff --git a/public/images/pinkball.gif b/app/assets/images/pinkball.gif
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diff --git a/public/images/pinkball.png b/app/assets/images/pinkball.png
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diff --git a/public/images/prev.gif b/app/assets/images/prev.gif
similarity index 100%
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diff --git a/public/images/prev.png b/app/assets/images/prev.png
similarity index 100%
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similarity index 100%
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similarity index 100%
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diff --git a/public/images/purpleball.gif b/app/assets/images/purpleball.gif
similarity index 100%
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diff --git a/public/images/purpleball.png b/app/assets/images/purpleball.png
similarity index 100%
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diff --git a/public/images/pv_grp.gif b/app/assets/images/pv_grp.gif
similarity index 100%
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diff --git a/public/images/pv_grp.png b/app/assets/images/pv_grp.png
similarity index 100%
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diff --git a/public/images/pv_grp_g.gif b/app/assets/images/pv_grp_g.gif
similarity index 100%
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diff --git a/public/images/pv_grp_g.png b/app/assets/images/pv_grp_g.png
similarity index 100%
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diff --git a/public/images/question.gif b/app/assets/images/question.gif
similarity index 100%
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diff --git a/public/images/red-circle_maps.png b/app/assets/images/red-circle_maps.png
similarity index 100%
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diff --git a/public/images/redball.gif b/app/assets/images/redball.gif
similarity index 100%
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diff --git a/public/images/redball.png b/app/assets/images/redball.png
similarity index 100%
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diff --git a/public/images/redcheck.png b/app/assets/images/redcheck.png
similarity index 100%
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diff --git a/public/images/register.jpg b/app/assets/images/register.jpg
similarity index 100%
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rename to app/assets/images/register.jpg
diff --git a/public/images/selectedcitation.png b/app/assets/images/selectedcitation.png
similarity index 100%
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rename to app/assets/images/selectedcitation.png
diff --git a/public/images/sites_new.png b/app/assets/images/sites_new.png
similarity index 100%
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diff --git a/public/images/soiltexture.png b/app/assets/images/soiltexture.png
similarity index 100%
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diff --git a/public/images/sort_asc.png b/app/assets/images/sort_asc.png
similarity index 100%
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diff --git a/public/images/sort_asc_disabled.png b/app/assets/images/sort_asc_disabled.png
similarity index 100%
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diff --git a/public/images/sort_both.png b/app/assets/images/sort_both.png
similarity index 100%
rename from public/images/sort_both.png
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diff --git a/public/images/sort_desc.png b/app/assets/images/sort_desc.png
similarity index 100%
rename from public/images/sort_desc.png
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diff --git a/public/images/sort_desc_disabled.png b/app/assets/images/sort_desc_disabled.png
similarity index 100%
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diff --git a/public/images/spinner.gif b/app/assets/images/spinner.gif
similarity index 100%
rename from public/images/spinner.gif
rename to app/assets/images/spinner.gif
diff --git a/public/images/starr2008.png b/app/assets/images/starr2008.png
similarity index 100%
rename from public/images/starr2008.png
rename to app/assets/images/starr2008.png
diff --git a/public/images/theme/bg-grain-grey.jpg b/app/assets/images/theme/bg-grain-grey.jpg
similarity index 100%
rename from public/images/theme/bg-grain-grey.jpg
rename to app/assets/images/theme/bg-grain-grey.jpg
diff --git a/public/images/theme/bg-nav-item.png b/app/assets/images/theme/bg-nav-item.png
similarity index 100%
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diff --git a/public/images/theme/bg-nav.jpg b/app/assets/images/theme/bg-nav.jpg
similarity index 100%
rename from public/images/theme/bg-nav.jpg
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diff --git a/public/images/theme/drop-over.png b/app/assets/images/theme/drop-over.png
similarity index 100%
rename from public/images/theme/drop-over.png
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diff --git a/public/images/theme/drop.png b/app/assets/images/theme/drop.png
similarity index 100%
rename from public/images/theme/drop.png
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diff --git a/public/images/theme/drop2.png b/app/assets/images/theme/drop2.png
similarity index 100%
rename from public/images/theme/drop2.png
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diff --git a/public/images/theme/logo-berkeley.png b/app/assets/images/theme/logo-berkeley.png
similarity index 100%
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diff --git a/public/images/theme/logo-bp.png b/app/assets/images/theme/logo-bp.png
similarity index 100%
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diff --git a/public/images/theme/logo-ebi-footer.jpg b/app/assets/images/theme/logo-ebi-footer.jpg
similarity index 100%
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diff --git a/public/images/theme/logo-ebi.png b/app/assets/images/theme/logo-ebi.png
similarity index 100%
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diff --git a/public/images/theme/logo-illinois.png b/app/assets/images/theme/logo-illinois.png
similarity index 100%
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diff --git a/public/images/theme/logo-lbl.png b/app/assets/images/theme/logo-lbl.png
similarity index 100%
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diff --git a/public/images/theme/nav-icon-admin.png b/app/assets/images/theme/nav-icon-admin.png
similarity index 100%
rename from public/images/theme/nav-icon-admin.png
rename to app/assets/images/theme/nav-icon-admin.png
diff --git a/public/images/theme/nav-icon-data.png b/app/assets/images/theme/nav-icon-data.png
similarity index 100%
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diff --git a/public/images/theme/nav-icon-docs.png b/app/assets/images/theme/nav-icon-docs.png
similarity index 100%
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diff --git a/public/images/theme/nav-icon-home.png b/app/assets/images/theme/nav-icon-home.png
similarity index 100%
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diff --git a/public/images/theme/nav-icon-logout.png b/app/assets/images/theme/nav-icon-logout.png
similarity index 100%
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diff --git a/public/images/theme/nav-icon-maps.png b/app/assets/images/theme/nav-icon-maps.png
similarity index 100%
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diff --git a/public/images/theme/nav-icon-new.png b/app/assets/images/theme/nav-icon-new.png
similarity index 100%
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diff --git a/public/images/theme/nav-separator.png b/app/assets/images/theme/nav-separator.png
similarity index 100%
rename from public/images/theme/nav-separator.png
rename to app/assets/images/theme/nav-separator.png
diff --git a/public/images/traits_new.png b/app/assets/images/traits_new.png
similarity index 100%
rename from public/images/traits_new.png
rename to app/assets/images/traits_new.png
diff --git a/public/images/treatment_new.png b/app/assets/images/treatment_new.png
similarity index 100%
rename from public/images/treatment_new.png
rename to app/assets/images/treatment_new.png
diff --git a/public/images/treatments_managements.png b/app/assets/images/treatments_managements.png
similarity index 100%
rename from public/images/treatments_managements.png
rename to app/assets/images/treatments_managements.png
diff --git a/public/images/uncheck.gif b/app/assets/images/uncheck.gif
similarity index 100%
rename from public/images/uncheck.gif
rename to app/assets/images/uncheck.gif
diff --git a/public/images/up.gif b/app/assets/images/up.gif
similarity index 100%
rename from public/images/up.gif
rename to app/assets/images/up.gif
diff --git a/public/images/up.png b/app/assets/images/up.png
similarity index 100%
rename from public/images/up.png
rename to app/assets/images/up.png
diff --git a/public/images/up_arrow.gif b/app/assets/images/up_arrow.gif
similarity index 100%
rename from public/images/up_arrow.gif
rename to app/assets/images/up_arrow.gif
diff --git a/public/images/up_g.gif b/app/assets/images/up_g.gif
similarity index 100%
rename from public/images/up_g.gif
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diff --git a/public/images/up_g.png b/app/assets/images/up_g.png
similarity index 100%
rename from public/images/up_g.png
rename to app/assets/images/up_g.png
diff --git a/public/images/update.jpg b/app/assets/images/update.jpg
similarity index 100%
rename from public/images/update.jpg
rename to app/assets/images/update.jpg
diff --git a/public/images/whiteball.gif b/app/assets/images/whiteball.gif
similarity index 100%
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diff --git a/public/images/whiteball.png b/app/assets/images/whiteball.png
similarity index 100%
rename from public/images/whiteball.png
rename to app/assets/images/whiteball.png
diff --git a/public/images/yellowball.gif b/app/assets/images/yellowball.gif
similarity index 100%
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diff --git a/public/images/yellowball.png b/app/assets/images/yellowball.png
similarity index 100%
rename from public/images/yellowball.png
rename to app/assets/images/yellowball.png
diff --git a/public/images/yield_maps/bz_sugarcane.png b/app/assets/images/yield_maps/bz_sugarcane.png
similarity index 100%
rename from public/images/yield_maps/bz_sugarcane.png
rename to app/assets/images/yield_maps/bz_sugarcane.png
diff --git a/public/images/yield_maps/us_miscanthus.png b/app/assets/images/yield_maps/us_miscanthus.png
similarity index 100%
rename from public/images/yield_maps/us_miscanthus.png
rename to app/assets/images/yield_maps/us_miscanthus.png
diff --git a/public/images/yields_new.png b/app/assets/images/yields_new.png
similarity index 100%
rename from public/images/yields_new.png
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diff --git a/public/images/ylw-circle_maps.png b/app/assets/images/ylw-circle_maps.png
similarity index 100%
rename from public/images/ylw-circle_maps.png
rename to app/assets/images/ylw-circle_maps.png
diff --git a/app/assets/javascripts/application.js b/app/assets/javascripts/application.js
new file mode 100644
index 000000000..66d868d2d
--- /dev/null
+++ b/app/assets/javascripts/application.js
@@ -0,0 +1,21 @@
+// Place your application-specific JavaScript functions and classes here
+// This file is automatically included by javascript_include_tag :defaults
+
+//= require jquery
+//= require rails-ujs
+//= require jquery-ui
+
+// Remove conflicting definition of $ before loading Prototype:
+//= require noconflict
+
+// defines Form:
+//= require prototype
+
+// defines Effect
+//= require effects
+
+// defines showHide
+//= require min
+
+//= require lazy/simple_search
+//= require lazy/application
diff --git a/public/javascripts/bootstrap.js b/app/assets/javascripts/bootstrap.js
similarity index 100%
rename from public/javascripts/bootstrap.js
rename to app/assets/javascripts/bootstrap.js
diff --git a/public/javascripts/cache/all.js-sample b/app/assets/javascripts/cache/all.js-sample
similarity index 100%
rename from public/javascripts/cache/all.js-sample
rename to app/assets/javascripts/cache/all.js-sample
diff --git a/public/javascripts/controls.js b/app/assets/javascripts/controls.js
similarity index 100%
rename from public/javascripts/controls.js
rename to app/assets/javascripts/controls.js
diff --git a/public/javascripts/dragdrop.js b/app/assets/javascripts/dragdrop.js
similarity index 100%
rename from public/javascripts/dragdrop.js
rename to app/assets/javascripts/dragdrop.js
diff --git a/public/javascripts/effects.js b/app/assets/javascripts/effects.js
similarity index 100%
rename from public/javascripts/effects.js
rename to app/assets/javascripts/effects.js
diff --git a/public/javascripts/lazy/application.js b/app/assets/javascripts/lazy/application.js
similarity index 100%
rename from public/javascripts/lazy/application.js
rename to app/assets/javascripts/lazy/application.js
diff --git a/public/javascripts/lazy/autocomplete.js b/app/assets/javascripts/lazy/autocomplete.js
similarity index 100%
rename from public/javascripts/lazy/autocomplete.js
rename to app/assets/javascripts/lazy/autocomplete.js
diff --git a/public/javascripts/lazy/bulk_upload.js b/app/assets/javascripts/lazy/bulk_upload.js
similarity index 100%
rename from public/javascripts/lazy/bulk_upload.js
rename to app/assets/javascripts/lazy/bulk_upload.js
diff --git a/public/javascripts/lazy/feedback.js b/app/assets/javascripts/lazy/feedback.js
similarity index 100%
rename from public/javascripts/lazy/feedback.js
rename to app/assets/javascripts/lazy/feedback.js
diff --git a/public/javascripts/lazy/jquery-1.11.0.js b/app/assets/javascripts/lazy/jquery-1.11.0.js
similarity index 100%
rename from public/javascripts/lazy/jquery-1.11.0.js
rename to app/assets/javascripts/lazy/jquery-1.11.0.js
diff --git a/public/javascripts/lazy/jquery-1.11.0.min.js b/app/assets/javascripts/lazy/jquery-1.11.0.min.js
similarity index 100%
rename from public/javascripts/lazy/jquery-1.11.0.min.js
rename to app/assets/javascripts/lazy/jquery-1.11.0.min.js
diff --git a/public/javascripts/lazy/jquery-1.7.2.js b/app/assets/javascripts/lazy/jquery-1.7.2.js
similarity index 100%
rename from public/javascripts/lazy/jquery-1.7.2.js
rename to app/assets/javascripts/lazy/jquery-1.7.2.js
diff --git a/public/javascripts/lazy/jquery-ui-1.10.4.min.js b/app/assets/javascripts/lazy/jquery-ui-1.10.4.min.js
similarity index 100%
rename from public/javascripts/lazy/jquery-ui-1.10.4.min.js
rename to app/assets/javascripts/lazy/jquery-ui-1.10.4.min.js
diff --git a/public/javascripts/lazy/login.js b/app/assets/javascripts/lazy/login.js
similarity index 100%
rename from public/javascripts/lazy/login.js
rename to app/assets/javascripts/lazy/login.js
diff --git a/public/javascripts/lazy/map_search.js b/app/assets/javascripts/lazy/map_search.js
similarity index 100%
rename from public/javascripts/lazy/map_search.js
rename to app/assets/javascripts/lazy/map_search.js
diff --git a/public/javascripts/lazy/schemaSpy.js b/app/assets/javascripts/lazy/schemaSpy.js
similarity index 100%
rename from public/javascripts/lazy/schemaSpy.js
rename to app/assets/javascripts/lazy/schemaSpy.js
diff --git a/public/javascripts/lazy/simple_search.js b/app/assets/javascripts/lazy/simple_search.js
similarity index 100%
rename from public/javascripts/lazy/simple_search.js
rename to app/assets/javascripts/lazy/simple_search.js
diff --git a/public/javascripts/libs/imgsizer.js b/app/assets/javascripts/libs/imgsizer.js
similarity index 100%
rename from public/javascripts/libs/imgsizer.js
rename to app/assets/javascripts/libs/imgsizer.js
diff --git a/public/javascripts/libs/jquery-1.6.2.min.js b/app/assets/javascripts/libs/jquery-1.6.2.min.js
similarity index 100%
rename from public/javascripts/libs/jquery-1.6.2.min.js
rename to app/assets/javascripts/libs/jquery-1.6.2.min.js
diff --git a/public/javascripts/libs/jquery-1.7.2.min.js b/app/assets/javascripts/libs/jquery-1.7.2.min.js
similarity index 100%
rename from public/javascripts/libs/jquery-1.7.2.min.js
rename to app/assets/javascripts/libs/jquery-1.7.2.min.js
diff --git a/public/javascripts/libs/jquery-1.8.1.min.js b/app/assets/javascripts/libs/jquery-1.8.1.min.js
similarity index 100%
rename from public/javascripts/libs/jquery-1.8.1.min.js
rename to app/assets/javascripts/libs/jquery-1.8.1.min.js
diff --git a/public/javascripts/libs/jquery-migrate-1.2.1.js b/app/assets/javascripts/libs/jquery-migrate-1.2.1.js
similarity index 100%
rename from public/javascripts/libs/jquery-migrate-1.2.1.js
rename to app/assets/javascripts/libs/jquery-migrate-1.2.1.js
diff --git a/public/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-1.10.2.js b/app/assets/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-1.10.2.js
similarity index 100%
rename from public/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-1.10.2.js
rename to app/assets/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-1.10.2.js
diff --git a/public/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.js b/app/assets/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.js
similarity index 100%
rename from public/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.js
rename to app/assets/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.js
diff --git a/public/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.min.js b/app/assets/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.min.js
similarity index 100%
rename from public/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.min.js
rename to app/assets/javascripts/libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.min.js
diff --git a/public/javascripts/libs/jquery.autocomplete.js b/app/assets/javascripts/libs/jquery.autocomplete.js
similarity index 100%
rename from public/javascripts/libs/jquery.autocomplete.js
rename to app/assets/javascripts/libs/jquery.autocomplete.js
diff --git a/public/javascripts/libs/jquery.dataTables.min.js b/app/assets/javascripts/libs/jquery.dataTables.min.js
similarity index 100%
rename from public/javascripts/libs/jquery.dataTables.min.js
rename to app/assets/javascripts/libs/jquery.dataTables.min.js
diff --git a/public/javascripts/libs/jquery.js b/app/assets/javascripts/libs/jquery.js
similarity index 100%
rename from public/javascripts/libs/jquery.js
rename to app/assets/javascripts/libs/jquery.js
diff --git a/public/javascripts/libs/modernizr-2.0.6.min.js b/app/assets/javascripts/libs/modernizr-2.0.6.min.js
similarity index 100%
rename from public/javascripts/libs/modernizr-2.0.6.min.js
rename to app/assets/javascripts/libs/modernizr-2.0.6.min.js
diff --git a/public/javascripts/libs/respond.min.js b/app/assets/javascripts/libs/respond.min.js
similarity index 100%
rename from public/javascripts/libs/respond.min.js
rename to app/assets/javascripts/libs/respond.min.js
diff --git a/public/javascripts/libs/selectivizr-min.js b/app/assets/javascripts/libs/selectivizr-min.js
similarity index 100%
rename from public/javascripts/libs/selectivizr-min.js
rename to app/assets/javascripts/libs/selectivizr-min.js
diff --git a/public/javascripts/min.js b/app/assets/javascripts/min.js
similarity index 100%
rename from public/javascripts/min.js
rename to app/assets/javascripts/min.js
diff --git a/public/javascripts/mylibs/helper.js b/app/assets/javascripts/mylibs/helper.js
similarity index 100%
rename from public/javascripts/mylibs/helper.js
rename to app/assets/javascripts/mylibs/helper.js
diff --git a/public/javascripts/mylibs/imgSizer.js b/app/assets/javascripts/mylibs/imgSizer.js
similarity index 100%
rename from public/javascripts/mylibs/imgSizer.js
rename to app/assets/javascripts/mylibs/imgSizer.js
diff --git a/public/javascripts/mylibs/maps.js b/app/assets/javascripts/mylibs/maps.js
similarity index 100%
rename from public/javascripts/mylibs/maps.js
rename to app/assets/javascripts/mylibs/maps.js
diff --git a/app/assets/javascripts/noconflict.js b/app/assets/javascripts/noconflict.js
new file mode 100644
index 000000000..f4b1f44e8
--- /dev/null
+++ b/app/assets/javascripts/noconflict.js
@@ -0,0 +1 @@
+jQuery.noConflict();
diff --git a/public/javascripts/plugins.js b/app/assets/javascripts/plugins.js
similarity index 100%
rename from public/javascripts/plugins.js
rename to app/assets/javascripts/plugins.js
diff --git a/public/javascripts/prototype.js b/app/assets/javascripts/prototype.js
similarity index 100%
rename from public/javascripts/prototype.js
rename to app/assets/javascripts/prototype.js
diff --git a/public/javascripts/rails.js b/app/assets/javascripts/rails.js
similarity index 100%
rename from public/javascripts/rails.js
rename to app/assets/javascripts/rails.js
diff --git a/public/javascripts/rails.js.bak b/app/assets/javascripts/rails.js.bak
similarity index 100%
rename from public/javascripts/rails.js.bak
rename to app/assets/javascripts/rails.js.bak
diff --git a/public/javascripts/script.js b/app/assets/javascripts/script.js
similarity index 100%
rename from public/javascripts/script.js
rename to app/assets/javascripts/script.js
diff --git a/public/javascripts/window.js b/app/assets/javascripts/window.js
similarity index 100%
rename from public/javascripts/window.js
rename to app/assets/javascripts/window.js
diff --git a/public/stylesheets/.gitkeep b/app/assets/stylesheets/.gitkeep
similarity index 100%
rename from public/stylesheets/.gitkeep
rename to app/assets/stylesheets/.gitkeep
diff --git a/app/assets/stylesheets/application.css b/app/assets/stylesheets/application.css
new file mode 100644
index 000000000..fc0b14604
--- /dev/null
+++ b/app/assets/stylesheets/application.css
@@ -0,0 +1,25 @@
+/*
+ * This is a manifest file that'll be compiled into application.css, which will include all the files
+ * listed below.
+ *
+ * Any CSS and SCSS file within this directory, lib/assets/stylesheets, or any plugin's
+ * vendor/assets/stylesheets directory can be referenced here using a relative path.
+ *
+ * You're free to add application-wide styles to this file and they'll appear at the bottom of the
+ * compiled file so the styles you add here take precedence over styles defined in any other CSS/SCSS
+ * files in this directory. Styles in this file should be added after the last require_* statement.
+ * It is generally better to create a new file per style scope.
+ *
+ * =require jquery-ui-1.10.4.min
+ * =require themes/default
+ * =require themes/alphacube
+ * =require scaffold
+ * =require base
+ * =require grid
+ * =require layout
+ * =require dropdown
+ * =require tables
+ * =require demo
+ * =require jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css
+ * =require_self
+ */
diff --git a/public/stylesheets/base.css b/app/assets/stylesheets/base.css.erb
similarity index 99%
rename from public/stylesheets/base.css
rename to app/assets/stylesheets/base.css.erb
index bb007ce18..7e3cc9bb5 100755
--- a/public/stylesheets/base.css
+++ b/app/assets/stylesheets/base.css.erb
@@ -1698,7 +1698,7 @@ table th[class*="span"],
 	*margin-right: .3em;
 	line-height: 14px;
 	vertical-align: text-top;
-	background-image: url("../images/glyphicons-halflings.png");
+	background-image: url(<%= asset_path("glyphicons-halflings.png") %>);
 	background-position: 14px 14px;
 	background-repeat: no-repeat;
 }
@@ -1718,7 +1718,7 @@ table th[class*="span"],
 .dropdown-menu > .active > a > [class*=" icon-"],
 .dropdown-submenu:hover > a > [class^="icon-"],
 .dropdown-submenu:hover > a > [class*=" icon-"] {
-	background-image: url("../images/glyphicons-halflings-white.png");
+	background-image: url(<%= asset_path("glyphicons-halflings-white.png") %>);
 }
 
 .icon-glass {
diff --git a/public/stylesheets/bulk_upload.css b/app/assets/stylesheets/bulk_upload.css
similarity index 100%
rename from public/stylesheets/bulk_upload.css
rename to app/assets/stylesheets/bulk_upload.css
diff --git a/public/stylesheets/demo.css b/app/assets/stylesheets/demo.css
similarity index 100%
rename from public/stylesheets/demo.css
rename to app/assets/stylesheets/demo.css
diff --git a/public/stylesheets/dropdown.css b/app/assets/stylesheets/dropdown.css.erb
similarity index 89%
rename from public/stylesheets/dropdown.css
rename to app/assets/stylesheets/dropdown.css.erb
index 7ec3e9b63..db7597988 100755
--- a/public/stylesheets/dropdown.css
+++ b/app/assets/stylesheets/dropdown.css.erb
@@ -148,7 +148,7 @@ ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul{
         width: 12.5%; /* this will need to be adjusted for your needs */
         height: 69px;
 		background-color: transparent;
-    	background-image: url('../images/nav-separator.png');
+    	background-image: url(<%= asset_path('nav-separator.png') %>);
 		background-position: 0 0;
 		background-repeat: repeat-y;
     }
@@ -169,7 +169,7 @@ ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul{
     /* new style for drop list items */
     .main-menu li li {
         background: #000;
-    	background-image: url('../images/nav-separator.png');
+    	background-image: url(<%= asset_path('nav-separator.png') %>);
         background-repeat: repeat-y;
         clear: left;
         width: 100%;
@@ -227,31 +227,31 @@ ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul{
 		font-size: 14px;
     }
 	.main-menu li.menu-home > a {
-		background: transparent url(../images/nav-icon-home.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-home.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-docs > a {
-		background: transparent url(../images/nav-icon-docs.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-docs.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-maps > a {
-		background: transparent url(../images/nav-icon-maps.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-maps.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-data > a {
-		background: transparent url(../images/nav-icon-data.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-data.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-new > a {
-		background: transparent url(../images/nav-icon-new.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-new.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-admin > a {
-		background: transparent url(../images/nav-icon-admin.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-admin.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-login > a {
-		background: transparent url(../images/nav-icon-logout.png) 100% 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-logout.png") %>) 100% 41px no-repeat;
 		width: 84%;
 		padding-right: 23px;
 	}
diff --git a/public/stylesheets/font-awesome.min.css b/app/assets/stylesheets/font-awesome.min.css
similarity index 100%
rename from public/stylesheets/font-awesome.min.css
rename to app/assets/stylesheets/font-awesome.min.css
diff --git a/public/stylesheets/grid.css b/app/assets/stylesheets/grid.css
similarity index 100%
rename from public/stylesheets/grid.css
rename to app/assets/stylesheets/grid.css
diff --git a/public/stylesheets/images/ui-bg_gloss-wave_35_f6a828_500x100.png b/app/assets/stylesheets/images/ui-bg_gloss-wave_35_f6a828_500x100.png
similarity index 100%
rename from public/stylesheets/images/ui-bg_gloss-wave_35_f6a828_500x100.png
rename to app/assets/stylesheets/images/ui-bg_gloss-wave_35_f6a828_500x100.png
diff --git a/public/stylesheets/images/ui-bg_highlight-soft_100_eeeeee_1x100.png b/app/assets/stylesheets/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
similarity index 100%
rename from public/stylesheets/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
rename to app/assets/stylesheets/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/animated-overlay.gif b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/animated-overlay.gif
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/animated-overlay.gif
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/animated-overlay.gif
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_flat_10_000000_40x100.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_flat_10_000000_40x100.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_flat_10_000000_40x100.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_flat_10_000000_40x100.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_222222_256x240.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_222222_256x240.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_222222_256x240.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_222222_256x240.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_228ef1_256x240.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_228ef1_256x240.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_228ef1_256x240.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_228ef1_256x240.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ef8c08_256x240.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ef8c08_256x240.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ef8c08_256x240.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ef8c08_256x240.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ffd27a_256x240.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ffd27a_256x240.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ffd27a_256x240.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ffd27a_256x240.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ffffff_256x240.png b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ffffff_256x240.png
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ffffff_256x240.png
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/images/ui-icons_ffffff_256x240.png
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css
diff --git a/public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.min.css b/app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.min.css
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.min.css
rename to app/assets/stylesheets/jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.min.css
diff --git a/public/stylesheets/jquery-ui-1.10.4.min.css b/app/assets/stylesheets/jquery-ui-1.10.4.min.css
similarity index 100%
rename from public/stylesheets/jquery-ui-1.10.4.min.css
rename to app/assets/stylesheets/jquery-ui-1.10.4.min.css
diff --git a/public/stylesheets/layout.css b/app/assets/stylesheets/layout.css.erb
similarity index 94%
rename from public/stylesheets/layout.css
rename to app/assets/stylesheets/layout.css.erb
index 4673a9591..5eeedd3dd 100755
--- a/public/stylesheets/layout.css
+++ b/app/assets/stylesheets/layout.css.erb
@@ -96,8 +96,7 @@ line-height:normal;
 		bottom: 0;
 		right: 0;
 		height: 80px;
-		width: 80px;
-		background: url(../../stylesheets/images/resize.png); }
+		width: 80px; }
 
 
 	img {
@@ -250,7 +249,7 @@ Bootstrap Styles
 }
 
 .header {
-	background: #dfdfdf url("../images/bg-grain-grey.jpg") top left repeat;
+	background: #dfdfdf url(<%= asset_path("bg-grain-grey.jpg") %>) top left repeat;
 	text-shadow: 0px 1px 1px rgba(255,255,255,1);
 }
 .header h1 {
@@ -273,7 +272,7 @@ Bootstrap Styles
 	width: 100px;
 	text-align: right;
 	display: inline-block;
-	background: url(../images/logo-ebi.png) top right no-repeat;
+	background: url(<%= asset_path("logo-ebi.png") %>) top right no-repeat;
 	padding-right: 45px;
 	height: 46px;
 	padding-top: 4px;
@@ -300,7 +299,7 @@ Bootstrap Styles
 	color: #444;
 }
 body > .nav {
-	background: #505050 url("../images/bg-nav.jpg") top left repeat-x;
+	background: #505050 url(<%= asset_path("bg-nav.jpg") %>) top left repeat-x;
 	color: #fff;
 	height: 75px;
 	padding-top: 6px;
@@ -383,7 +382,7 @@ body > .nav {
 }
 .sidenav .active .icon-chevron-right,
 .sidenav .active a:hover .icon-chevron-right {
-  background-image: url(../images/glyphicons-halflings-white.png);
+  background-image: url(<%= asset_path("glyphicons-halflings-white.png") %>);
   opacity: 1;
 }
 .sidenav.affix {
@@ -463,7 +462,7 @@ border-bottom-color: transparent;
 	padding-top: 40px;
 	line-height: 13px;
 	font-size: 11px;
-	background: url("../images/logo-ebi-footer.jpg") top center no-repeat;
+	background: url(<%= asset_path("logo-ebi-footer.jpg") %>) top center no-repeat;
 }
 .footer .six.columns.omega p:first-child {
 	margin-bottom: 10px;
@@ -612,22 +611,22 @@ border-bottom-color: transparent;
 		  overflow: hidden;
 	  }
 	  .footer .footnotes a.illinois {
-		  background: url(../images/logo-illinois.png) 0 0 no-repeat;
+		  background: url(<%= asset_path("logo-illinois.png") %>) 0 0 no-repeat;
 		  width: 246px;
 	  
 	  }
 	  .footer .footnotes a.berkeley {
-		  background: url(../images/logo-berkeley.png) 0 0 no-repeat;
+		  background: url(<%= asset_path("logo-berkeley.png") %>) 0 0 no-repeat;
 		  width: 145px;
 		  margin-left: 20%;
 	  }
 	  .footer .footnotes a.lbl {
-		  background: url(../images/logo-lbl.png) 0 0 no-repeat;
+		  background: url(<%= asset_path("logo-lbl.png") %>) 0 0 no-repeat;
 		  width: 232px;
 	  
 	  }
 	  .footer .footnotes a.bp {
-		  background: url(../images/logo-bp.png) 0 0 no-repeat;
+		  background: url(<%= asset_path("logo-bp.png") %>) 0 0 no-repeat;
 		  width: 54px;
 		  margin-right: 40%;
 	  }
diff --git a/public/stylesheets/mobile.css b/app/assets/stylesheets/mobile.css
similarity index 100%
rename from public/stylesheets/mobile.css
rename to app/assets/stylesheets/mobile.css
diff --git a/public/stylesheets/scaffold.css b/app/assets/stylesheets/scaffold.css
similarity index 99%
rename from public/stylesheets/scaffold.css
rename to app/assets/stylesheets/scaffold.css
index d1bc40749..a649d0da2 100644
--- a/public/stylesheets/scaffold.css
+++ b/app/assets/stylesheets/scaffold.css
@@ -225,7 +225,7 @@ div#banner a.logo {
   width: 213px;
   height: 109px;
   text-indent: -9999em;
- top left no-repeat;
+  background: top left no-repeat;
 }
 
 div#banner a.bety-db {
diff --git a/public/stylesheets/schemaSpy.css b/app/assets/stylesheets/schemaSpy.css
similarity index 100%
rename from public/stylesheets/schemaSpy.css
rename to app/assets/stylesheets/schemaSpy.css
diff --git a/public/stylesheets/tables.css b/app/assets/stylesheets/tables.css.erb
similarity index 93%
rename from public/stylesheets/tables.css
rename to app/assets/stylesheets/tables.css.erb
index ddaaa2df5..20210e590 100755
--- a/public/stylesheets/tables.css
+++ b/app/assets/stylesheets/tables.css.erb
@@ -110,25 +110,25 @@ div.dataTables_filter label {
 }
 
 .paginate_disabled_previous {
-	background: url('../images/back_disabled.png') no-repeat top left;
+	background: url(<%= asset_path("back_disabled.png") %>) no-repeat top left;
 }
 
 .paginate_enabled_previous {
-	background: url('../images/back_enabled.png') no-repeat top left;
+	background: url(<%= asset_path("back_enabled.png") %>) no-repeat top left;
 }
 .paginate_enabled_previous:hover {
-	background: url('../images/back_enabled_hover.png') no-repeat top left;
+	background: url(<%= asset_path("back_enabled_hover.png") %>) no-repeat top left;
 }
 
 .paginate_disabled_next {
-	background: url('../images/forward_disabled.png') no-repeat top right;
+	background: url(<%= asset_path("forward_disabled.png") %>) no-repeat top right;
 }
 
 .paginate_enabled_next {
-	background: url('../images/forward_enabled.png') no-repeat top right;
+	background: url(<%= asset_path("forward_enabled.png") %>) no-repeat top right;
 }
 .paginate_enabled_next:hover {
-	background: url('../images/forward_enabled_hover.png') no-repeat top right;
+	background: url(<%= asset_path("forward_enabled_hover.png") %>) no-repeat top right;
 }
 
 
@@ -239,27 +239,27 @@ table.table thead .sorting_desc_disabled {
 	*cursor: hand;
 }
 table.table .sorting_asc {
-	background: url('../images/sort_asc.png') no-repeat center right;
+	background: url(<%= asset_path("sort_asc.png") %>) no-repeat center right;
 	
 	color: #007eac;
 }
 
 table.table .sorting_desc {
-	background: url('../images/sort_desc.png') no-repeat center right;
+	background: url(<%= asset_path("sort_desc.png") %>) no-repeat center right;
 	
 	color: #007eac;
 }
 
 table.table .sorting {
-	background: url('../images/sort_both.png') no-repeat center right;
+	background: url(<%= asset_path("sort_both.png") %>) no-repeat center right;
 }
 
 table.table .sorting_asc_disabled {
-	background: url('../images/sort_asc_disabled.png') no-repeat center right;
+	background: url(<%= asset_path("sort_asc_disabled.png") %>) no-repeat center right;
 }
 
 table.table .sorting_desc_disabled {
-	background: url('../images/sort_desc_disabled.png') no-repeat center right;
+	background: url(<%= asset_path("sort_desc_disabled.png") %>) no-repeat center right;
 }
  
 table.table thead th:active,
diff --git a/public/stylesheets/themes/alert.css b/app/assets/stylesheets/themes/alert.css
similarity index 100%
rename from public/stylesheets/themes/alert.css
rename to app/assets/stylesheets/themes/alert.css
diff --git a/public/stylesheets/themes/alert/bottom.gif b/app/assets/stylesheets/themes/alert/bottom.gif
similarity index 100%
rename from public/stylesheets/themes/alert/bottom.gif
rename to app/assets/stylesheets/themes/alert/bottom.gif
diff --git a/public/stylesheets/themes/alert/bottom_left.gif b/app/assets/stylesheets/themes/alert/bottom_left.gif
similarity index 100%
rename from public/stylesheets/themes/alert/bottom_left.gif
rename to app/assets/stylesheets/themes/alert/bottom_left.gif
diff --git a/public/stylesheets/themes/alert/bottom_right.gif b/app/assets/stylesheets/themes/alert/bottom_right.gif
similarity index 100%
rename from public/stylesheets/themes/alert/bottom_right.gif
rename to app/assets/stylesheets/themes/alert/bottom_right.gif
diff --git a/public/stylesheets/themes/alert/left.gif b/app/assets/stylesheets/themes/alert/left.gif
similarity index 100%
rename from public/stylesheets/themes/alert/left.gif
rename to app/assets/stylesheets/themes/alert/left.gif
diff --git a/public/stylesheets/themes/alert/overlay.png b/app/assets/stylesheets/themes/alert/overlay.png
similarity index 100%
rename from public/stylesheets/themes/alert/overlay.png
rename to app/assets/stylesheets/themes/alert/overlay.png
diff --git a/public/stylesheets/themes/alert/progress.gif b/app/assets/stylesheets/themes/alert/progress.gif
similarity index 100%
rename from public/stylesheets/themes/alert/progress.gif
rename to app/assets/stylesheets/themes/alert/progress.gif
diff --git a/public/stylesheets/themes/alert/right.gif b/app/assets/stylesheets/themes/alert/right.gif
similarity index 100%
rename from public/stylesheets/themes/alert/right.gif
rename to app/assets/stylesheets/themes/alert/right.gif
diff --git a/public/stylesheets/themes/alert/top.gif b/app/assets/stylesheets/themes/alert/top.gif
similarity index 100%
rename from public/stylesheets/themes/alert/top.gif
rename to app/assets/stylesheets/themes/alert/top.gif
diff --git a/public/stylesheets/themes/alert/top_left.gif b/app/assets/stylesheets/themes/alert/top_left.gif
similarity index 100%
rename from public/stylesheets/themes/alert/top_left.gif
rename to app/assets/stylesheets/themes/alert/top_left.gif
diff --git a/public/stylesheets/themes/alert/top_right.gif b/app/assets/stylesheets/themes/alert/top_right.gif
similarity index 100%
rename from public/stylesheets/themes/alert/top_right.gif
rename to app/assets/stylesheets/themes/alert/top_right.gif
diff --git a/public/stylesheets/themes/alert_lite.css b/app/assets/stylesheets/themes/alert_lite.css
similarity index 100%
rename from public/stylesheets/themes/alert_lite.css
rename to app/assets/stylesheets/themes/alert_lite.css
diff --git a/public/stylesheets/themes/alphacube.css b/app/assets/stylesheets/themes/alphacube.css
similarity index 100%
rename from public/stylesheets/themes/alphacube.css
rename to app/assets/stylesheets/themes/alphacube.css
diff --git a/public/stylesheets/themes/alphacube/bottom-left-c.gif b/app/assets/stylesheets/themes/alphacube/bottom-left-c.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/bottom-left-c.gif
rename to app/assets/stylesheets/themes/alphacube/bottom-left-c.gif
diff --git a/public/stylesheets/themes/alphacube/bottom-middle.gif b/app/assets/stylesheets/themes/alphacube/bottom-middle.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/bottom-middle.gif
rename to app/assets/stylesheets/themes/alphacube/bottom-middle.gif
diff --git a/public/stylesheets/themes/alphacube/bottom-right-c.gif b/app/assets/stylesheets/themes/alphacube/bottom-right-c.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/bottom-right-c.gif
rename to app/assets/stylesheets/themes/alphacube/bottom-right-c.gif
diff --git a/public/stylesheets/themes/alphacube/button-close-focus.gif b/app/assets/stylesheets/themes/alphacube/button-close-focus.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/button-close-focus.gif
rename to app/assets/stylesheets/themes/alphacube/button-close-focus.gif
diff --git a/public/stylesheets/themes/alphacube/button-max-focus.gif b/app/assets/stylesheets/themes/alphacube/button-max-focus.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/button-max-focus.gif
rename to app/assets/stylesheets/themes/alphacube/button-max-focus.gif
diff --git a/public/stylesheets/themes/alphacube/button-min-focus.gif b/app/assets/stylesheets/themes/alphacube/button-min-focus.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/button-min-focus.gif
rename to app/assets/stylesheets/themes/alphacube/button-min-focus.gif
diff --git a/public/stylesheets/themes/alphacube/frame-left.gif b/app/assets/stylesheets/themes/alphacube/frame-left.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/frame-left.gif
rename to app/assets/stylesheets/themes/alphacube/frame-left.gif
diff --git a/public/stylesheets/themes/alphacube/frame-right.gif b/app/assets/stylesheets/themes/alphacube/frame-right.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/frame-right.gif
rename to app/assets/stylesheets/themes/alphacube/frame-right.gif
diff --git a/public/stylesheets/themes/alphacube/left-top.gif b/app/assets/stylesheets/themes/alphacube/left-top.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/left-top.gif
rename to app/assets/stylesheets/themes/alphacube/left-top.gif
diff --git a/public/stylesheets/themes/alphacube/right-top.gif b/app/assets/stylesheets/themes/alphacube/right-top.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/right-top.gif
rename to app/assets/stylesheets/themes/alphacube/right-top.gif
diff --git a/public/stylesheets/themes/alphacube/top-middle.gif b/app/assets/stylesheets/themes/alphacube/top-middle.gif
similarity index 100%
rename from public/stylesheets/themes/alphacube/top-middle.gif
rename to app/assets/stylesheets/themes/alphacube/top-middle.gif
diff --git a/public/stylesheets/themes/behavior.htc b/app/assets/stylesheets/themes/behavior.htc
similarity index 100%
rename from public/stylesheets/themes/behavior.htc
rename to app/assets/stylesheets/themes/behavior.htc
diff --git a/public/stylesheets/themes/darkX.css b/app/assets/stylesheets/themes/darkX.css
similarity index 100%
rename from public/stylesheets/themes/darkX.css
rename to app/assets/stylesheets/themes/darkX.css
diff --git a/public/stylesheets/themes/darkX/button-close-focused.png b/app/assets/stylesheets/themes/darkX/button-close-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/button-close-focused.png
rename to app/assets/stylesheets/themes/darkX/button-close-focused.png
diff --git a/public/stylesheets/themes/darkX/button-maximize-focused.png b/app/assets/stylesheets/themes/darkX/button-maximize-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/button-maximize-focused.png
rename to app/assets/stylesheets/themes/darkX/button-maximize-focused.png
diff --git a/public/stylesheets/themes/darkX/button-minimize-focused.png b/app/assets/stylesheets/themes/darkX/button-minimize-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/button-minimize-focused.png
rename to app/assets/stylesheets/themes/darkX/button-minimize-focused.png
diff --git a/public/stylesheets/themes/darkX/frame-bottom-left-focused.png b/app/assets/stylesheets/themes/darkX/frame-bottom-left-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/frame-bottom-left-focused.png
rename to app/assets/stylesheets/themes/darkX/frame-bottom-left-focused.png
diff --git a/public/stylesheets/themes/darkX/frame-bottom-mid-focused.png b/app/assets/stylesheets/themes/darkX/frame-bottom-mid-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/frame-bottom-mid-focused.png
rename to app/assets/stylesheets/themes/darkX/frame-bottom-mid-focused.png
diff --git a/public/stylesheets/themes/darkX/frame-bottom-right-focused.png b/app/assets/stylesheets/themes/darkX/frame-bottom-right-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/frame-bottom-right-focused.png
rename to app/assets/stylesheets/themes/darkX/frame-bottom-right-focused.png
diff --git a/public/stylesheets/themes/darkX/frame-left-focused.png b/app/assets/stylesheets/themes/darkX/frame-left-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/frame-left-focused.png
rename to app/assets/stylesheets/themes/darkX/frame-left-focused.png
diff --git a/public/stylesheets/themes/darkX/frame-right-focused.png b/app/assets/stylesheets/themes/darkX/frame-right-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/frame-right-focused.png
rename to app/assets/stylesheets/themes/darkX/frame-right-focused.png
diff --git a/public/stylesheets/themes/darkX/titlebar-left-focused.png b/app/assets/stylesheets/themes/darkX/titlebar-left-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/titlebar-left-focused.png
rename to app/assets/stylesheets/themes/darkX/titlebar-left-focused.png
diff --git a/public/stylesheets/themes/darkX/titlebar-mid-focused.png b/app/assets/stylesheets/themes/darkX/titlebar-mid-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/titlebar-mid-focused.png
rename to app/assets/stylesheets/themes/darkX/titlebar-mid-focused.png
diff --git a/public/stylesheets/themes/darkX/titlebar-right-focused.png b/app/assets/stylesheets/themes/darkX/titlebar-right-focused.png
similarity index 100%
rename from public/stylesheets/themes/darkX/titlebar-right-focused.png
rename to app/assets/stylesheets/themes/darkX/titlebar-right-focused.png
diff --git a/public/stylesheets/themes/debug.css b/app/assets/stylesheets/themes/debug.css
similarity index 100%
rename from public/stylesheets/themes/debug.css
rename to app/assets/stylesheets/themes/debug.css
diff --git a/public/stylesheets/themes/default.css b/app/assets/stylesheets/themes/default.css
similarity index 100%
rename from public/stylesheets/themes/default.css
rename to app/assets/stylesheets/themes/default.css
diff --git a/public/stylesheets/themes/default/bottom_left.gif b/app/assets/stylesheets/themes/default/bottom_left.gif
similarity index 100%
rename from public/stylesheets/themes/default/bottom_left.gif
rename to app/assets/stylesheets/themes/default/bottom_left.gif
diff --git a/public/stylesheets/themes/default/bottom_mid.gif b/app/assets/stylesheets/themes/default/bottom_mid.gif
similarity index 100%
rename from public/stylesheets/themes/default/bottom_mid.gif
rename to app/assets/stylesheets/themes/default/bottom_mid.gif
diff --git a/public/stylesheets/themes/default/bottom_right.gif b/app/assets/stylesheets/themes/default/bottom_right.gif
similarity index 100%
rename from public/stylesheets/themes/default/bottom_right.gif
rename to app/assets/stylesheets/themes/default/bottom_right.gif
diff --git a/public/stylesheets/themes/default/bottom_right_resize.gif b/app/assets/stylesheets/themes/default/bottom_right_resize.gif
similarity index 100%
rename from public/stylesheets/themes/default/bottom_right_resize.gif
rename to app/assets/stylesheets/themes/default/bottom_right_resize.gif
diff --git a/public/stylesheets/themes/default/center_left.gif b/app/assets/stylesheets/themes/default/center_left.gif
similarity index 100%
rename from public/stylesheets/themes/default/center_left.gif
rename to app/assets/stylesheets/themes/default/center_left.gif
diff --git a/public/stylesheets/themes/default/center_right.gif b/app/assets/stylesheets/themes/default/center_right.gif
similarity index 100%
rename from public/stylesheets/themes/default/center_right.gif
rename to app/assets/stylesheets/themes/default/center_right.gif
diff --git a/public/stylesheets/themes/default/clear.gif b/app/assets/stylesheets/themes/default/clear.gif
similarity index 100%
rename from public/stylesheets/themes/default/clear.gif
rename to app/assets/stylesheets/themes/default/clear.gif
diff --git a/public/stylesheets/themes/default/close.gif b/app/assets/stylesheets/themes/default/close.gif
similarity index 100%
rename from public/stylesheets/themes/default/close.gif
rename to app/assets/stylesheets/themes/default/close.gif
diff --git a/public/stylesheets/themes/default/inspect.gif b/app/assets/stylesheets/themes/default/inspect.gif
similarity index 100%
rename from public/stylesheets/themes/default/inspect.gif
rename to app/assets/stylesheets/themes/default/inspect.gif
diff --git a/public/stylesheets/themes/default/maximize.gif b/app/assets/stylesheets/themes/default/maximize.gif
similarity index 100%
rename from public/stylesheets/themes/default/maximize.gif
rename to app/assets/stylesheets/themes/default/maximize.gif
diff --git a/public/stylesheets/themes/default/minimize.gif b/app/assets/stylesheets/themes/default/minimize.gif
similarity index 100%
rename from public/stylesheets/themes/default/minimize.gif
rename to app/assets/stylesheets/themes/default/minimize.gif
diff --git a/public/stylesheets/themes/default/overlay.png b/app/assets/stylesheets/themes/default/overlay.png
similarity index 100%
rename from public/stylesheets/themes/default/overlay.png
rename to app/assets/stylesheets/themes/default/overlay.png
diff --git a/public/stylesheets/themes/default/resize.gif b/app/assets/stylesheets/themes/default/resize.gif
similarity index 100%
rename from public/stylesheets/themes/default/resize.gif
rename to app/assets/stylesheets/themes/default/resize.gif
diff --git a/public/stylesheets/themes/default/sizer.gif b/app/assets/stylesheets/themes/default/sizer.gif
similarity index 100%
rename from public/stylesheets/themes/default/sizer.gif
rename to app/assets/stylesheets/themes/default/sizer.gif
diff --git a/public/stylesheets/themes/default/top_left.gif b/app/assets/stylesheets/themes/default/top_left.gif
similarity index 100%
rename from public/stylesheets/themes/default/top_left.gif
rename to app/assets/stylesheets/themes/default/top_left.gif
diff --git a/public/stylesheets/themes/default/top_mid.gif b/app/assets/stylesheets/themes/default/top_mid.gif
similarity index 100%
rename from public/stylesheets/themes/default/top_mid.gif
rename to app/assets/stylesheets/themes/default/top_mid.gif
diff --git a/public/stylesheets/themes/default/top_right.gif b/app/assets/stylesheets/themes/default/top_right.gif
similarity index 100%
rename from public/stylesheets/themes/default/top_right.gif
rename to app/assets/stylesheets/themes/default/top_right.gif
diff --git a/public/stylesheets/themes/iefix/blank.gif b/app/assets/stylesheets/themes/iefix/blank.gif
similarity index 100%
rename from public/stylesheets/themes/iefix/blank.gif
rename to app/assets/stylesheets/themes/iefix/blank.gif
diff --git a/public/stylesheets/themes/iefix/iepngfix.css b/app/assets/stylesheets/themes/iefix/iepngfix.css
similarity index 100%
rename from public/stylesheets/themes/iefix/iepngfix.css
rename to app/assets/stylesheets/themes/iefix/iepngfix.css
diff --git a/public/stylesheets/themes/iefix/iepngfix.htc b/app/assets/stylesheets/themes/iefix/iepngfix.htc
similarity index 100%
rename from public/stylesheets/themes/iefix/iepngfix.htc
rename to app/assets/stylesheets/themes/iefix/iepngfix.htc
diff --git a/public/stylesheets/themes/lighting.css b/app/assets/stylesheets/themes/lighting.css
similarity index 100%
rename from public/stylesheets/themes/lighting.css
rename to app/assets/stylesheets/themes/lighting.css
diff --git a/public/stylesheets/themes/lighting/background_buttons.gif b/app/assets/stylesheets/themes/lighting/background_buttons.gif
similarity index 100%
rename from public/stylesheets/themes/lighting/background_buttons.gif
rename to app/assets/stylesheets/themes/lighting/background_buttons.gif
diff --git a/public/stylesheets/themes/lighting/bottom-left-blue.png b/app/assets/stylesheets/themes/lighting/bottom-left-blue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-left-blue.png
rename to app/assets/stylesheets/themes/lighting/bottom-left-blue.png
diff --git a/public/stylesheets/themes/lighting/bottom-left-darkblue.png b/app/assets/stylesheets/themes/lighting/bottom-left-darkblue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-left-darkblue.png
rename to app/assets/stylesheets/themes/lighting/bottom-left-darkblue.png
diff --git a/public/stylesheets/themes/lighting/bottom-left-green.png b/app/assets/stylesheets/themes/lighting/bottom-left-green.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-left-green.png
rename to app/assets/stylesheets/themes/lighting/bottom-left-green.png
diff --git a/public/stylesheets/themes/lighting/bottom-left-grey.png b/app/assets/stylesheets/themes/lighting/bottom-left-grey.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-left-grey.png
rename to app/assets/stylesheets/themes/lighting/bottom-left-grey.png
diff --git a/public/stylesheets/themes/lighting/bottom-middle-blue.png b/app/assets/stylesheets/themes/lighting/bottom-middle-blue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-middle-blue.png
rename to app/assets/stylesheets/themes/lighting/bottom-middle-blue.png
diff --git a/public/stylesheets/themes/lighting/bottom-middle-darkblue.png b/app/assets/stylesheets/themes/lighting/bottom-middle-darkblue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-middle-darkblue.png
rename to app/assets/stylesheets/themes/lighting/bottom-middle-darkblue.png
diff --git a/public/stylesheets/themes/lighting/bottom-middle-green.png b/app/assets/stylesheets/themes/lighting/bottom-middle-green.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-middle-green.png
rename to app/assets/stylesheets/themes/lighting/bottom-middle-green.png
diff --git a/public/stylesheets/themes/lighting/bottom-middle-grey.png b/app/assets/stylesheets/themes/lighting/bottom-middle-grey.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-middle-grey.png
rename to app/assets/stylesheets/themes/lighting/bottom-middle-grey.png
diff --git a/public/stylesheets/themes/lighting/bottom-right-blue.png b/app/assets/stylesheets/themes/lighting/bottom-right-blue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-right-blue.png
rename to app/assets/stylesheets/themes/lighting/bottom-right-blue.png
diff --git a/public/stylesheets/themes/lighting/bottom-right-darkblue.png b/app/assets/stylesheets/themes/lighting/bottom-right-darkblue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-right-darkblue.png
rename to app/assets/stylesheets/themes/lighting/bottom-right-darkblue.png
diff --git a/public/stylesheets/themes/lighting/bottom-right-green.png b/app/assets/stylesheets/themes/lighting/bottom-right-green.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-right-green.png
rename to app/assets/stylesheets/themes/lighting/bottom-right-green.png
diff --git a/public/stylesheets/themes/lighting/bottom-right-grey.png b/app/assets/stylesheets/themes/lighting/bottom-right-grey.png
similarity index 100%
rename from public/stylesheets/themes/lighting/bottom-right-grey.png
rename to app/assets/stylesheets/themes/lighting/bottom-right-grey.png
diff --git a/public/stylesheets/themes/lighting/button-close-blue.png b/app/assets/stylesheets/themes/lighting/button-close-blue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/button-close-blue.png
rename to app/assets/stylesheets/themes/lighting/button-close-blue.png
diff --git a/public/stylesheets/themes/lighting/button-close-darkblue.png b/app/assets/stylesheets/themes/lighting/button-close-darkblue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/button-close-darkblue.png
rename to app/assets/stylesheets/themes/lighting/button-close-darkblue.png
diff --git a/public/stylesheets/themes/lighting/button-close-green.png b/app/assets/stylesheets/themes/lighting/button-close-green.png
similarity index 100%
rename from public/stylesheets/themes/lighting/button-close-green.png
rename to app/assets/stylesheets/themes/lighting/button-close-green.png
diff --git a/public/stylesheets/themes/lighting/button-close-grey.png b/app/assets/stylesheets/themes/lighting/button-close-grey.png
similarity index 100%
rename from public/stylesheets/themes/lighting/button-close-grey.png
rename to app/assets/stylesheets/themes/lighting/button-close-grey.png
diff --git a/public/stylesheets/themes/lighting/button-maximize-blue.png b/app/assets/stylesheets/themes/lighting/button-maximize-blue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/button-maximize-blue.png
rename to app/assets/stylesheets/themes/lighting/button-maximize-blue.png
diff --git a/public/stylesheets/themes/lighting/button-maximize-darkblue.png b/app/assets/stylesheets/themes/lighting/button-maximize-darkblue.png
similarity index 100%
rename from public/stylesheets/themes/lighting/button-maximize-darkblue.png
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diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread.css b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread.css
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread.css
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread.css
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-left-c.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-left-c.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-left-c.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-left-c.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-middle.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-middle.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-middle.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-middle.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-right-c.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-right-c.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-right-c.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/bottom-right-c.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/button-close-focus.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-close-focus.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/button-close-focus.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-close-focus.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/button-max-focus.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-max-focus.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/button-max-focus.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-max-focus.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/button-min-focus.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-min-focus.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/button-min-focus.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-min-focus.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/frame-left.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/frame-left.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/frame-left.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/frame-left.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/frame-right.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/frame-right.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/frame-right.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/frame-right.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/left-top.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/left-top.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/left-top.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/left-top.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/right-top.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/right-top.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/right-top.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/right-top.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/top-middle.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/top-middle.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/top-middle.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/top-middle.gif
diff --git a/public/stylesheets/windows_js_1.3/helper/prototype_window_class_helper.rb b/app/assets/stylesheets/windows_js_1.3/helper/prototype_window_class_helper.rb
similarity index 100%
rename from public/stylesheets/windows_js_1.3/helper/prototype_window_class_helper.rb
rename to app/assets/stylesheets/windows_js_1.3/helper/prototype_window_class_helper.rb
diff --git a/public/stylesheets/windows_js_1.3/javascripts/debug.js b/app/assets/stylesheets/windows_js_1.3/javascripts/debug.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/debug.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/debug.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/effects.js b/app/assets/stylesheets/windows_js_1.3/javascripts/effects.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/effects.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/effects.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/extended_debug.js b/app/assets/stylesheets/windows_js_1.3/javascripts/extended_debug.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/extended_debug.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/extended_debug.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/prototype.js b/app/assets/stylesheets/windows_js_1.3/javascripts/prototype.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/prototype.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/prototype.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/tooltip.js b/app/assets/stylesheets/windows_js_1.3/javascripts/tooltip.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/tooltip.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/tooltip.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/window_effects.js b/app/assets/stylesheets/windows_js_1.3/javascripts/window_effects.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/window_effects.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/window_effects.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/window_ext.js b/app/assets/stylesheets/windows_js_1.3/javascripts/window_ext.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/window_ext.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/window_ext.js
diff --git a/public/stylesheets/windows_js_1.3/samples/constraint.html b/app/assets/stylesheets/windows_js_1.3/samples/constraint.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/constraint.html
rename to app/assets/stylesheets/windows_js_1.3/samples/constraint.html
diff --git a/public/stylesheets/windows_js_1.3/samples/dialog.html b/app/assets/stylesheets/windows_js_1.3/samples/dialog.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/dialog.html
rename to app/assets/stylesheets/windows_js_1.3/samples/dialog.html
diff --git a/public/stylesheets/windows_js_1.3/samples/dialog_ajax.html b/app/assets/stylesheets/windows_js_1.3/samples/dialog_ajax.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/dialog_ajax.html
rename to app/assets/stylesheets/windows_js_1.3/samples/dialog_ajax.html
diff --git a/public/stylesheets/windows_js_1.3/samples/inframe.html b/app/assets/stylesheets/windows_js_1.3/samples/inframe.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/inframe.html
rename to app/assets/stylesheets/windows_js_1.3/samples/inframe.html
diff --git a/public/stylesheets/windows_js_1.3/samples/inset.html b/app/assets/stylesheets/windows_js_1.3/samples/inset.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/inset.html
rename to app/assets/stylesheets/windows_js_1.3/samples/inset.html
diff --git a/public/stylesheets/windows_js_1.3/samples/multi_modal.html b/app/assets/stylesheets/windows_js_1.3/samples/multi_modal.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/multi_modal.html
rename to app/assets/stylesheets/windows_js_1.3/samples/multi_modal.html
diff --git a/public/stylesheets/windows_js_1.3/samples/oldFirstSampleCode.html b/app/assets/stylesheets/windows_js_1.3/samples/oldFirstSampleCode.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/oldFirstSampleCode.html
rename to app/assets/stylesheets/windows_js_1.3/samples/oldFirstSampleCode.html
diff --git a/public/stylesheets/windows_js_1.3/samples/openInside.html b/app/assets/stylesheets/windows_js_1.3/samples/openInside.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/openInside.html
rename to app/assets/stylesheets/windows_js_1.3/samples/openInside.html
diff --git a/public/stylesheets/windows_js_1.3/samples/parent.html b/app/assets/stylesheets/windows_js_1.3/samples/parent.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/parent.html
rename to app/assets/stylesheets/windows_js_1.3/samples/parent.html
diff --git a/public/stylesheets/windows_js_1.3/samples/popup_open.html b/app/assets/stylesheets/windows_js_1.3/samples/popup_open.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/popup_open.html
rename to app/assets/stylesheets/windows_js_1.3/samples/popup_open.html
diff --git a/public/stylesheets/windows_js_1.3/samples/rico/index.html b/app/assets/stylesheets/windows_js_1.3/samples/rico/index.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/rico/index.html
rename to app/assets/stylesheets/windows_js_1.3/samples/rico/index.html
diff --git a/public/stylesheets/windows_js_1.3/samples/rico/properties_1.gif b/app/assets/stylesheets/windows_js_1.3/samples/rico/properties_1.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/rico/properties_1.gif
rename to app/assets/stylesheets/windows_js_1.3/samples/rico/properties_1.gif
diff --git a/public/stylesheets/windows_js_1.3/samples/rico/rico.css b/app/assets/stylesheets/windows_js_1.3/samples/rico/rico.css
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/rico/rico.css
rename to app/assets/stylesheets/windows_js_1.3/samples/rico/rico.css
diff --git a/public/stylesheets/windows_js_1.3/samples/rico/rico_change.js b/app/assets/stylesheets/windows_js_1.3/samples/rico/rico_change.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/rico/rico_change.js
rename to app/assets/stylesheets/windows_js_1.3/samples/rico/rico_change.js
diff --git a/public/stylesheets/windows_js_1.3/samples/tooltips/tooltip.html b/app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/tooltips/tooltip.html
rename to app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip.html
diff --git a/public/stylesheets/windows_js_1.3/samples/tooltips/tooltip_ajax.html b/app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip_ajax.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/tooltips/tooltip_ajax.html
rename to app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip_ajax.html
diff --git a/public/stylesheets/windows_js_1.3/samples/tooltips/tooltip_url.html b/app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip_url.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/tooltips/tooltip_url.html
rename to app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip_url.html
diff --git a/public/stylesheets/windows_js_1.3/samples/window_key.html b/app/assets/stylesheets/windows_js_1.3/samples/window_key.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/window_key.html
rename to app/assets/stylesheets/windows_js_1.3/samples/window_key.html
diff --git a/public/stylesheets/windows_js_1.3/samples/window_key_url_content.html b/app/assets/stylesheets/windows_js_1.3/samples/window_key_url_content.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/window_key_url_content.html
rename to app/assets/stylesheets/windows_js_1.3/samples/window_key_url_content.html
diff --git a/public/stylesheets/windows_js_1.3/samples/window_store.html b/app/assets/stylesheets/windows_js_1.3/samples/window_store.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/window_store.html
rename to app/assets/stylesheets/windows_js_1.3/samples/window_store.html
diff --git a/app/controllers/api/base_controller.rb b/app/controllers/api/base_controller.rb
index 06dcbf205..6b75dff5a 100644
--- a/app/controllers/api/base_controller.rb
+++ b/app/controllers/api/base_controller.rb
@@ -7,7 +7,7 @@ class Api::BaseController < ActionController::Base
   protect_from_forgery with: :null_session
 
   #  before_action :destroy_session <-- Rails 4
-  before_filter :destroy_session
+  before_action :destroy_session
 
   def destroy_session
     request.session_options[:skip] = true
@@ -47,7 +47,7 @@ def bad_url
   # clause "key = value" is replaced by "key::text ~ value*", where "value*" is
   # "value" with the tilde removed.
   def query(model, params)
-    where_params = params.slice(*model.column_names)
+    where_params = params.permit!.to_hash.slice(*model.column_names)
 
     limit = nil
     if params.has_key? "limit"
@@ -129,7 +129,7 @@ def fuzzy_match_restrictions(model_or_relation, where_params)
     # remove these from where_params
     where_params.delete_if { |k, v| fuzzy_params.has_key?(k) }
 
-    kv_pairs = fuzzy_params.to_a
+    kv_pairs = fuzzy_params.to_unsafe_h.to_a
     
     where_clause_array = kv_pairs.map { |kv| "#{kv[0]}::text ~* ?" }
     where_clause = where_clause_array.join(" AND ")
diff --git a/app/controllers/api/v1/base_controller.rb b/app/controllers/api/v1/base_controller.rb
index 2a88c72ec..a417fae24 100644
--- a/app/controllers/api/v1/base_controller.rb
+++ b/app/controllers/api/v1/base_controller.rb
@@ -3,8 +3,8 @@
 class Api::V1::BaseController < Api::BaseController
   include ApiAuthenticationSystem
 
-  before_filter :set_content_type # IMPORTANT: Run this filter first!
-  before_filter :login_required
+  before_action :set_content_type # IMPORTANT: Run this filter first!
+  before_action :login_required
 
   NO_CONSTRAINT = lambda { |value| true }
 
diff --git a/app/controllers/api/v1/traits_controller.rb b/app/controllers/api/v1/traits_controller.rb
index 9d5221092..e38c3bd93 100644
--- a/app/controllers/api/v1/traits_controller.rb
+++ b/app/controllers/api/v1/traits_controller.rb
@@ -38,7 +38,7 @@ def create
     end
     create_from_xml_string(xml_data)
 
-    render status: 201, content_type: "application/xml"
+    render status: 201
 
   rescue Nokogiri::XML::SyntaxError, InvalidDocument, InvalidData,
     Yajl::ParseError, Api::CsvHandler::BadHeading
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index cbd8e08ef..fa43257db 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -24,8 +24,7 @@ class ApplicationController < ActionController::Base
       flash[:error] = e.message
     end
 
-
-    redirect_to :back
+    redirect_back(fallback_location: root_path)
   end
 
   # Be sure to include AuthenticationSystem in Application Controller instead
@@ -117,7 +116,7 @@ def log_searches(m, arg = params[:search])
     search_info += "\nsearch string: \"" + (params['search'] || "") + "\""
     search_info += "\nformat: " + (params['format'] || 'html')
     search_info += "\nSQL query: " + sql # method_object.call(arg).send(additional_method).to_sql
-    search_info += "\nall parameters: " + params.inspect
+    search_info += "\nall parameters: " + params.permit!.inspect
 
     logger.info(search_info)
 
@@ -170,7 +169,7 @@ def handle_constraint_violations(e)
     logger.info(e)
     match = e.message.match /The value of .*? for .*? .*? must be between .*? and .*?\./
     flash[:error] = match && match[0] || e.message
-    redirect_to :back
+    redirect_back(fallback_location: root_path)
   end
 
   # Given a model class, a list of columns (attributes) of the model,
diff --git a/app/controllers/bulk_upload_controller.rb b/app/controllers/bulk_upload_controller.rb
index 198c48f04..55ebbc76d 100644
--- a/app/controllers/bulk_upload_controller.rb
+++ b/app/controllers/bulk_upload_controller.rb
@@ -44,12 +44,12 @@
 # of the session variable.
 class BulkUploadController < ApplicationController
 
-  before_filter :login_required
-  before_filter :record_stage
-  before_filter :clear_session_data, only: :start_upload
-  before_filter :valid_file_required, only: [ :choose_global_data_values, :confirm_data, :insert_data ]
+  before_action :login_required
+  before_action :record_stage
+  before_action :clear_session_data, only: :start_upload
+  before_action :valid_file_required, only: [ :choose_global_data_values, :confirm_data, :insert_data ]
 
-  after_filter :record_bulk_upload_citation
+  after_action :record_bulk_upload_citation
 
   private
 
@@ -207,7 +207,7 @@ def choose_global_citation
   def display_csv_file
 
     uploaded_io = params["CSV file"]
-    if uploaded_io
+    if !uploaded_io.blank?
       # we got here via the "upload file" button
       @data_set = BulkUploadDataSet.new(session, uploaded_io)
     elsif session[:csvpath]
diff --git a/app/controllers/citations_controller.rb b/app/controllers/citations_controller.rb
index 8d188b9dc..415e49973 100644
--- a/app/controllers/citations_controller.rb
+++ b/app/controllers/citations_controller.rb
@@ -1,6 +1,6 @@
 class CitationsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/citations_sites_controller.rb b/app/controllers/citations_sites_controller.rb
index da9bd4e3b..9d442b342 100644
--- a/app/controllers/citations_sites_controller.rb
+++ b/app/controllers/citations_sites_controller.rb
@@ -1,5 +1,5 @@
 class CitationsSitesController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/citations_treatments_controller.rb b/app/controllers/citations_treatments_controller.rb
index f0ddd02df..9f1b48c2b 100644
--- a/app/controllers/citations_treatments_controller.rb
+++ b/app/controllers/citations_treatments_controller.rb
@@ -1,5 +1,5 @@
 class CitationsTreatmentsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/covariates_controller.rb b/app/controllers/covariates_controller.rb
index 4a160add1..7ef6845ec 100644
--- a/app/controllers/covariates_controller.rb
+++ b/app/controllers/covariates_controller.rb
@@ -1,5 +1,5 @@
 class CovariatesController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /covariates
diff --git a/app/controllers/cultivars_controller.rb b/app/controllers/cultivars_controller.rb
index ec3aa5654..f8b4f28c8 100644
--- a/app/controllers/cultivars_controller.rb
+++ b/app/controllers/cultivars_controller.rb
@@ -1,5 +1,5 @@
 class CultivarsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/dbfiles_controller.rb b/app/controllers/dbfiles_controller.rb
index 14a74ab83..92f2c2983 100644
--- a/app/controllers/dbfiles_controller.rb
+++ b/app/controllers/dbfiles_controller.rb
@@ -1,6 +1,6 @@
 class DbfilesController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
@@ -34,12 +34,12 @@ def unlink
     respond_to do |format|
       if dbfile.save
         flash[:notice] = "File unlinked"
-        format.html { redirect_to :back }
+        format.html { redirect_back(fallback_location: root_path) }
         format.xml  { render :xml => 'File unlinked' }
         format.json  { render :json => 'File unlinked' }
       else
         flash[:notice] = "File not removed"
-        format.html {redirect_to :back }
+        format.html {redirect_back(fallback_location: root_path) }
         format.xml  { render :xml => 'File not removed' }
         format.json  { render :json => 'File not removed' }
       end
diff --git a/app/controllers/ensembles_controller.rb b/app/controllers/ensembles_controller.rb
index e956a1090..96f27175f 100644
--- a/app/controllers/ensembles_controller.rb
+++ b/app/controllers/ensembles_controller.rb
@@ -1,6 +1,6 @@
 class EnsemblesController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /ensembles
diff --git a/app/controllers/entities_controller.rb b/app/controllers/entities_controller.rb
index a147fef19..6486079bd 100644
--- a/app/controllers/entities_controller.rb
+++ b/app/controllers/entities_controller.rb
@@ -1,7 +1,7 @@
 class EntitiesController < ApplicationController
   require 'will_paginate/array' 
 
-  before_filter :login_required
+  before_action :login_required
 
   # GET /entitys
   # GET /entitys.xml
diff --git a/app/controllers/experiments_controller.rb b/app/controllers/experiments_controller.rb
index ca7817515..c63a63392 100644
--- a/app/controllers/experiments_controller.rb
+++ b/app/controllers/experiments_controller.rb
@@ -1,6 +1,6 @@
 class ExperimentsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /experiments
diff --git a/app/controllers/formats_controller.rb b/app/controllers/formats_controller.rb
index 8a6a3b2fc..edfe78dad 100644
--- a/app/controllers/formats_controller.rb
+++ b/app/controllers/formats_controller.rb
@@ -1,18 +1,17 @@
 class FormatsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   def rem_formats_variables
-    @formats_variable = FormatsVariable.find(params[:id])
-    @format = @formats_variable.format
+    formats_variable = FormatsVariable.find(params[:id])
+    @format = formats_variable.format
+    formats_variable.destroy
 
-    render :update do |page|
-      if @formats_variable.destroy
-        page.replace_html 'edit_formats_variables', :partial => 'edit_formats_variables'
-      else
-        page.replace_html 'edit_formats_variables', :partial => 'edit_formats_variables'
-      end
+    respond_to do |format|
+      format.js {
+        render "edit_formats_variables", layout: false
+      }
     end
   end
 
@@ -23,8 +22,10 @@ def add_formats_variables
     formats_variable.variable = Variable.find(params[:variable_id])
     formats_variable.save
 
-    render :update do |page|
-      page.replace_html 'edit_formats_variables', :partial => 'edit_formats_variables'
+    respond_to do |format|
+      format.js {
+        render "edit_formats_variables", layout: false
+      }
     end
   end
 
@@ -33,8 +34,10 @@ def edit_formats_variables
     @format = formats_variable.format
     formats_variable.update_attributes(params[:formats_variable])
 
-    render :update do |page|
-      page.replace_html 'edit_formats_variables', :partial => 'edit_formats_variables'
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
diff --git a/app/controllers/inputs_controller.rb b/app/controllers/inputs_controller.rb
index 2798af258..5b5688bed 100644
--- a/app/controllers/inputs_controller.rb
+++ b/app/controllers/inputs_controller.rb
@@ -1,6 +1,6 @@
 class InputsController < ApplicationController
 
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_direction, :sort_column
 
   # general autocompletion
@@ -69,9 +69,10 @@ def edit_inputs_files
       @files = DBFile.where(search_cond).select("id, file_name").page(params[:page])
     end
 
-    render :update do |page|
-      page.replace_html :files_index_table, :partial => "edit_inputs_files_table"
-      page.replace_html :files_search_term, search
+    respond_to do |format|
+      format.js {
+        render layout: false, locals: { search: search }
+      }
     end
   end
 
diff --git a/app/controllers/inputs_runs_controller.rb b/app/controllers/inputs_runs_controller.rb
index 6c244eb2d..5bb2237cc 100644
--- a/app/controllers/inputs_runs_controller.rb
+++ b/app/controllers/inputs_runs_controller.rb
@@ -1,5 +1,5 @@
 class InputsRunsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/likelihoods_controller.rb b/app/controllers/likelihoods_controller.rb
index d0133eab6..f412ac12c 100644
--- a/app/controllers/likelihoods_controller.rb
+++ b/app/controllers/likelihoods_controller.rb
@@ -1,6 +1,6 @@
 class LikelihoodsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /likelihoods
diff --git a/app/controllers/machines_controller.rb b/app/controllers/machines_controller.rb
index 0f7dae1b1..ad125b4a0 100644
--- a/app/controllers/machines_controller.rb
+++ b/app/controllers/machines_controller.rb
@@ -1,6 +1,6 @@
 class MachinesController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /machines
diff --git a/app/controllers/managements_controller.rb b/app/controllers/managements_controller.rb
index 43df41b40..596a3a15c 100644
--- a/app/controllers/managements_controller.rb
+++ b/app/controllers/managements_controller.rb
@@ -1,5 +1,5 @@
 class ManagementsController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/managements_treatments_controller.rb b/app/controllers/managements_treatments_controller.rb
index b53abdd58..d6d609694 100644
--- a/app/controllers/managements_treatments_controller.rb
+++ b/app/controllers/managements_treatments_controller.rb
@@ -1,5 +1,5 @@
 class ManagementsTreatmentsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/methods_controller.rb b/app/controllers/methods_controller.rb
index 7a4fd5837..5666682a9 100644
--- a/app/controllers/methods_controller.rb
+++ b/app/controllers/methods_controller.rb
@@ -1,7 +1,7 @@
 # coding: utf-8
 class MethodsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # This action acts as a _source_ for the jQuery UI autocompletion widgets on
diff --git a/app/controllers/models_controller.rb b/app/controllers/models_controller.rb
index 48bea5e8a..c81ca9d24 100644
--- a/app/controllers/models_controller.rb
+++ b/app/controllers/models_controller.rb
@@ -1,6 +1,6 @@
 class ModelsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   def edit_models_files
@@ -52,9 +52,11 @@ def edit_models_files
       @files = DBFile.where(search_cond).select("id,file_name").page(params[:page])
     end
 
-    render :update do |page|
-      page.replace_html :files_index_table, :partial => "edit_models_files_table"
-      page.replace_html :files_search_term, search
+
+    respond_to do |format|
+      format.js {
+        render layout: false, locals: { search: search }
+      }
     end
   end
 
diff --git a/app/controllers/modeltypes_controller.rb b/app/controllers/modeltypes_controller.rb
index 2c4ae3d11..9ce1962c6 100644
--- a/app/controllers/modeltypes_controller.rb
+++ b/app/controllers/modeltypes_controller.rb
@@ -1,18 +1,18 @@
 class ModeltypesController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   def remove_modeltypes_format
     @modeltypes_format = ModeltypesFormat.find(params[:id])
     @modeltype = @modeltypes_format.modeltype
 
-    render :update do |page|
-      if @modeltypes_format.destroy
-        page.replace_html 'edit_formats', :partial => 'edit_formats'
-      else
-        page.replace_html 'edit_formats', :partial => 'edit_formats'
-      end
+    @modeltypes_format.destroy
+
+    respond_to do |format|
+      format.js {
+        render "edit_modeltypes_format", layout: false
+      }
     end
   end
 
@@ -23,8 +23,10 @@ def add_modeltypes_format
     @modeltypes_format.format = Format.find(params[:format_id])
     @modeltypes_format.save
 
-    render :update do |page|
-      page.replace_html 'edit_formats', :partial => 'edit_formats'
+    respond_to do |format|
+      format.js {
+        render "edit_modeltypes_format", layout: false
+      }
     end
   end
 
@@ -33,8 +35,10 @@ def edit_modeltypes_format
     @modeltype = @modeltypes_format.modeltype
     @modeltypes_format.update_attributes(params[:modeltypes_format])
 
-    render :update do |page|
-      page.replace_html 'edit_formats', :partial => 'edit_formats'
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
diff --git a/app/controllers/pfts_controller.rb b/app/controllers/pfts_controller.rb
index 6ac964bd3..cbea9d48a 100644
--- a/app/controllers/pfts_controller.rb
+++ b/app/controllers/pfts_controller.rb
@@ -1,5 +1,5 @@
 class PftsController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
@@ -96,9 +96,10 @@ def edit2_pfts_species
       @species = Specie.where(search_cond).select("id, scientificname").page(params[:page])
     end
 
-    render :update do |page|
-      page.replace_html :index_table, :partial => "edit2_pfts_species_table"
-      page.replace_html :search_term, search
+    respond_to do |format|
+      format.js {
+        render layout: false, locals: { search: search }
+      }
     end
   end
 
diff --git a/app/controllers/pfts_priors_controller.rb b/app/controllers/pfts_priors_controller.rb
index a03570bb0..58b2d19b1 100644
--- a/app/controllers/pfts_priors_controller.rb
+++ b/app/controllers/pfts_priors_controller.rb
@@ -1,5 +1,5 @@
 class PftsPriorsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/pfts_species_controller.rb b/app/controllers/pfts_species_controller.rb
index 2cfacc78b..5361a64f5 100644
--- a/app/controllers/pfts_species_controller.rb
+++ b/app/controllers/pfts_species_controller.rb
@@ -1,5 +1,5 @@
 class PftsSpeciesController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/posteriors_controller.rb b/app/controllers/posteriors_controller.rb
index 96559de37..78fec86c2 100644
--- a/app/controllers/posteriors_controller.rb
+++ b/app/controllers/posteriors_controller.rb
@@ -1,6 +1,6 @@
 class PosteriorsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /posteriors
diff --git a/app/controllers/priors_controller.rb b/app/controllers/priors_controller.rb
index e09c67ec1..5da91b59a 100644
--- a/app/controllers/priors_controller.rb
+++ b/app/controllers/priors_controller.rb
@@ -1,5 +1,5 @@
 class PriorsController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
@@ -107,9 +107,15 @@ def preview
         # On ebi-forecast, the version of R we want to use is in
         # /usr/local/R-3.1.0/bin, so put it first in the path so that that version
         # gets used if it exists:
-        ENV["PATH"] = "/usr/local/R-3.1.0/bin:/usr/bin:/usr/local/bin"                                                                                 
-        o, error_output, s = Open3.capture3("R", "--vanilla", "--args", imgfile, distname, aparam.to_s, bparam.to_s, n.to_s,                           
-                                            stdin_data: Rails.root.join('script/previewhelp.R').read)
+        path_additions = "/usr/local/R-3.1.0/bin:"
+
+        o, error_output, s = Open3.capture3(
+                           {"PATH" => path_additions + ENV["PATH"]},
+                           "R", "--vanilla", "--args", imgfile, distname,
+                           aparam.to_s, bparam.to_s, n.to_s,
+                           stdin_data: Rails.root.join('script/previewhelp.R').read
+                         )
+
       else
         error_output = sprintf("Invalid argument set:\n\timgfile = %s\n\tdistname = %s\n\taparam = %s\n\tbparam = %s\n\tn = %s\n", 
                                imgfile, distname, aparam, bparam, n)
diff --git a/app/controllers/runs_controller.rb b/app/controllers/runs_controller.rb
index be5425bbf..d11e54441 100644
--- a/app/controllers/runs_controller.rb
+++ b/app/controllers/runs_controller.rb
@@ -1,6 +1,6 @@
 class RunsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /runs
diff --git a/app/controllers/sitegroups_controller.rb b/app/controllers/sitegroups_controller.rb
index 55ecf4666..1b69108f6 100644
--- a/app/controllers/sitegroups_controller.rb
+++ b/app/controllers/sitegroups_controller.rb
@@ -1,6 +1,6 @@
 class SitegroupsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   def edit_sitegroups_sites
@@ -52,9 +52,10 @@ def edit_sitegroups_sites
       @sites = Site.where(search_cond).paginate :page => params[:page]
     end
 
-    render :update do |page|
-      page.replace_html :sites_index_table, :partial => "edit_sitegroups_sites_table"
-      page.replace_html :sites_search_term, search
+    respond_to do |format|
+      format.js {
+        render layout: false, locals: { search: search }
+      }
     end
   end
 
diff --git a/app/controllers/sites_controller.rb b/app/controllers/sites_controller.rb
index 782316158..38902d794 100644
--- a/app/controllers/sites_controller.rb
+++ b/app/controllers/sites_controller.rb
@@ -1,5 +1,5 @@
 class SitesController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   layout 'application', :except => [ :map ]
@@ -15,13 +15,16 @@ def linked
 
     if exists
       @citation.sites.delete(@site)
+      @linking = false
     else
       @citation.sites<<@site
+      @linking = true
     end
 
-    render :update do |page|
-      page.replace_html "site-#{ @site.id }", ""
-      page.replace_html "linked", :partial => 'linked'
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
diff --git a/app/controllers/species_controller.rb b/app/controllers/species_controller.rb
index 03a624afb..3a616c5e2 100644
--- a/app/controllers/species_controller.rb
+++ b/app/controllers/species_controller.rb
@@ -2,7 +2,7 @@
 # RAILS3 added above encoding (actually this is needed with Ruby 1.9.2)
 
 class SpeciesController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
@@ -51,29 +51,16 @@ def species_search
       @species = Specie.where('LOWER(scientificname) LIKE LOWER(:query) OR LOWER(genus) LIKE LOWER(:query) OR LOWER("AcceptedSymbol") LIKE LOWER(:query) OR LOWER(commonname) LIKE LOWER(:query)' +
                               ' OR LOWER(scientificname) LIKE LOWER(:query2) OR LOWER(genus) LIKE LOWER(:query2) OR LOWER("AcceptedSymbol") LIKE LOWER(:query2) OR LOWER(commonname) LIKE LOWER(:query2)', 
                               {:query => @query + "%", :query2 => "%" + @query + "%"}).limit(100).order("scientificname")
-      @species.uniq!
+      @species.distinct!
     else
-      @species = []
+      @species = Specie.none
     end
 
-    render :update do |page|
-      if params[:cont] == "species"
-        page.replace_html "search_results", :partial => 'search', :object => @species
-      else
-        if @species.empty?
-          page.replace_html "#{params[:cont]}_specie_id", "<option value=''>There are no species that match your query.</option>"
-        else
-          page.replace_html "#{params[:cont]}_specie_id", options_from_collection_for_select(@species, :id, :select_default)
-        end
-      end
-      if params[:symbol].length > 3
-        page.replace_html "results", "<h3>Search results for #{sanitize(@query)}</h3>"
-      else
-        page.replace_html "results", "<h3>Search must be longer then 3 characters</h3>"
-      end
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
-
-#    render :partial => 'species/species_search'
   end
 
 
diff --git a/app/controllers/traits_controller.rb b/app/controllers/traits_controller.rb
index 6b873e369..9e72fc604 100644
--- a/app/controllers/traits_controller.rb
+++ b/app/controllers/traits_controller.rb
@@ -1,5 +1,5 @@
 class TraitsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
@@ -11,6 +11,7 @@ def trait_search
 
       @trait = Trait.all_limited(current_user).
         includes([:specie,:variable,:cultivar,:treatment,:citation]).
+        references([:specie,:variable,:treatment,:citation]).
         where(%q{   species.scientificname LIKE :query
                  OR species.genus LIKE :query
                  OR species."AcceptedSymbol" LIKE :query
@@ -24,52 +25,71 @@ def trait_search
       @trait = nil
     end
 
-
-    render :update do |page|
-      if params[:symbol].length > 3
-        if @trait.length == 100
-          page.replace_html "results", "<h3>Search results for #{@query}. More then 100 results, please narrow your search.</h3>"
-        else
-          page.replace_html "results", "<h3>Search results for #{@query}</h3>"
-        end
-      else
-        page.replace_html "results", "<h3>Search must be longer then 3 characters</h3>"
-      end
-      if @trait.nil?
-        page.replace_html "#{params[:cont]}_trait_id", "<option value=''>There are no traits that match your query.</option>"
+    if params[:symbol].length > 3
+      if @trait.length == 100
+        @message = "<h3>Search results for #{@query}. More then 100 results, please narrow your search.</h3>"
       else
-        page.replace_html "#{params[:cont]}_trait_id", options_from_collection_for_select(@trait, :id, :select_default)
+        @message = "<h3>Search results for #{@query}</h3>"
       end
+    else
+      @message = "<h3>Search must be longer then 3 characters</h3>"
+    end
+
+    if @trait.nil?
+      @options = "<option value=''>There are no traits that match your query.</option>"
+    else
+      @options = ActionController::Base.helpers.options_from_collection_for_select(@trait, :id, :select_default)
     end
 
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
+    end
   end
 
   def access_level
 
     t = Trait.all_limited(current_user).find(params[:id])
-
+    t.current_user = current_user
     t.access_level = params[:trait][:access_level] if t
 
-    render :update do |page|
-      if t and t.save
-        page['access_level-'+t.id.to_s].visual_effect :pulsate
-      else
-        page['access_level-'+t.id.to_s].visual_effect :shake
-      end
+    @element_id = "access_level-#{t.id}"
+
+    if t && t.save
+      @saved = true
+    else
+      @saved = false
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
   def checked
-    t = Trait.all_limited(current_user).find(params[:id])
-    t.current_user = current_user
-    t.checked = params[:trait][:checked] if t
+    id = params[:id]
+    t = Trait.all_limited(current_user).find_by_id(id)
 
-    render :update do |page|
-      if t and t.save
-        page.replace_html 'checked_notify-'+t.id.to_s, "<br />Updated to #{t.checked}"
-      else
-        page.replace_html 'checked_notify-'+t.id.to_s, "<br />Something went wrong, not updated!"
-      end
+    if t
+      t.current_user = current_user
+      t.checked = params[:trait][:checked]
+    end
+
+    @element_id = "checked_notify-#{id}"
+
+    if t && t.save
+      @message = "<br />Updated to #{t.checked}"
+    else
+      @message = "<br />Something went wrong, not updated!"
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
@@ -209,7 +229,7 @@ def update
               # these "saved" covariates are rolled back if any save errors occur
               saved_covariates << @covariate
             else
-              @trait.errors.add(:covariates, (@covariate.errors.get(:level))[0])
+              @trait.errors.add(:covariates, (@covariate.errors[:level])[0])
             end
           end
         end
@@ -254,11 +274,10 @@ def unlink_covariate
     @trait = Trait.all_limited(current_user).find(params[:id])
     Covariate.find(params[:covariate]).destroy
     respond_to do |format|
-      format.html {
-        render :action =>"edit" do |page|
-          page.replace_html "edit_covariates_traits", :partial =>"edit_covariates_traits"
-        end
+      format.js {
+        render layout: false
       }
+      format.html { head :ok }
       format.xml  { head :ok }
       format.csv  { head :ok }
     end
diff --git a/app/controllers/treatments_controller.rb b/app/controllers/treatments_controller.rb
index b9aac1311..1ff2b1a56 100644
--- a/app/controllers/treatments_controller.rb
+++ b/app/controllers/treatments_controller.rb
@@ -1,7 +1,7 @@
 require 'will_paginate/array'
 
 class TreatmentsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   helper_method :sort_column, :sort_direction
 
@@ -50,24 +50,17 @@ def create_new_management
 
     @management = Management.new(params[:management])
 
-    render :update do |page|
-      if @management.save
-        @treatment.managements << @management
-        flash[:notice] = "Management was successfully created"
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-
-        # After we've added the newly-created management to the collection, we
-        # have to pass an unsaved copy of it to the 'new_management' partial so the
-        # form it contains doesn't try to to a PUT instead of a POST:
-        @management = @management.dup
+    if @management.save
+      @treatment.managements << @management
+      flash.now[:notice] = "Management was successfully created"
+    else
+      flash.now[:error] = "Management was not created"
+    end
 
-        page.replace_html 'new_management', :partial => 'new_management'
-        page.call 'showHide', 'new_management'
-      else
-        flash[:notice] = "Management was not created"
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-        page.replace_html 'new_management', :partial => 'new_management'
-      end
+    respond_to do |format|
+      format.js {
+        render layout: false, locals: { flash: flash }
+      }
     end
    end
 
@@ -75,12 +68,12 @@ def rem_managements_treatments
     @treatment = Treatment.find(params[:id])
     @management = Management.find(params[:management])
 
-    render :update do |page|
-      if @management.treatments.delete(@treatment)
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-      else
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-      end
+    @management.treatments.delete(@treatment)
+
+    respond_to do |format|
+      format.js {
+        render "edit_managements_treatments", layout: false
+      }
     end
   end
 
@@ -88,17 +81,18 @@ def edit_managements_treatments
 
     @treatment = Treatment.find(params[:id])
 
-    render :update do |page|
-      if !params[:management].nil?
-        params[:management][:id].each do |c|
-          next if c.empty?
-          @treatment.managements << Management.find(c)
-        end
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-      else
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
+    if !params[:management].nil?
+      params[:management][:id].each do |c|
+        next if c.empty?
+        @treatment.managements << Management.find(c)
       end
     end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
+    end
   end
 
   def flag_control
@@ -113,12 +107,12 @@ def flag_control
     respond_to do |format|
       if @treatment.save
         flash[:notice] = 'Treatment was successfully updated.'
-        format.html { redirect_to :back }
+        format.html { redirect_back(fallback_location: root_path) }
         format.xml  { head :ok }
         format.csv  { head :ok }
         format.json  { head :ok }
       else
-        format.html { redirect_to :back }
+        format.html { redirect_back(fallback_location: root_path) }
         format.xml  { render :xml => @treatment.errors, :status => :unprocessable_entity }
         format.csv  { render :csv => @treatment.errors, :status => :unprocessable_entity }
         format.json  { render :json => @treatment.errors, :status => :unprocessable_entity }
diff --git a/app/controllers/users_controller.rb b/app/controllers/users_controller.rb
index d76604555..b2f7fda54 100644
--- a/app/controllers/users_controller.rb
+++ b/app/controllers/users_controller.rb
@@ -1,7 +1,7 @@
 class UsersController < ApplicationController
 
-  before_filter :login_required, :except => [:create,:new]
-  #before_filter :login_required
+  before_action :login_required, :except => [:create,:new]
+
   helper_method :sort_column, :sort_direction
 
   def index
diff --git a/app/controllers/variables_controller.rb b/app/controllers/variables_controller.rb
index 2e7510635..b02db28c9 100644
--- a/app/controllers/variables_controller.rb
+++ b/app/controllers/variables_controller.rb
@@ -1,5 +1,5 @@
 class VariablesController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb
index f87094c37..900ab9c0e 100644
--- a/app/controllers/workflows_controller.rb
+++ b/app/controllers/workflows_controller.rb
@@ -1,5 +1,5 @@
 class WorkflowsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/yields_controller.rb b/app/controllers/yields_controller.rb
index 1aae1a9d5..4d08e5641 100644
--- a/app/controllers/yields_controller.rb
+++ b/app/controllers/yields_controller.rb
@@ -1,35 +1,50 @@
 class YieldsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
 
   def checked
-    y = Yield.all_limited(current_user).find(params[:id])
-    
-    y.checked = params[:y][:checked]
+    id = params[:id]
+    y = Yield.all_limited(current_user).find(id)
 
-    render :update do |page|
-      if y and y.save
-        page.replace_html 'checked_notify-'+y.id.to_s, "<br />Updated to #{y.checked}"
-      else 
-        page.replace_html 'checked_notify-'+y.id.to_s, "<br />Something went wrong, not updated!"
-      end
+    if y
+      y.checked = params[:y][:checked]
+    end
+
+    @element_id = "checked_notify-#{id}"
+    binding.pry
+    if y && y.save
+      @message = "<br />Updated to #{y.checked}"
+    else
+      @message = "<br />Something went wrong, not updated!"
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
   def access_level
 
     y = Yield.all_limited(current_user).find(params[:id])
-
     y.access_level = params[:yield][:access_level] if y
     
-    render :update do |page|
-      if y and y.save
-        page['access_level-'+y.id.to_s].visual_effect :pulsate
-      else 
-        page['access_level-'+y.id.to_s].visual_effect :shake
-      end
+
+    @element_id = "access_level-#{y.id}"
+
+    if y && y.save
+      @saved = true
+    else
+      @saved = false
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
diff --git a/app/controllers/yieldsviews_controller.rb b/app/controllers/yieldsviews_controller.rb
index 99ee39737..b03d920a9 100644
--- a/app/controllers/yieldsviews_controller.rb
+++ b/app/controllers/yieldsviews_controller.rb
@@ -1,5 +1,5 @@
 class YieldsviewsController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
 
   require 'csv'
 
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index ef633e230..8a5fdc5f2 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -44,7 +44,7 @@ def sortable(column, title = nil)
     title ||= column.titleize
     css_class = (column == sort_column) ? "current #{sort_direction}" : nil
     direction = (column == sort_column && sort_direction == "asc") ? "desc" : "asc"
-    link_to title, params.merge(:sort => column, :direction => direction, :page => nil), {:class => css_class}
+    link_to title, params.permit(:sort, :direction, :page, :_).merge(:sort => column, :direction => direction, :page => nil), {:class => css_class}
   end
 
   def format_stat(record)
@@ -65,7 +65,7 @@ def format_stat(record)
 
 # Call this to make a link inside a form that submits the form.
 def link_to_submit(*args, &block)
-  link_to_function (block_given? ? capture(&block) : args[0]), "jQuery(this).closest('form').submit()", args.extract_options!
+  link_to (block_given? ? capture(&block) : args[0]), "#", args.extract_options!.merge(onclick: "jQuery(this).closest('form').submit(); return false")
 end
 
 # Given a FormBuilder object `f`, a string `label`, an SQL table name
@@ -157,3 +157,80 @@ def commit_date
   e = ENV['BETY_GIT_DATE']
   e.nil? || e.empty? ? `git log --pretty=format:"%ad" -1` : e
 end
+
+# Replacement for the Prototype method of this name.
+def observe_field(element_id, **options)
+
+  observed_event = options[:event_name] || "keyup"
+
+  # We assume options has either the key :url or the key :function (but not
+  # both).
+  if options.has_key? :url
+    url = url_for(options[:url])
+    connector = url.match(/\?/) ? '&' : '?'
+    confirmation = options[:confirmation] || "true"
+    raw(
+      %Q{<script>
+             var data_access_level = #{current_user.access_level};
+             jQuery(document).ready(function() {
+                 jQuery("##{element_id.to_s}").bind("focus", function() {
+                     previous = this.value;
+                 }).bind("#{observed_event}", function(event) {
+                     var newvalue = this.value;
+                     jQuery.ajax({
+                         type: "POST",
+                         url: "#{url}" + "#{connector}" + #{options[:with]},
+                         beforeSend: function() {
+                             var returnValue;
+                             if ("##{element_id.to_s}".search("access_level-") == 1) {
+                                 // We are dealing with an element having an id of the form "access_level-...":
+                                 if (data_access_level > newvalue) {
+                                     var confirmation_message = "Really " +
+                                         "change the access level of this " +
+                                         "trait to " + newvalue + "?  " +
+                                         "You will lose access to it if you " +
+                                         "do so.";
+                                     var answer = confirm(confirmation_message);
+                                     if (answer == false) {
+                                         jQuery("##{element_id.to_s}").val(previous);
+                                         jQuery("##{element_id.to_s}").addClass('alert-error', 500);
+                                         jQuery("##{element_id.to_s}").removeClass('alert-error', 500);
+                                     }
+                                     returnValue = answer;
+                                 }
+                                 else {
+                                     returnValue = true;
+                                 }
+                             }
+                             else {
+                                 // This is not an element that changes the
+                                 // access level.  Just allow it to be changed.
+                                 returnValue = true;
+                             }
+                             previous = jQuery("##{element_id.to_s}").val();
+                             return returnValue;
+
+                         },
+                         success: function() {
+                             if ("##{element_id.to_s}".search("access_level-") == 1 &&
+                                 data_access_level > newvalue) {
+                                 jQuery("##{element_id}").closest('tr').fadeOut(1000, function() { jQuery(this).remove(); });
+                             }
+                         }
+                     });
+                 })
+             })
+         </script>}
+      ).html_safe
+  else
+    raw(
+      %Q{<script>
+             jQuery(document).ready(function() {
+                 jQuery("##{element_id.to_s}").bind("#{observed_event}", function() {
+                     #{options[:function]}
+                 })
+             })
+         </script>}
+      ).html_safe
+  end
+end
diff --git a/app/models/bulk_upload_data_set.rb b/app/models/bulk_upload_data_set.rb
index a6cbd8259..f1367c972 100644
--- a/app/models/bulk_upload_data_set.rb
+++ b/app/models/bulk_upload_data_set.rb
@@ -1896,7 +1896,7 @@ def get_insertion_data
     # Get interactively-specified values, or set to empty hash if nil; since we
     # are going to alter interactively_specified_values, we use clone to make a
     # copy so that the session value remains as is.
-    interactively_specified_values = @session["global_values"].clone rescue {}
+    interactively_specified_values = @session["global_values"].clone rescue ActionController::Parameters.new
 
     # TO DO: decide if this code serves any useful purpose:
     # Double-check that all form fields are were non-empty:
@@ -1954,7 +1954,8 @@ def get_insertion_data
       csv_row_as_hash.merge!(id_values)
 
       # Merge the global interactively-specified values into this row:
-      csv_row_as_hash.merge!(global_values)
+      # To-Do: Be more specific about which values to permit.
+      csv_row_as_hash.merge!(global_values.permit!)
 
       if csv_row_as_hash.has_key?("SE")
         # apply rounding to the standard error
diff --git a/app/models/experiment.rb b/app/models/experiment.rb
index 20bea7b1d..38e7532e8 100644
--- a/app/models/experiment.rb
+++ b/app/models/experiment.rb
@@ -1,4 +1,5 @@
 class Experiment < ActiveRecord::Base
+  attr_protected []
 
   extend SimpleSearch
 
diff --git a/app/models/modeltypes_format.rb b/app/models/modeltypes_format.rb
index a3166b714..a78a8ba2c 100644
--- a/app/models/modeltypes_format.rb
+++ b/app/models/modeltypes_format.rb
@@ -1,4 +1,6 @@
 class ModeltypesFormat < ActiveRecord::Base
+  attr_protected []
+
   validates :tag,
       presence: { message: "tag can't be blank" },
       format: { with: /\A[a-z]+\z/,
diff --git a/app/views/formats/edit_formats_variables.js.erb b/app/views/formats/edit_formats_variables.js.erb
new file mode 100644
index 000000000..2a9651e4d
--- /dev/null
+++ b/app/views/formats/edit_formats_variables.js.erb
@@ -0,0 +1 @@
+jQuery('#edit_formats_variables').html("<%= escape_javascript(render 'edit_formats_variables', format: @format) %>")
diff --git a/app/views/inputs/edit_inputs_files.js.erb b/app/views/inputs/edit_inputs_files.js.erb
new file mode 100644
index 000000000..f52c48d5a
--- /dev/null
+++ b/app/views/inputs/edit_inputs_files.js.erb
@@ -0,0 +1,3 @@
+jQuery('#files_index_table').html("<%= escape_javascript(render 'edit_inputs_files_table', files: @files, input: @input, searchparam: @searchparam) %>")
+
+jQuery('#files_search_term').html("<%= search %>")
diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index edf8e5b35..450989e8d 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -2,7 +2,7 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml">
 <head>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
   <title><%= if @title then @title else "BETYdb: #{request.env['PATH_INFO']}" end %></title>
   <meta name="verify-v1" content="T7Z0mdC+KbUOu+J0CJ6oBySKYz1WUJQJLH0BOtUn1QA=" />
   <meta name="keywords" content="biofuel, biofuels, agriculture, pecan, pecanproject, miscanthus, switchgrass, willow, poplar, sugarcane, ecosystem, crop modeling" />
@@ -11,17 +11,23 @@
 
   <%= csrf_meta_tag %>
 
+  <% if params[:controller] == 'bulk_upload' %>
+    <%= stylesheet_link_tag 'bulk_upload', media: 'all', 'data-turbolinks-track': 'reload' %>
+  <% end %>
+  <%= stylesheet_link_tag 'application', media: 'all', 'data-turbolinks-track': 'reload' %>
+  <%= javascript_include_tag 'application', 'data-turbolinks-track': 'reload' %>
+
   <!-- to do: reconcile these two sets of includes: -->
 
   <!-- Set One -->
-  <%= javascript_include_tag 'lazy/jquery-1.11.0.js' %>
-  <%= javascript_include_tag 'libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.js' %>
-  <%= javascript_include_tag 'libs/jquery-migrate-1.2.1.js' %>
+  <%#= javascript_include_tag 'lazy/jquery-1.11.0.js' %>
+  <%#= javascript_include_tag 'libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.js' %>
+  <%#= javascript_include_tag 'libs/jquery-migrate-1.2.1.js' %>
 
   <!-- Set Two -->
-  <%= javascript_include_tag 'lazy/jquery-1.7.2.js' %>
-  <%= javascript_include_tag 'lazy/jquery-ui-1.10.4.min.js' %>
-  <%= stylesheet_link_tag "jquery-ui-1.10.4.min" %>
+  <%#= javascript_include_tag 'lazy/jquery-1.7.2.js' %>
+  <%#= javascript_include_tag 'lazy/jquery-ui-1.10.4.min.js' %>
+  <%#= stylesheet_link_tag "jquery-ui-1.10.4.min" %>
 
   <!--  It seems so far that everything works in 1.7.2.-->
 
@@ -31,26 +37,26 @@
 
   <!-- Since as of Rails 4, javascript_include_tag doesn't recognize the :all option, we have to do this: -->
   <% if Rails.env == "production" %>
-    <%= javascript_include_tag "cache/all" %>
+    <%#= javascript_include_tag "cache/all" %>
   <% else %>
-    <%= javascript_include_tag 'prototype.js' %>
-    <%= javascript_include_tag 'effects.js' %>
-    <%= javascript_include_tag 'bootstrap.js' %>
-    <%= javascript_include_tag 'controls.js' %>
-    <%= javascript_include_tag 'dragdrop.js' %>
-    <%= javascript_include_tag 'min.js' %>
-    <%= javascript_include_tag 'plugins.js' %>
-    <%= javascript_include_tag 'rails.js' %>
-    <%= javascript_include_tag 'script.js' %>
-    <%= javascript_include_tag 'window.js' %>
-    <%= javascript_include_tag 'application.js' %>
+    <%#= javascript_include_tag 'prototype.js' %>
+    <%#= javascript_include_tag 'effects.js' %>
+    <%#= javascript_include_tag 'bootstrap.js' %>
+    <%#= javascript_include_tag 'controls.js' %>
+    <%#= javascript_include_tag 'dragdrop.js' %>
+    <%#= javascript_include_tag 'min.js' %>
+    <%#= javascript_include_tag 'plugins.js' %>
+    <%#= javascript_include_tag 'rails.js' %>
+    <%#= javascript_include_tag 'script.js' %>
+    <%#= javascript_include_tag 'window.js' %>
+    <%#= javascript_include_tag 'application.js' %>
   <% end %>
 
   <!-- ############## BEGAN verifying all JS imports from here ############## -->
   <!--[if (lt IE 9) & (!IEMobile)]>
     <script src="js/libs/selectivizr-min.js"></script>
   <![endif]-->
-  <%= javascript_include_tag 'libs/respond.min.js', 'libs/modernizr-2.0.6.min.js' %>
+  <%#= javascript_include_tag 'libs/respond.min.js', 'libs/modernizr-2.0.6.min.js' %>
 
   <%= yield :autocomplete_javascript %>
 
@@ -68,10 +74,10 @@
   <!-- ############## ENDED verifying all JS imports from here ############## -->
 
   <!--  This disables the use of $ as the jQuery alias-->
-  <script> jQuery.noConflict(); </script>
 
-  <%= javascript_include_tag 'lazy/simple_search.js' %>
-  <%= javascript_include_tag 'lazy/application.js' %>
+
+  <%#= javascript_include_tag 'lazy/simple_search.js' %>
+  <%#= javascript_include_tag 'lazy/application.js' %>
 
   <% if params[:controller] == 'sessions' %>
     <%= javascript_include_tag 'lazy/login' %>
@@ -84,8 +90,8 @@
   <% end %>
 
   <meta name="verify-v1" content="T7Z0mdC+KbUOu+J0CJ6oBySKYz1WUJQJLH0BOtUn1QA=" />
-  <%= stylesheet_link_tag 'themes/default' %>
-  <%= stylesheet_link_tag 'themes/alphacube' %>
+  <%#= stylesheet_link_tag 'themes/default' %>
+  <%#= stylesheet_link_tag 'themes/alphacube' %>
 
   <script type="text/javascript">
     var _gaq = _gaq || [];
@@ -101,16 +107,16 @@
 
   <!-- Maintain the order of the following CSS until we can gut the "scaffold" CSS -->
   <!-- Old CSS -->
-  <%= stylesheet_link_tag "scaffold" %>
+  <%#= stylesheet_link_tag "scaffold" %>
   <!-- Redesign CSS -->
   <%= yield :schemaCSS %>
-  <%= stylesheet_link_tag "base", "grid", "layout", "dropdown", "tables", "demo" %>
+  <%#= stylesheet_link_tag "base", "grid", "layout", "dropdown", "tables", "demo" %>
 
-  <% if params[:controller] == 'bulk_upload' %>
-    <%= stylesheet_link_tag "bulk_upload" %>
-  <% end %>
+  <%# if params[:controller] == 'bulk_upload' %>
+    <%#= stylesheet_link_tag "bulk_upload" %>
+  <%# end %>
 
-  <%= stylesheet_link_tag "jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css" %>
+  <%#= stylesheet_link_tag "jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css" %>
 
 </head>
 
@@ -172,6 +178,7 @@
                 <li><%= link_to "Citations", citations_path %></li>
                 <li><%= link_to "Covariates", covariates_path %></li>
                 <li><%= link_to "Cultivars", cultivars_path %></li>
+                <li><%= link_to "Experiments", experiments_path %></li>
                 <li><%= link_to "Managements", managements_path %></li>
                 <% if current_user.page_access_level <= 2 %>
                   <li><%= link_to "Methods", methods_path %></li>
diff --git a/app/views/models/edit_models_files.js.erb b/app/views/models/edit_models_files.js.erb
new file mode 100644
index 000000000..1ccf1d780
--- /dev/null
+++ b/app/views/models/edit_models_files.js.erb
@@ -0,0 +1,3 @@
+jQuery('#files_index_table').html("<%= escape_javascript(render 'edit_models_files_table', files: @files, model: @model, searchparam: @searchparam) %>")
+
+jQuery('#files_search_term').html("<%= search %>")
diff --git a/app/views/modeltypes/edit_modeltypes_format.js.erb b/app/views/modeltypes/edit_modeltypes_format.js.erb
new file mode 100644
index 000000000..90af12094
--- /dev/null
+++ b/app/views/modeltypes/edit_modeltypes_format.js.erb
@@ -0,0 +1 @@
+jQuery("#edit_formats").html("<%= escape_javascript(render 'edit_formats', modeltype: @modeltype, modeltypes_format: @modeltypes_format) %>")
diff --git a/app/views/pfts/edit2_pfts_species.js.erb b/app/views/pfts/edit2_pfts_species.js.erb
new file mode 100644
index 000000000..8eb447348
--- /dev/null
+++ b/app/views/pfts/edit2_pfts_species.js.erb
@@ -0,0 +1,3 @@
+jQuery('#index_table').html("<%= escape_javascript(render 'edit2_pfts_species_table', species: @species, pft: @pft, search: @search) %>")
+
+jQuery('#search_term').html("<%= search %>")
diff --git a/app/views/sitegroups/edit_sitegroups_sites.js.erb b/app/views/sitegroups/edit_sitegroups_sites.js.erb
new file mode 100644
index 000000000..eedf99105
--- /dev/null
+++ b/app/views/sitegroups/edit_sitegroups_sites.js.erb
@@ -0,0 +1,3 @@
+jQuery('#sites_index_table').html("<%= escape_javascript(render 'edit_sitegroups_sites_table', sitegroup: @sitegroup, sites: @sites, searchparam: @searchparam) %>")
+
+jQuery('#search_term').html("<%= search %>")
diff --git a/app/views/sites/linked.js.erb b/app/views/sites/linked.js.erb
new file mode 100644
index 000000000..8fd35b40b
--- /dev/null
+++ b/app/views/sites/linked.js.erb
@@ -0,0 +1,7 @@
+jQuery("#site-<%= @site.id %>").remove()
+<% if @linking %>
+  jQuery("#linked").html("<%= escape_javascript(render "linked", citation: @citation) %>")
+<% end %>
+// (If unlinking, removing the site from the "linked sites" list is probably
+// sufficient even though this means we won't see the newly-unlinked sites in
+// the non-associated sites list right away.)
diff --git a/app/views/species/species_search.js.erb b/app/views/species/species_search.js.erb
new file mode 100644
index 000000000..88c0c5b79
--- /dev/null
+++ b/app/views/species/species_search.js.erb
@@ -0,0 +1,18 @@
+<% options = escape_javascript options_from_collection_for_select(@species, :id, :select_default) %>
+
+<% if params[:cont] == "species" %>
+  // This branch may be obsolete.
+  jQuery('#search_results').html(<%= @species %>)
+<% else %>
+  <% if @species.empty? == true %>
+    jQuery("<%= "#" + params[:cont] + "_specie_id" %>").html("<option value=''>There are no species that match your query.</option>")
+  <% else %>
+    jQuery("<%= "#" + params[:cont] + "_specie_id" %>").html('<%= options %>')
+  <% end %>
+<% end %>
+<% if params[:symbol].length > 3 %>
+    jQuery("#results").html("<h3>Search results for <%= sanitize(@query) %></h3>")
+<% else %>
+    jQuery("#results").html("<h3>Search must be longer then 3 characters</h3>")
+<% end %>
+
diff --git a/app/views/traits/_index_table.html.erb b/app/views/traits/_index_table.html.erb
index 61caeb48a..704705588 100644
--- a/app/views/traits/_index_table.html.erb
+++ b/app/views/traits/_index_table.html.erb
@@ -80,9 +80,11 @@
    <%= observe_field("access_level-" + trait.id.to_s,
                   :frequency => 1,
                   :with => "'id=' + #{trait.id} + '&trait[access_level]=' + Form.Element.getValue('access_level-#{trait.id.to_s}')",
-                  :url => { :action => :access_level }) %>
+                  :url => { :action => :access_level },
+                  :event_name => "change") %>
    <%= observe_field("checked-" + trait.id.to_s,
                   :frequency => 1,
                   :with => "'id=' + #{trait.id} + '&trait[checked]=' + Form.Element.getValue('checked-#{trait.id.to_s}')",
-                  :url => { :action => :checked }) %>
+                  :url => { :action => :checked },
+                  :event_name => "change") %>
 <% end %>
diff --git a/app/views/traits/_new_covariate.html.erb b/app/views/traits/_new_covariate.html.erb
index 9d266d16e..458f2517e 100644
--- a/app/views/traits/_new_covariate.html.erb
+++ b/app/views/traits/_new_covariate.html.erb
@@ -1,6 +1,6 @@
 <div class="row">
   <% if covariate.errors.size >0 %>
-    <%= content_tag(:div, "<b>Error</b> : #{(covariate.errors.get(:level))[0]}".html_safe) %>
+    <%= content_tag(:div, "<b>Error</b> : #{(covariate.errors[:level])[0]}".html_safe) %>
   <% end %>
   <div class="three columns alpha">
     <%= label_tag :variable_id %>
diff --git a/app/views/traits/access_level.js.erb b/app/views/traits/access_level.js.erb
new file mode 100644
index 000000000..6cda1274b
--- /dev/null
+++ b/app/views/traits/access_level.js.erb
@@ -0,0 +1,7 @@
+<% if @saved %>
+  jQuery("#<%= @element_id %>").addClass('alert-success', 500)
+  jQuery("#<%= @element_id %>").removeClass('alert-success', 500)
+<% else %>
+  jQuery("#<%= @element_id %>").addClass('alert-error', 500)
+  jQuery("#<%= @element_id %>").removeClass('alert-error', 500)
+<% end %>
diff --git a/app/views/traits/checked.js.erb b/app/views/traits/checked.js.erb
new file mode 100644
index 000000000..96ef48ba7
--- /dev/null
+++ b/app/views/traits/checked.js.erb
@@ -0,0 +1 @@
+jQuery("#<%= @element_id %>").html("<%= raw @message %>")
diff --git a/app/views/traits/trait_search.js.erb b/app/views/traits/trait_search.js.erb
new file mode 100644
index 000000000..4155f5f88
--- /dev/null
+++ b/app/views/traits/trait_search.js.erb
@@ -0,0 +1,2 @@
+jQuery("#results").html("<%= raw @message %>")
+jQuery("#<%= "#{params[:cont]}_trait_id" %>").html("<%= escape_javascript(@options) %>")
diff --git a/app/views/traits/unlink_covariate.js.erb b/app/views/traits/unlink_covariate.js.erb
new file mode 100644
index 000000000..f14cf7488
--- /dev/null
+++ b/app/views/traits/unlink_covariate.js.erb
@@ -0,0 +1 @@
+jQuery('#edit_covariates_traits').html("<%= escape_javascript(render 'edit_covariates_traits', trait: @trait) %>")
diff --git a/app/views/treatments/_alert.html.erb b/app/views/treatments/_alert.html.erb
new file mode 100644
index 000000000..177dd0907
--- /dev/null
+++ b/app/views/treatments/_alert.html.erb
@@ -0,0 +1,8 @@
+<% flash.each do |key, value| %>
+  <%= content_tag(:div, class: "alert alert-#{key} fade in centered") do %>
+    <div style="width:850px; margin:auto">
+      <button class="close" data-dismiss="alert">×</button>
+      <%= value %>
+    </div>
+  <% end %>
+<% end %>
diff --git a/app/views/treatments/_new_management.html.erb b/app/views/treatments/_new_management.html.erb
index cb34df395..f8140e648 100644
--- a/app/views/treatments/_new_management.html.erb
+++ b/app/views/treatments/_new_management.html.erb
@@ -1,6 +1,6 @@
 <h1>New management</h1>
 
-<%= form_for(@management) do |f| %>
+<%= form_for @management, :url => create_new_management_treatments_path, :remote => true do |f| %>
   <%= f.error_messages %>
 
 <table>
@@ -41,7 +41,7 @@
   </p>
   <p>
     <%= f.hidden_field :id, :value => @treatment.id %>
-    <%= submit_to_remote f, 'Create', :url => { :action => "create_new_management" } %>
+    <%= button_tag 'Create', :type => 'submit' %>
   </p>
     </td>
   </tr>
diff --git a/app/views/treatments/create_new_management.js.erb b/app/views/treatments/create_new_management.js.erb
new file mode 100644
index 000000000..8616301ed
--- /dev/null
+++ b/app/views/treatments/create_new_management.js.erb
@@ -0,0 +1,15 @@
+jQuery('#edit_managements_treatments').html("<%= escape_javascript(render 'edit_managements_treatments', management: @management, treatment: @treatment) %>")
+
+<% if @management.persisted? %>
+  <% @management = @management.dup %>
+  jQuery('#new_management').slideUp(800);
+<% end %>
+
+jQuery('#new_management').html("<%= escape_javascript(render 'new_management', management: @management, treatment: @treatment) %>");
+
+jQuery('div.alert').detach();
+jQuery('div.nav').after("<%= escape_javascript(render 'alert', flash: flash) %>")
+
+jQuery('button.close').on('click', function(){
+  jQuery(this).closest('div.alert').hide();
+})
diff --git a/app/views/treatments/edit.html.erb b/app/views/treatments/edit.html.erb
index fd6f19d21..12d515bc5 100644
--- a/app/views/treatments/edit.html.erb
+++ b/app/views/treatments/edit.html.erb
@@ -11,7 +11,7 @@
         <%= render 'edit_managements_treatments' %>
       </div>
       <hr />
-      <a style="text-decoration: none" href="#" onclick="showHide('new_management')" id="show_new_management">[+] Create New Management</a>
+      <a style="text-decoration: none" href="#" onclick="jQuery('#new_management').slideToggle(800)" id="show_new_management">[+] Create New Management</a>
       <br/>
       <div id="new_management" class="hidden notvisible">
         <%= render 'new_management' %>
diff --git a/app/views/treatments/edit_managements_treatments.js.erb b/app/views/treatments/edit_managements_treatments.js.erb
new file mode 100644
index 000000000..6f4b2c69a
--- /dev/null
+++ b/app/views/treatments/edit_managements_treatments.js.erb
@@ -0,0 +1 @@
+jQuery('#edit_managements_treatments').html("<%= escape_javascript(render 'edit_managements_treatments', management: @management, treatment: @treatment) %>")
diff --git a/app/views/users/edit.html.erb b/app/views/users/edit.html.erb
index c10acca02..847701451 100644
--- a/app/views/users/edit.html.erb
+++ b/app/views/users/edit.html.erb
@@ -98,8 +98,8 @@
 
 <%= observe_field("change_password",
                   :frequency => 1,
-                  :function => "var u = $('user_password'); u.disabled = !u.disabled;$('user_password_confirmation').disabled = u.disabled;") %>
-
+                  :event_name => "change",
+                  :function => "var u = jQuery('#user_password')[0]; u.disabled = !u.disabled; jQuery('#user_password_confirmation')[0].disabled = u.disabled;") %>
 
 
 
diff --git a/app/views/yields/_index_table.html.erb b/app/views/yields/_index_table.html.erb
index 4a004ca80..aefdfd0e1 100644
--- a/app/views/yields/_index_table.html.erb
+++ b/app/views/yields/_index_table.html.erb
@@ -93,11 +93,13 @@
    <%= observe_field("access_level-" + y.id.to_s,
                   :frequency => 1,
                   :with => "'id=' + #{y.id} + '&yield[access_level]=' + Form.Element.getValue('access_level-#{y.id.to_s}')",
-                  :url => { :action => :access_level }) %>
+                  :url => { :action => :access_level },
+                  :event_name => "change") %>
      <%= observe_field("checked-" + y.id.to_s,
                   :frequency => 1,
                   :with => "'id=' + #{y.id} + '&y[checked]=' + Form.Element.getValue('checked-#{y.id.to_s}')",
-                  :url => { :action => :checked }) %>
+                  :url => { :action => :checked },
+                  :event_name => "change") %>
 <% end %>
 
 
diff --git a/app/views/yields/access_level.js.erb b/app/views/yields/access_level.js.erb
new file mode 100644
index 000000000..6cda1274b
--- /dev/null
+++ b/app/views/yields/access_level.js.erb
@@ -0,0 +1,7 @@
+<% if @saved %>
+  jQuery("#<%= @element_id %>").addClass('alert-success', 500)
+  jQuery("#<%= @element_id %>").removeClass('alert-success', 500)
+<% else %>
+  jQuery("#<%= @element_id %>").addClass('alert-error', 500)
+  jQuery("#<%= @element_id %>").removeClass('alert-error', 500)
+<% end %>
diff --git a/app/views/yields/checked.js.erb b/app/views/yields/checked.js.erb
new file mode 100644
index 000000000..96ef48ba7
--- /dev/null
+++ b/app/views/yields/checked.js.erb
@@ -0,0 +1 @@
+jQuery("#<%= @element_id %>").html("<%= raw @message %>")
diff --git a/config.ru b/config.ru
index 52aeeab9d..762cedca0 100644
--- a/config.ru
+++ b/config.ru
@@ -1,4 +1,4 @@
 # This file is used by Rack-based servers to start the application.
 
 require ::File.expand_path('../config/environment',  __FILE__)
-run BetyRails3::Application
+run BetyRails5::Application
diff --git a/config/application.rb b/config/application.rb
index 4d7430fc5..d25f4194b 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -1,4 +1,4 @@
-require File.expand_path('../boot', __FILE__)
+require_relative 'boot'
 
 require 'rails/all'
 
@@ -6,7 +6,7 @@
 # you've limited to :test, :development, or :production.
 Bundler.require(*Rails.groups)
 
-module BetyRails3
+module BetyRails5
   class Application < Rails::Application
 
     # Enable Hash#deep_symbolize_keys method defined in lib/symbolize_helper.rb.
@@ -74,8 +74,5 @@ class Application < Rails::Application
 #    config.action_view.javascript_expansions[:defaults] = ['prototype', 'effects']
     # Enable the asset pipeline
     # config.assets.enabled = true
-
-    # Do not swallow errors in after_commit/after_rollback callbacks.
-    config.active_record.raise_in_transactional_callbacks = true
   end
 end
diff --git a/config/boot.rb b/config/boot.rb
index 6b750f00b..30f5120df 100644
--- a/config/boot.rb
+++ b/config/boot.rb
@@ -1,3 +1,3 @@
-ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__)
 
 require 'bundler/setup' # Set up gems listed in the Gemfile.
diff --git a/config/environment.rb b/config/environment.rb
index 01de3b5bb..0448b3ca0 100644
--- a/config/environment.rb
+++ b/config/environment.rb
@@ -1,5 +1,5 @@
 # Load the Rails application.
-require File.expand_path('../application', __FILE__)
+require_relative 'application'
 
 # Initialize the Rails application.
 Rails.application.initialize!
diff --git a/config/environments/development.rb b/config/environments/development.rb
index b55e2144b..fb101a451 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -9,13 +9,28 @@
   # Do not eager load code on boot.
   config.eager_load = false
 
-  # Show full error reports and disable caching.
-  config.consider_all_requests_local       = true
-  config.action_controller.perform_caching = false
+  # Show full error reports.
+  config.consider_all_requests_local = true
+
+  # Enable/disable caching. By default caching is disabled.
+  if Rails.root.join('tmp/caching-dev.txt').exist?
+    config.action_controller.perform_caching = true
+
+    config.cache_store = :memory_store
+    config.public_file_server.headers = {
+      'Cache-Control' => 'public, max-age=172800'
+    }
+  else
+    config.action_controller.perform_caching = false
+
+    config.cache_store = :null_store
+  end
 
   # Don't care if the mailer can't send.
   config.action_mailer.raise_delivery_errors = false
 
+  config.action_mailer.perform_caching = false
+
   # Print deprecation notices to the Rails logger.
   config.active_support.deprecation = :log
 
@@ -29,13 +44,20 @@
 
   # Asset digests allow you to set far-future HTTP expiration dates on all assets,
   # yet still be able to expire them through the digest params.
-  config.assets.digest = true
+  ## config.assets.digest = true
 
   # Adds additional error checking when serving assets at runtime.
   # Checks for improperly declared sprockets dependencies.
   # Raises helpful error messages.
-  config.assets.raise_runtime_errors = true
+  ## config.assets.raise_runtime_errors = true
+
+  # Suppress logger output for asset requests.
+  config.assets.quiet = true
 
   # Raises error for missing translations
   # config.action_view.raise_on_missing_translations = true
+
+  # Use an evented file watcher to asynchronously detect changes in source code,
+  # routes, locales, etc. This feature depends on the listen gem.
+  # config.file_watcher = ActiveSupport::EventedFileUpdateChecker
 end
diff --git a/config/environments/production.rb b/config/environments/production.rb
index 46aa8e419..bcb67ff4a 100644
--- a/config/environments/production.rb
+++ b/config/environments/production.rb
@@ -1,7 +1,6 @@
 Rails.application.configure do
   # Settings specified here will take precedence over those in config/application.rb.
 
-  # The production environment is meant for finished, "live" apps.
   # Code is not reloaded between requests.
   config.cache_classes = true
 
@@ -15,18 +14,9 @@
   config.consider_all_requests_local       = false
   config.action_controller.perform_caching = true
 
-  # Enable Rack::Cache to put a simple HTTP cache in front of your application
-  # Add `rack-cache` to your Gemfile before enabling this.
-  # For large-scale production use, consider using a caching reverse proxy like
-  # NGINX, varnish or squid.
-  # config.action_dispatch.rack_cache = true
-
   # Disable serving static files from the `/public` folder by default since
   # Apache or NGINX already handles this.
-  config.serve_static_files = ENV['RAILS_SERVE_STATIC_FILES'].present?
-
-  # Compress JavaScripts and CSS
-  ## config.assets.compress = true
+  config.public_file_server.enabled = ENV['RAILS_SERVE_STATIC_FILES'].present?
 
   # Compress JavaScripts and CSS.
   config.assets.js_compressor = :uglifier
@@ -35,16 +25,20 @@
   # Do not fallback to assets pipeline if a precompiled asset is missed.
   ## config.assets.compile = false
 
-  # Asset digests allow you to set far-future HTTP expiration dates on all assets,
-  # yet still be able to expire them through the digest params.
-  config.assets.digest = true
-
   # `config.assets.precompile` and `config.assets.version` have moved to config/initializers/assets.rb
 
+  # Enable serving of images, stylesheets, and JavaScripts from an asset server.
+  # config.action_controller.asset_host = 'http://assets.example.com'
+
   # 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
 
+  # Mount Action Cable outside main process or domain
+  # config.action_cable.mount_path = nil
+  # config.action_cable.url = 'wss://example.com/cable'
+  # config.action_cable.allowed_request_origins = [ 'http://example.com', /http:\/\/example.*/ ]
+
   # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
   # config.force_ssl = true
 
@@ -53,10 +47,7 @@
   config.log_level = :info
 
   # Prepend all log lines with the following tags.
-  # config.log_tags = [ :subdomain, :uuid ]
-
-  # Use a different logger for distributed setups.
-  # config.logger = ActiveSupport::TaggedLogging.new(SyslogLogger.new)
+  config.log_tags = [ :request_id ]
 
   # Use a different cache store in production.
   # config.cache_store = :mem_cache_store
@@ -64,8 +55,10 @@
   # set assets path
   ## config.assets.prefix = (ENV['RAILS_RELATIVE_URL_ROOT'] || "") + "/assets"
 
-  # Enable serving of images, stylesheets, and JavaScripts from an asset server.
-  # config.action_controller.asset_host = 'http://assets.example.com'
+  # Use a real queuing backend for Active Job (and separate queues per environment)
+  # config.active_job.queue_adapter     = :resque
+  # config.active_job.queue_name_prefix = "bety_rails3_#{Rails.env}"
+  config.action_mailer.perform_caching = false
 
   # Ignore bad email addresses and do not raise email delivery errors.
   # Set this to true and configure the email server for immediate delivery to raise delivery errors.
@@ -78,12 +71,19 @@
   # Send deprecation notices to registered listeners.
   config.active_support.deprecation = :notify
 
-  # Disable automatic flushing of the log to improve performance.
-  # config.autoflush_log = false
-
   # Use default logging formatter so that PID and timestamp are not suppressed.
   config.log_formatter = ::Logger::Formatter.new
 
+  # Use a different logger for distributed setups.
+  # require 'syslog/logger'
+  # config.logger = ActiveSupport::TaggedLogging.new(Syslog::Logger.new 'app-name')
+
+  if ENV["RAILS_LOG_TO_STDOUT"].present?
+    logger           = ActiveSupport::Logger.new(STDOUT)
+    logger.formatter = config.log_formatter
+    config.logger = ActiveSupport::TaggedLogging.new(logger)
+  end
+
   # Do not dump schema after migrations.
   config.active_record.dump_schema_after_migration = false
 end
diff --git a/config/environments/test.rb b/config/environments/test.rb
index 2acb5eb97..ff7c69fda 100644
--- a/config/environments/test.rb
+++ b/config/environments/test.rb
@@ -12,9 +12,11 @@
   # preloads Rails for running tests, you may have to set it to true.
   config.eager_load = false
 
-  # Configure static file server for tests with Cache-Control for performance.
-  config.serve_static_files   = true
-  config.static_cache_control = 'public, max-age=3600'
+  # Configure public file server for tests with Cache-Control for performance.
+  config.public_file_server.enabled = true
+  config.public_file_server.headers = {
+    'Cache-Control' => 'public, max-age=3600'
+  }
 
   # Show full error reports and disable caching.
   config.consider_all_requests_local       = true
@@ -25,6 +27,7 @@
 
   # Disable request forgery protection in test environment.
   config.action_controller.allow_forgery_protection = false
+  config.action_mailer.perform_caching = false
 
   # Tell Action Mailer not to deliver emails to the real world.
   # The :test delivery method accumulates sent emails in the
diff --git a/config/initializers/apipie.rb b/config/initializers/apipie.rb
index 9f3dbac94..5b3b120d1 100644
--- a/config/initializers/apipie.rb
+++ b/config/initializers/apipie.rb
@@ -6,4 +6,6 @@
   # where is your API defined?
   config.api_controllers_matcher = "#{Rails.root}/app/controllers/api/v1/*.rb"
 
+  config.translate               = false
+  config.default_locale          = nil
 end
diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb
index a459b7d5f..0098a0d6a 100644
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@@ -1,13 +1,24 @@
 # Be sure to restart your server when you modify this file.
 
 # Version of your assets, change this if you want to expire all your assets.
-# Rails.application.config.assets.version = '1.0'
+Rails.application.config.assets.version = '1.0'
+
+# Add additional assets to the asset load path
+# Rails.application.config.assets.paths << Emoji.images_path
 
 # Precompile additional assets.
 # application.js, application.css, and all non-JS/CSS in app/assets folder are already added.
 Rails.application.config.assets.precompile += %w(
-  prototype.js
-  effects.js
-  controls.js
-  dragdrop.js
-)
+  bulk_upload.css
+  schemaSpy.css
+
+  lazy/login.js
+  lazy/map_search.js
+  lazy/feedback.js
+  lazy/autocomplete.js
+  lazy/bulk_upload.js
+ )
+
+Rails.application.config.assets.paths <<
+  Rails.root.join("app", "assets", "stylesheets", "jquery-ui-1.10.4.custom",
+                  "css", "ui-lightness").to_s
diff --git a/config/routes.rb b/config/routes.rb
index c20776539..f29d908e2 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -1,4 +1,5 @@
 Rails.application.routes.draw do
+  # For details on the DSL available within this file, see http://guides.rubyonrails.org/routing.html
   apipie
   # The priority is based upon order of creation: first created -> highest priority.
   # See how all your routes lay out with "rake routes".
@@ -55,15 +56,15 @@
   #     resources :products
   #   end
 
-  # 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)))'
-
-  # route for autocompletion actions used by the bulk upload wizard:
-  get ':controller/bu_autocomplete', action: 'bu_autocomplete'
+  # routes for autocompletion actions used by the bulk upload wizard:
+  %w{citations cultivars sites species treatments}.each do |controller|
+    get "#{controller}/bu_autocomplete", controller: controller
+  end
 
-  # route for other autocompletion actions:
-  get ':controller/autocomplete', action: 'autocomplete'
+  # routes for other autocompletion actions:
+  %w{citations mimetypes inputs sites variables}.each do |controller|
+    get "#{controller}/autocomplete", controller: controller
+  end
 
   resources :yieldsviews, :only => [:show]
   resources :workflows
diff --git a/config/unicorn.rb b/config/unicorn.rb
new file mode 100644
index 000000000..a19c1d143
--- /dev/null
+++ b/config/unicorn.rb
@@ -0,0 +1,97 @@
+# Sample verbose configuration file for Unicorn (not Rack)
+#
+# This configuration file documents many features of Unicorn
+# that may not be needed for some applications. See
+# http://unicorn.bogomips.org/examples/unicorn.conf.minimal.rb
+# for a much simpler configuration file.
+#
+# See http://unicorn.bogomips.org/Unicorn/Configurator.html for complete
+# documentation.
+
+# Go with at least 1 per CPU core, a higher amount will usually help for fast
+# responses such as reading from a cache.
+worker_processes ENV['UNICORN_WORKER_PROCESSES'].to_i
+
+# Help ensure your application will always spawn in the symlinked
+# "current" directory that Capistrano sets up.
+#working_directory "/home/bety" # available in 0.94.0+
+
+# feel free to point this anywhere accessible on the filesystem
+#pid "/home/bety/tmp/pids/unicorn.pid"
+
+# Listen on both a Unix domain socket and a TCP port.
+# If you are load-balancing multiple Unicorn masters, lower the backlog
+# setting to e.g. 64 for faster failover.
+#listen "/home/git/gitlab/tmp/sockets/gitlab.socket", :backlog => 1024
+#listen "127.0.0.1:8080", :tcp_nopush => true
+listen "0.0.0.0:" + ENV['UNICORN_PORT']
+
+# nuke workers after 30 seconds instead of 60 seconds (the default)
+timeout 30
+
+# By default, the Unicorn logger will write to stderr.
+# Additionally, some applications/frameworks log to stderr or stdout,
+# so prevent them from going to /dev/null when daemonized here:
+#stderr_path "/home/bety/log/unicorn.stderr.log"
+#stdout_path "/home/bety/log/unicorn.stdout.log"
+
+# combine Ruby 2.0.0dev or REE with "preload_app true" for memory savings
+# http://rubyenterpriseedition.com/faq.html#adapt_apps_for_cow
+preload_app true
+GC.respond_to?(:copy_on_write_friendly=) and
+  GC.copy_on_write_friendly = true
+
+# Enable this flag to have unicorn test client connections by writing the
+# beginning of the HTTP headers before calling the application.  This
+# prevents calling the application for connections that have disconnected
+# while queued.  This is only guaranteed to detect clients on the same
+# host unicorn runs on, and unlikely to detect disconnects even on a
+# fast LAN.
+check_client_connection false
+
+before_fork do |server, worker|
+  # the following is highly recommended for Rails + "preload_app true"
+  # as there's no need for the master process to hold a connection
+  defined?(ActiveRecord::Base) and
+    ActiveRecord::Base.connection.disconnect!
+
+  # The following is only recommended for memory/DB-constrained
+  # installations.  It is not needed if your system can house
+  # twice as many worker_processes as you have configured.
+  #
+  # This allows a new master process to incrementally
+  # phase out the old master process with SIGTTOU to avoid a
+  # thundering herd (especially in the "preload_app false" case)
+  # when doing a transparent upgrade.  The last worker spawned
+  # will then kill off the old master process with a SIGQUIT.
+  old_pid = "#{server.config[:pid]}.oldbin"
+  if old_pid != server.pid
+    begin
+      sig = (worker.nr + 1) >= server.worker_processes ? :QUIT : :TTOU
+      Process.kill(sig, File.read(old_pid).to_i)
+    rescue Errno::ENOENT, Errno::ESRCH
+    end
+  end
+  #
+  # Throttle the master from forking too quickly by sleeping.  Due
+  # to the implementation of standard Unix signal handlers, this
+  # helps (but does not completely) prevent identical, repeated signals
+  # from being lost when the receiving process is busy.
+  # sleep 1
+end
+
+after_fork do |server, worker|
+  # per-process listener ports for debugging/admin/migrations
+  # addr = "127.0.0.1:#{9293 + worker.nr}"
+  # server.listen(addr, :tries => -1, :delay => 5, :tcp_nopush => true)
+
+  # the following is *required* for Rails + "preload_app true",
+  defined?(ActiveRecord::Base) and
+    ActiveRecord::Base.establish_connection
+
+  # if preload_app is true, then you may also want to check and
+  # restart any other shared sockets/descriptors such as Memcached,
+  # and Redis.  TokyoCabinet file handles are safe to reuse
+  # between any number of forked children (assuming your kernel
+  # correctly implements pread()/pwrite() system calls)
+end
diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 000000000..e85ac47c2
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,46 @@
+version: "3"
+
+services:
+  # BETY rails frontend to the database
+  bety:
+    image: pecan/bety:unicorn
+    networks:
+      - bety
+    ports:
+      - 8000
+    environment:
+      - UNICORN_WORKER_PROCESSES=1
+      - SECRET_KEY_BASE=thisissomereallllllylongsecretkeyandshouldbelongerthanthis
+    depends_on:
+      - postgres
+    restart: unless-stopped
+    deploy:
+      mode: replicated
+      restart_policy:
+        condition: any
+      placement:
+        constraints: [node.role == manager]
+
+  # postgresql + postgis to hold all the data
+  postgres:
+    image: mdillon/postgis:9.5
+    networks:
+      - bety
+    #ports:
+    #  - 5432
+    volumes:
+      - postgres:/var/lib/postgresql/data
+    restart: unless-stopped
+    deploy:
+      mode: replicated
+      restart_policy:
+        condition: any
+      placement:
+        constraints: [node.role == worker]
+
+networks:
+  bety:
+
+volumes:
+  postgres:
+
diff --git a/docker/config.ru b/docker/config.ru
new file mode 100644
index 000000000..bbdec59fd
--- /dev/null
+++ b/docker/config.ru
@@ -0,0 +1,7 @@
+# This file is used by Rack-based servers to start the application.
+
+require ::File.expand_path('../config/environment',  __FILE__)
+
+map (ENV['RAILS_RELATIVE_URL_ROOT'] || "") + "/" do
+    run BetyRails5::Application
+end
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
deleted file mode 100644
index 1ca4e4d45..000000000
--- a/docker/docker-compose.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-# ruby & bety
-bety:
-  image: pecan/bety:develop
-  ports:
-    - "3000"
-  links:
-    - postgres:pg
-
-# postgres database
-postgres:
-  image: mdillon/postgis:9.4
-  ports:
-    - "5432"
diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh
index 83ba8859e..3b7551474 100755
--- a/docker/entrypoint.sh
+++ b/docker/entrypoint.sh
@@ -1,33 +1,14 @@
 #!/bin/bash
 
-function wait_for_postgres() {
-    echo "Waiting for postgres"
-    # Wait for Postgres to start
-    # http://www.onegeek.com.au/articles/waiting-for-dependencies-in-docker-compose
-    WAIT=0
-    while ! nc -w 1 -z postgres 5432; do
-      sleep 1
-      WAIT=$(($WAIT + 1))
-      echo "Try ${WAIT}"
-      if [ "$WAIT" -gt 15 ]; then
-        echo "Error: Timeout wating for Postgres to start"
-        exit 1
-      fi
-    done
-}
-
 # start right job
 case $1 in
     "initialize" )
-        wait_for_postgres
-        SERVER=$( echo ${REMOTE_SERVERS} | awk '{print $1}' )
-        echo "Create new database, initialized from server ${SERVER}"
+        echo "Create new database, initialized from all data."
         psql -h postgres -p 5432 -U postgres -c "CREATE ROLE bety WITH LOGIN CREATEDB NOSUPERUSER NOCREATEROLE PASSWORD 'bety'"
         psql -h postgres -p 5432 -U postgres -c "CREATE DATABASE bety WITH OWNER bety"
-        ./load.bety.sh -a "postgres" -d "bety" -p "-h postgres -p 5432" -o bety -c -u -g -m ${LOCAL_SERVER} -r ${SERVER}
+        ./load.bety.sh -a "postgres" -d "bety" -p "-h postgres -p 5432" -o bety -c -u -g -m ${LOCAL_SERVER} -r 0 -w https://ebi-forecast.igb.illinois.edu/pecan/dumpall/bety.tar.gz
         ;;
     "sync" )
-        wait_for_postgres
         echo "Synchronize with servers ${REMOTE_SERVERS}"
         for r in ${REMOTE_SERVERS}; do
             echo "Synchronizing with server ${r}"
@@ -35,28 +16,48 @@ case $1 in
         done
         ;;
     "dump" )
-        wait_for_postgres
         echo "Dump data from server ${LOCAL_SERVER}"
         ./dump.bety.sh -d "bety" -p "-h postgres -p 5432 -U postgres" -m ${LOCAL_SERVER} -o dump
         ;;
     "migrate" )
-        wait_for_postgres
-        echo "Migrate databae."
+        echo "Migrate database."
         rake db:migrate SKIP_SCHEMASPY=YES
         ;;
     "server" )
-        wait_for_postgres
-        echo "Start running BETY"
+        echo "Start running BETY (rails server)"
         exec rails s
         ;;
+    "unicorn" )
+        if [ "$RAILS_RELATIVE_URL_ROOT" != "" ]; then
+            echo "Compiling assests."
+            bundle exec rake assets:precompile
+        fi
+        echo "Start running BETY (unicorn)"
+        exec bundle exec unicorn -c config/unicorn.rb
+        ;;
+    "autoserver" )
+        echo "Migrate database."
+        rake db:migrate SKIP_SCHEMASPY=YES
+        if [ "$RAILS_RELATIVE_URL_ROOT" != "" ]; then
+            echo "Compiling assests."
+            bundle exec rake assets:precompile
+        fi
+        echo "Start running BETY (unicorn)"
+        exec bundle exec unicorn -c config/unicorn.rb
+        ;;
     "help" )
-        echo "initialize : create a new database and initialize with data from server 0"
+        echo "initialize : create a new database and initialize with all data from server 0"
         echo "sync       : synchronize database with remote servers ${REMOTE_SERVERS}"
         echo "dump       : dumps local database"
         echo "migrate    : migrates the database to a new version of bety"
-        echo "server     : runs the server"
+        echo "server     : runs the server (using rails server)"
+        echo "unicorn    : runs the server (using unicorn)"
+        echo "autoserver : runs the server (using unicorn) after running a migrate"
         echo "help       : this text"
+        echo ""
+        echo "Default is to run bety using unicorn. no automatic migrations."
         ;;
     * )
         exec "$@"
+        ;;
 esac
diff --git a/lib/tasks/databases-hack.rake b/lib/tasks/databases-hack.rake
index 05c8219c8..16ef144ef 100644
--- a/lib/tasks/databases-hack.rake
+++ b/lib/tasks/databases-hack.rake
@@ -22,16 +22,6 @@
 end
 =end
 
-# gems/activerecord-3.2.21/lib/active_record/railties/databases.rake:521
-# defines db:test:clone_structure with prerequisites db:structure:dump
-# and db:test:load_structure and no actions.  The postgis adapter Gem
-# overrides this in
-# "gems/activerecord-postgis-adapter-0.6.6/lib/active_record/connection_adapters/postgis_adapter/rails3/databases.rake",
-# adding an action to set run the structure file directly.  This is
-# redundant, so we clear out that action.
-Rake::Task["db:test:clone_structure"].clear_actions
-
-
 # Add descriptions for test-database-related tasks:
 Rake::Task["db:test:load_structure"].add_description(<<DESC
 Loads the test database with database structure defined in the file "db/<RAILS_ENV>_structure.sql",
@@ -41,15 +31,6 @@ recreate it.
 DESC
 )
 
-Rake::Task["db:test:clone_structure"].add_description(<<DESC
-Clones the structure of the current environment and then loads it into the test database.
-It will first run db:test:purge to drop the test database (if it exists) and
-recreate it.  Then it creates (or recreates) the structure.sql file for the
-current environment ("db/<RAILS_ENV>_structure.sql") and loads it into the test
-database.
-DESC
-)
-
 namespace :db do
   namespace :fixtures do
     task :load => :block_for_non_test_env
diff --git a/public/javascripts/application.js b/public/javascripts/application.js
deleted file mode 100644
index 767991890..000000000
--- a/public/javascripts/application.js
+++ /dev/null
@@ -1,4 +0,0 @@
-// Place your application-specific JavaScript functions and classes here
-// This file is automatically included by javascript_include_tag :defaults
-
-
diff --git a/script/update-betydb.sh b/script/update-betydb.sh
index d1984562b..4aaa12e6d 100755
--- a/script/update-betydb.sh
+++ b/script/update-betydb.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # The source for load.bety.sh:
-SCRIPT_SOURCE_LOCATION=https://raw.githubusercontent.com/PecanProject/pecan/master/scripts/load.bety.sh
+SCRIPT_SOURCE_LOCATION=https://raw.githubusercontent.com/PecanProject/pecan/develop/scripts/load.bety.sh
 
 # These are options we want to pass through to load.bety.sh.  Update this as
 # needed if load.bety.sh is revised:
diff --git a/spec/api/trait_insertion_api_spec.rb b/spec/api/trait_insertion_api_spec.rb
index cc14432b2..88855ee7c 100644
--- a/spec/api/trait_insertion_api_spec.rb
+++ b/spec/api/trait_insertion_api_spec.rb
@@ -24,7 +24,7 @@
 
         aggregate_failures "Insertion works correctly" do
           expect {
-            post "#{path}?key=3333333333333333333333333333333333333333", valid_data_doc
+            post "#{path}?key=3333333333333333333333333333333333333333", params: valid_data_doc
           }.to change { Trait.count }.by(num_new_traits)
             .and change { Entity.count }.by(num_new_entities)
             .and change { Covariate.count }.by(num_new_covariates)
@@ -51,7 +51,7 @@
 
         aggregate_failures "Insertion fails without proper authorization" do
           expect {
-            post "#{path}?key=4444444444444444444444444444444444444444", valid_data_doc
+            post "#{path}?key=4444444444444444444444444444444444444444", params: valid_data_doc
           }.to change { Trait.count }.by(0)
             .and change { Entity.count }.by(0)
             .and change { Covariate.count }.by(0)
@@ -75,7 +75,7 @@
     include_examples "format", "spec/fixtures/files/api/v1/valid-test-data.json", "JSON", "", "application/json"
 
     specify "Sending a malformed JSON document should return a Bad Request status" do
-      post "/api/v1/traits?key=3333333333333333333333333333333333333333", "{ no-closing-brace "
+      post "/api/v1/traits?key=3333333333333333333333333333333333333333", params: "{ no-closing-brace "
       aggregate_failures do
         expect(response.status).to eq 400
         expect(response.content_type).to eq "application/json"
@@ -93,7 +93,7 @@
     include_examples "format", "spec/fixtures/files/api/v1/valid-test-data.xml", "XML", ".xml", "application/xml"
 
     specify "Sending a malformed XML document should return a Bad Request status" do
-      post "/api/v1/traits.xml?key=3333333333333333333333333333333333333333", "<no-closing-tag>"
+      post "/api/v1/traits.xml?key=3333333333333333333333333333333333333333", params: "<no-closing-tag>"
       aggregate_failures do
         expect(response.status).to eq 400
         expect(response.content_type).to eq "application/xml"
@@ -106,7 +106,7 @@
     end
 
     specify "Sending an invalid XML document should return a Bad Request status" do
-      post "/api/v1/traits.xml?key=3333333333333333333333333333333333333333", "<xml-doc-not-conforming-to-schema/>"
+      post "/api/v1/traits.xml?key=3333333333333333333333333333333333333333", params: "<xml-doc-not-conforming-to-schema/>"
       aggregate_failures do
         expect(response.status).to eq 400
         expect(response.content_type).to eq "application/xml"
@@ -128,7 +128,7 @@
 
       expect {
         post "/api/v1/traits.csv?key=3333333333333333333333333333333333333333",
-          File.open(Rails.root.join "spec/fixtures/files/api/v1/missing-meta-data.csv").read
+          params: File.open(Rails.root.join "spec/fixtures/files/api/v1/missing-meta-data.csv").read
       }.not_to change { Trait.count }
 
     end
@@ -137,7 +137,7 @@
 
       expect {
         post "/api/v1/traits.csv?key=3333333333333333333333333333333333333333",
-          File.open(Rails.root.join "spec/fixtures/files/api/v1/missing-meta-data.csv").read
+          params: File.open(Rails.root.join "spec/fixtures/files/api/v1/missing-meta-data.csv").read
       }.not_to change { Entity.count }
 
     end
@@ -146,7 +146,7 @@
 
       expect {
         post "/api/v1/traits.csv?key=3333333333333333333333333333333333333333",
-          File.open(Rails.root.join "spec/fixtures/files/api/v1/out-of-range-data.csv").read
+          params: File.open(Rails.root.join "spec/fixtures/files/api/v1/out-of-range-data.csv").read
       }.not_to change { Entity.count }
 
     end
diff --git a/spec/controllers/bulk_upload_controller_spec.rb b/spec/controllers/bulk_upload_controller_spec.rb
index e033ec77f..2dc77c361 100644
--- a/spec/controllers/bulk_upload_controller_spec.rb
+++ b/spec/controllers/bulk_upload_controller_spec.rb
@@ -3,7 +3,7 @@
 
   class BulkUploadController
     # override the login requirement for testing:
-    before_filter :login_required, only: []
+    before_action :login_required, only: []
   end
 
   describe "display csv file" do
@@ -16,7 +16,7 @@ class BulkUploadController
 
       it "should display an error when no file has been uploaded" do
 
-        post 'display_csv_file', { 'new upload' => true }
+        post 'display_csv_file', params: { 'new upload' => true }
         assert_equal("No file chosen", flash[:error] )
         assert_operator(200, :!=, response.status) # Since this is a redirect, we should get 302; this test is somewhat redundant in view of the next.
         assert_redirected_to '/bulk_upload/start_upload', "Failed to redirect when no file chosen"
@@ -25,7 +25,7 @@ class BulkUploadController
       it "should create a data set when a well-formed CSV file is uploaded" do
 
         @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
-        post 'display_csv_file', { 'new upload' => true, "CSV file" => @file }
+        post 'display_csv_file', params: { 'new upload' => true, "CSV file" => @file }
         assert(!assigns(:data_set).nil?)
         assert_instance_of BulkUploadDataSet, assigns(:data_set), "Failed to return dataset instance"
       end
@@ -35,7 +35,7 @@ class BulkUploadController
 
         @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
         session[:csvpath] = @file.path
-        post 'display_csv_file', { 'new upload' => false }
+        post 'display_csv_file', params: { 'new upload' => false }
         assert(!assigns(:data_set).nil?)
         assert_instance_of BulkUploadDataSet, assigns(:data_set), "Failed to return dataset instance"
       end
@@ -45,7 +45,7 @@ class BulkUploadController
         @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
         session[:csvpath] = @file.path
         get 'start_upload'
-        post 'display_csv_file', { 'CSV file' => nil }
+        post 'display_csv_file', params: { 'CSV file' => nil }
         assert_equal("No file chosen", flash[:error])
         assert_operator(200, :!=, response.status)
         assert_redirected_to '/bulk_upload/start_upload', "Failed to redirect when no file chosen"
@@ -66,14 +66,14 @@ class BulkUploadController
         it "should remove a linked citation when a file is uploaded that includes citation information" do
 
           session[:citation] = 1
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           assert_nil session[:citation], "Failed to remove citation from session"
           expect(flash[:warning]).to match(/^Removing/i)
         end
 
         it "should validate the file data" do
 
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           @dataset = assigns(:data_set)
           @validated_data = @dataset.validated_data
           assert(!@validated_data.nil?, "Failed to validate rows")
@@ -95,7 +95,7 @@ class BulkUploadController
         ## some error at the data insertion step if they have a null or wrong citation...
         it "should not allow visiting the 'choose_global_data_values' page without having choosen a citation" do
 
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           session[:citation] = nil
           get 'choose_global_data_values'
           assert_operator(200, :!=, response.status, "Failed to stop when no citation present")
@@ -105,7 +105,7 @@ class BulkUploadController
         it "should not allow visiting the 'choose_global_data_values' page when a citation inconsistent with the data set has been chosen" do
 
           session[:citation] = 4
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           @dataset = assigns(:data_set)
           # Ensure the citation we set actually *is* inconsistent:
           assert(@dataset.validation_summary.has_key?("Site is inconsistent with citation") && 
@@ -123,7 +123,7 @@ class BulkUploadController
 
           @file = fixture_file_upload("/files/bulk_upload/invalid_file.csv", "text/csv")
           @form = { 'new upload' => true, "CSV file" => @file }
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           assert(!flash[:error].nil?, "Failed to display error message")
           assert_redirected_to '/bulk_upload/start_upload', "Failed to redirect to start upload"
         end
@@ -139,7 +139,7 @@ class BulkUploadController
       get 'start_upload'
       @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
       @form = { 'new upload' => true, "CSV file" => @file }
-      post 'display_csv_file', @form
+      post 'display_csv_file', params: @form
       get 'choose_global_data_values'
     end
 
@@ -156,11 +156,11 @@ class BulkUploadController
     before(:each) do
       get 'start_upload'
       @file = fixture_file_upload("/files/bulk_upload/rounding_demo.csv", "text/csv")
-      post 'display_csv_file', { 'new upload' => true, "CSV file" => @file }
+      post 'display_csv_file', params: { 'new upload' => true, "CSV file" => @file }
       get 'choose_global_data_values'
       @values ={ "global_values" => {}, "rounding" => { "yields" => "2" } }
       request.env["HTTP_REFERER"] = 'choose_global_data_values'
-      post 'confirm_data', @values
+      post 'confirm_data', params: @values
     end
 
     it "should return a new dataset" do
@@ -190,11 +190,11 @@ class BulkUploadController
     before(:each) do
       @count = Yield.count
       @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
-      post 'display_csv_file', { 'new upload' => true, "CSV file" => @file }
+      post 'display_csv_file', params: { 'new upload' => true, "CSV file" => @file }
       get 'choose_global_data_values'
       @values ={ "global_values" => {}, "rounding" => { "yields" => "2" } }
       request.env["HTTP_REFERER"] = 'choose_global_data_values'
-      post 'confirm_data', @values
+      post 'confirm_data', params: @values
       session[:user_id] = 1 # needed for the insertion step
       post 'insert_data'
     end
diff --git a/spec/controllers/traits_controller_spec.rb b/spec/controllers/traits_controller_spec.rb
index 983cdd99e..3635d1aba 100644
--- a/spec/controllers/traits_controller_spec.rb
+++ b/spec/controllers/traits_controller_spec.rb
@@ -21,13 +21,13 @@
 	context'message on invalid input' do
     it 'should not return success message' do
 			trait = Trait.find_by_id('2')
-	    post :update,{:id =>trait.to_param,:trait => invalid_attr},session
+	    post :update, params: {:id =>trait.to_param, :trait => invalid_attr}, session: session
 	    assert_operator(flash[:notice], :!=, "Trait was successfully updated.")
 	  end
 
     it 'should return error message' do
 	    trait = Trait.find_by_id('2')
-	    post :update,{:id =>trait.to_param,:covariate => invalid_covariate},session
+	    post :update, params: {:id =>trait.to_param, :covariate => invalid_covariate}, session: session
 	    assert(!flash[:error].nil?)
 	  end
 	end
@@ -38,21 +38,21 @@
     end
 
     it 'should not modify attribute if covariate is invalid' do
-	    post :update,{:id =>@trait.to_param, :covariate => invalid_covariate, :trait =>valid_attr},session
+	    post :update, params: {:id => @trait.to_param, :covariate => invalid_covariate, :trait =>valid_attr}, session: session
       new_trait = Trait.find_by_id('2')
       assert_equal(@trait.mean, new_trait.mean)
     end
 
     it 'should not modify covariate list if attribute is invalid' do
       old_size = @trait.covariates.size
-	    post :update,{:id =>@trait.to_param, :covariate => valid_covariate, :trait => invalid_attr},session
+	    post :update, params: {:id => @trait.to_param, :covariate => valid_covariate, :trait => invalid_attr}, session: session
       new_trait = Trait.find_by_id('2')
       assert_equal(old_size, new_trait.covariates.size)
     end
 
     it 'should not modify covariate list if any covariate is invalid' do
       old_size = @trait.covariates.size
-	    post :update,{:id =>@trait.to_param, :covariate => mixed_covariate, :trait =>valid_attr},session
+	    post :update, params: {:id => @trait.to_param, :covariate => mixed_covariate, :trait =>valid_attr}, session: session
       new_trait = Trait.find_by_id('2')
       assert_equal(old_size, new_trait.covariates.size)
     end
@@ -65,22 +65,22 @@
     end
 
     it "should render edit action" do
-	    post :update,{:id =>@trait.to_param,:trait => invalid_attr},session
+	    post :update, params: {:id => @trait.to_param, :trait => invalid_attr}, session: session
 	    assert_template 'edit', "Failed to render edit action"
     end
 
     it "should display error messages" do
-	    post :update,{:id =>@trait.to_param,:trait => invalid_attr},session
+	    post :update, params: {:id => @trait.to_param, :trait => invalid_attr}, session: session
 	    expect(response.body).to have_content("2 errors")
     end
 
     it "should not change attribute inputs" do
-	    post :update,{:id =>@trait.to_param,:trait => invalid_attr},session
+	    post :update, params: {:id => @trait.to_param, :trait => invalid_attr}, session: session
       expect(response.body).to have_selector("input#trait_mean[value = '#{invalid_attr[:mean]}']")
     end
 
     it "should not change covariate inputs" do
-	    post :update,{:id =>@trait.to_param,:trait => invalid_attr, :covariate =>invalid_covariate},session
+	    post :update, params: {:id => @trait.to_param, :trait => invalid_attr, :covariate =>invalid_covariate}, session: session
 	    expect(response.body).to have_xpath(".//select[@id='covariate__variable_id']/option[@value='404' and @selected='selected']")
     end
   end
diff --git a/spec/controllers/treatments_controller_spec.rb b/spec/controllers/treatments_controller_spec.rb
index bf857c510..15bcdeb60 100644
--- a/spec/controllers/treatments_controller_spec.rb
+++ b/spec/controllers/treatments_controller_spec.rb
@@ -24,6 +24,8 @@
   # adjust the attributes here as well.
   let(:valid_attributes) { { name: "bogus" } }
 
+  let(:invalid_attribute_set) { { name: nil } }
+
   # This should return the minimal set of values that should be in the session
   # in order to pass any filters (e.g. authentication) defined in
   # TreatmentsController. Be sure to keep this updated too.
@@ -35,24 +37,24 @@
   }
 
   describe "GET index" do
-    it "assigns all treatments as @treatments" do
-      treatment = Treatment.first
-      get :index, {}, valid_session
-      expect(assigns(:treatments)).to eq([treatment])
+    it "assigns all treatments associated with the session citation as @treatments" do
+      treatments = Citation.find(valid_session[:citation]).treatments
+      get :index, params: {}, session: valid_session
+      expect(assigns(:treatments)).to eq(treatments)
     end
   end
 
   describe "GET show" do
     it "assigns the requested treatment as @treatment" do
       treatment = Treatment.create! valid_attributes
-      get :show, {:id => treatment.to_param}, valid_session
+      get :show, params: {:id => treatment.to_param}, session: valid_session
       expect(assigns(:treatment)).to eq(treatment)
     end
   end
 
   describe "GET new" do
     it "assigns a new treatment as @treatment" do
-      get :new, {}, valid_session
+      get :new, params: {}, session: valid_session
       expect(assigns(:treatment)).to be_a_new(Treatment)
     end
   end
@@ -60,7 +62,7 @@
   describe "GET edit" do
     it "assigns the requested treatment as @treatment" do
       treatment = Treatment.create! valid_attributes
-      get :edit, {:id => treatment.to_param}, valid_session
+      get :edit, params: {:id => treatment.to_param}, session: valid_session
       expect(assigns(:treatment)).to eq(treatment)
     end
   end
@@ -69,18 +71,18 @@
     describe "with valid params" do
       it "creates a new Treatment" do
         expect {
-          post :create, {:treatment => valid_attributes}, valid_session
+          post :create, params: {:treatment => valid_attributes}, session: valid_session
         }.to change(Treatment, :count).by(1)
       end
 
       it "assigns a newly created treatment as @treatment" do
-        post :create, {:treatment => valid_attributes}, valid_session
+        post :create, params: {:treatment => valid_attributes}, session: valid_session
         expect(assigns(:treatment)).to be_a(Treatment)
         expect(assigns(:treatment)).to be_persisted
       end
 
       it "redirects to the treatment index page" do
-        post :create, {:treatment => valid_attributes}, valid_session
+        post :create, params: {:treatment => valid_attributes}, session: valid_session
         expect(response).to redirect_to(action: :index)
       end
     end
@@ -89,14 +91,14 @@
       it "assigns a newly created but unsaved treatment as @treatment" do
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        post :create, {:treatment => {  }}, valid_session
+        post :create, params: {}, session: valid_session
         expect(assigns(:treatment)).to be_a_new(Treatment)
       end
 
       it "re-renders the 'new' template" do
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        post :create, {:treatment => {  }}, valid_session
+        post :create, params: {}, session: valid_session
         expect(response).to render_template("new")
       end
     end
@@ -110,19 +112,19 @@
         # specifies that the Treatment created on the previous line
         # receives the :update_attributes message with whatever params are
         # submitted in the request.
-        expect_any_instance_of(Treatment).to receive(:update_attributes).with({ "these" => "params" })
-        put :update, {:id => treatment.to_param, :treatment => { "these" => "params" }}, valid_session
+        expect_any_instance_of(Treatment).to receive(:update_attributes).with(ActionController::Parameters.new({ "these" => "params" }))
+        put :update, params: {:id => treatment.to_param, :treatment => { "these" => "params" }}, session: valid_session
       end
 
       it "assigns the requested treatment as @treatment" do
         treatment = Treatment.create! valid_attributes
-        put :update, {:id => treatment.to_param, :treatment => valid_attributes}, valid_session
+        put :update, params: {:id => treatment.to_param, :treatment => valid_attributes}, session: valid_session
         expect(assigns(:treatment)).to eq(treatment)
       end
 
       it "redirects to the treatment index page" do
         treatment = Treatment.create! valid_attributes
-        put :update, {:id => treatment.to_param, :treatment => valid_attributes}, valid_session
+        put :update, params: {:id => treatment.to_param, :treatment => valid_attributes}, session: valid_session
         expect(response).to redirect_to(treatments_path)
       end
     end
@@ -132,7 +134,7 @@
         treatment = Treatment.create! valid_attributes
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        put :update, {:id => treatment.to_param, :treatment => {  }}, valid_session
+        put :update, params: {:id => treatment.to_param, :treatment => invalid_attribute_set}, session: valid_session
         expect(assigns(:treatment)).to eq(treatment)
       end
 
@@ -140,7 +142,7 @@
         treatment = Treatment.create! valid_attributes
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        put :update, {:id => treatment.to_param, :treatment => {  }}, valid_session
+        put :update, params: {:id => treatment.to_param, :treatment => invalid_attribute_set}, session: valid_session
         expect(response).to render_template("edit")
       end
     end
@@ -150,13 +152,13 @@
     it "destroys the requested treatment" do
       treatment = Treatment.create! valid_attributes
       expect {
-        delete :destroy, {:id => treatment.to_param}, valid_session
+        delete :destroy, params: {:id => treatment.to_param}, session: valid_session
       }.to change(Treatment, :count).by(-1)
     end
 
     it "redirects to the treatments list" do
       treatment = Treatment.create! valid_attributes
-      delete :destroy, {:id => treatment.to_param}, valid_session
+      delete :destroy, params: {:id => treatment.to_param}, session: valid_session
       expect(response).to redirect_to(treatments_path)
     end
   end
diff --git a/spec/features/bulk_upload_integration_2_spec.rb b/spec/features/bulk_upload_integration_2_spec.rb
index 0ecbe017a..af934850c 100644
--- a/spec/features/bulk_upload_integration_2_spec.rb
+++ b/spec/features/bulk_upload_integration_2_spec.rb
@@ -447,7 +447,7 @@
                      : 30 # than for WebKit
         begin
           # Wrap while loops in timeout in case some deletion fails
-          timeout time_limit do
+          Timeout.timeout time_limit do
 
             # Remove covariates before traits because they refer to traits:
             visit '/covariates'
diff --git a/spec/features/site_integration_spec.rb b/spec/features/site_integration_spec.rb
index fa956ace4..cd488431d 100644
--- a/spec/features/site_integration_spec.rb
+++ b/spec/features/site_integration_spec.rb
@@ -56,7 +56,7 @@
       it 'show allow adding new related citations', js: true do
         click_link 'View Related Citations'
         fill_in 'search_citations', with: 'Wood'
-        sleep 1
+        sleep 2 # 1 often isn't enough
         click_link '+'
         click_button 'Update'
         # reopen related citations listing
diff --git a/spec/features/treatment_integration_spec.rb b/spec/features/treatment_integration_spec.rb
index 01ab0f585..d5dc634d1 100644
--- a/spec/features/treatment_integration_spec.rb
+++ b/spec/features/treatment_integration_spec.rb
@@ -58,7 +58,7 @@
         click_link 'View Related Managements'
         page.select 'planting', from: 'management_id'
         click_button 'Select'
-        expect(page).to have_content 'planting'
+        expect(page.find('table table')).to have_content 'planting'
 
       # now do clean-up:
       page.find(:xpath, ".//table/tbody/tr[preceding-sibling::tr/th/text() = 'Type'][contains(td[last()], 'planting')]/td/a[text() = 'X']").click
diff --git a/spec/support/helpers.rb b/spec/support/helpers.rb
index f744ba912..c477a54d3 100644
--- a/spec/support/helpers.rb
+++ b/spec/support/helpers.rb
@@ -41,7 +41,7 @@ def choose_citation_from_dropdown(author = 'Adler')
     sleep 1 # maybe not needed
     page.execute_script("jQuery('#autocomplete_citation').trigger('keydown', {keyCode: 40})")
     sleep 1 # necessary!
-    first("#ui-id-1 li.ui-menu-item a").click
+    first("#ui-id-1 li.ui-menu-item > *").click
     click_button "View Validation Results"
   end
 end
@@ -49,7 +49,7 @@ def choose_citation_from_dropdown(author = 'Adler')
 module AutocompletionHelper
   def fill_autocomplete(field_id, options = {})
     fill_in field_id, :with => options[:with]
-    selector = "ul.ui-autocomplete a:contains('#{options[:select]}')"
+    selector = "ul.ui-autocomplete div:contains('#{options[:select]}')"
 
     # RSpec doesn't seem to recognize the :contains syntax for selectors
     #page.should have_selector selector
diff --git a/test/fixtures/machines.yml b/test/fixtures/machines.yml
index 061f9c015..f70798465 100644
--- a/test/fixtures/machines.yml
+++ b/test/fixtures/machines.yml
@@ -1,4 +1,5 @@
 test_machine:
+  id: 1
   hostname: "ebi-cluster.igb.illinois.edu"
   created_at: "2012-04-26 13:07:08"
   updated_at: "2012-12-26 23:53:39"