merge with helma/development

46 files changed, 2163 insertions, 0 deletions

diff --git a/application.rb b/application.rb
new file mode 100644
index 0000000..fe9b8b4
--- /dev/null
+++ b/application.rb
@@ -0,0 +1,354 @@
+['rubygems', "haml", "sass", "rack-flash"].each do |lib|
+  require lib
+end
+gem "opentox-ruby", "~> 0"
+require 'opentox-ruby'
+gem 'sinatra-static-assets'
+require 'sinatra/static_assets'
+require 'ftools'
+require File.join(File.dirname(__FILE__),'model.rb')
+require File.join(File.dirname(__FILE__),'helper.rb')
+#require File.join(File.dirname(__FILE__),'parser.rb')
+
+use Rack::Flash
+set :sessions, true
+
+helpers do 
+
+  def error(message)
+    @model.error_messages = message
+    LOGGER.error message
+    @model.status = "Error"
+    @model.save
+    #@dataset.delete
+    flash[:notice] = message
+    redirect url_for('/create')
+  end
+
+end
+
+get '/?' do
+  redirect url_for('/create')
+end
+
+get '/models/?' do
+  @models = ToxCreateModel.all(:order => [ :created_at.desc ])
+  #@models.each { |model| model.process }
+  haml :models
+end
+
+get '/model/:id/status/?' do
+  response['Content-Type'] = 'text/plain'
+  model = ToxCreateModel.get(params[:id])
+  begin
+    haml :model_status, :locals=>{:model=>model}, :layout => false
+  rescue
+    return "unavailable"
+  end
+end
+
+get '/model/:id/:view/?' do
+  response['Content-Type'] = 'text/plain'
+  model = ToxCreateModel.get(params[:id])
+
+  begin
+    #model.process
+    #model.save
+    case params[:view]
+      when "model"
+        haml :model, :locals=>{:model=>model}, :layout => false
+      when /validation/
+        haml :validation, :locals=>{:model=>model}, :layout => false
+      else
+        return "unable to render model: id #{params[:id]}, view #{params[:view]}"
+    end
+  rescue
+    return "unable to render model: id #{params[:id]}, view #{params[:view]}"
+  end
+end
+
+get '/predict/?' do 
+  @models = ToxCreateModel.all(:order => [ :created_at.desc ])
+  @models = @models.collect{|m| m if m.status == 'Completed'}.compact
+  haml :predict
+end
+
+get '/create' do
+  haml :create
+end
+
+get '/help' do
+  haml :help
+end
+
+get "/confidence" do
+  haml :confidence
+end
+
+# proxy to get data from compound service
+# (jQuery load does not work with external URIs)
+get %r{/compound/(.*)} do |inchi|
+  inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'')
+  OpenTox::Compound.from_inchi(inchi).to_names.join(', ')
+end
+
+post '/models' do # create a new model
+
+  unless params[:file] and params[:file][:tempfile] #params[:endpoint] and 
+    flash[:notice] = "Please upload a Excel or CSV file."
+    redirect url_for('/create')
+  end
+
+  @model = ToxCreateModel.create(:name => params[:file][:filename].sub(/\..*$/,""))
+  task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do
+
+    @model.update :status => "Uploading and saving dataset"
+    begin
+      @dataset = OpenTox::Dataset.create
+      # check format by extension - not all browsers provide correct content-type]) 
+      case File.extname(params[:file][:filename])
+      when ".csv"
+        csv = params[:file][:tempfile].read
+        LOGGER.debug csv
+        @dataset.load_csv(csv)
+      when ".xls", ".xlsx"
+        @dataset.load_spreadsheet(Excel.new params[:file][:tempfile].path)
+      else
+        error "#{params[:file][:filename]} has a unsupported file type."
+      end
+    rescue => e
+      error "Dataset creation failed with #{e.message}"
+    end
+    @dataset.save
+    if @dataset.compounds.size < 10
+      error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/excel_format"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
+    end
+    if @dataset.features.keys.size != 1
+      error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again."
+    end
+    if @dataset.metadata[OT.Errors]
+      error "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} formats."
+    end
+    @model.training_dataset = @dataset.uri
+    @model.nr_compounds = @dataset.compounds.size
+    @model.warnings = @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings].empty?
+    @model.save
+
+    @model.update :status => "Creating prediction model"
+    begin
+      lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri)
+    rescue => e
+      error "Model creation failed with '#{e.message}'. Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format."
+    end
+    LOGGER.debug lazar.metadata.to_yaml
+    @model.feature_dataset = lazar.metadata[OT.featureDataset]
+    @model.uri = lazar.uri
+    case lazar.metadata[OT.isA]
+    when /Classification/
+      @model.type = "classification"
+    when /Regression/
+      @model.type = "regression"
+    else
+      @model.type = "unknown"
+    end
+    @model.save
+
+    unless url_for("",:full).match(/localhost/)
+      @model.update :status => "Validating model"
+      begin
+        validation = OpenTox::Validation.create_crossvalidation(
+          :algorithm_uri => OpenTox::Algorithm::Lazar.uri,
+          :dataset_uri => lazar.parameter("dataset_uri"),
+          :prediction_feature => lazar.parameter("prediction_feature"),
+          :algorithm_params => "feature_generation_uri=#{lazar.parameter("feature_generation_uri")}"
+        )
+        @model.update(:validation_uri => validation.uri)
+        LOGGER.debug "Validation URI: #{@model.validation_uri}"
+      rescue => e
+        LOGGER.debug "Model validation failed with #{e.message}."
+        @model.warnings += "Model validation failed with #{e.message}."
+      end
+
+      # create summary
+      validation.summary(@model.type).each{|k,v| eval "@model.#{k.to_s} = v"}
+      @model.save
+      
+      @model.update :status => "Creating validation report"
+      begin
+        @model.update(:validation_report_uri => validation.create_report)
+      rescue => e
+        LOGGER.debug "Validation report generation failed with #{e.message}."
+        @model.warnings += "Validation report generation failed with #{e.message}."
+      end
+
+      @model.update :status => "Creating QMRF report"
+      begin
+        @model.update(:validation_qmrf_report_uri => validation.create_qmrf_report)
+      rescue => e
+        LOGGER.debug "Validation QMRF report generation failed with #{e.message}."
+        @model.warnings += "Validation QMRF report generation failed with #{e.message}."
+      end
+    end
+
+
+
+    #@model.warnings += "<p>Incorrect Smiles structures (ignored):</p>" + parser.smiles_errors.join("<br/>") unless parser.smiles_errors.empty?
+    #@model.warnings += "<p>Irregular activities (ignored):</p>" + parser.activity_errors.join("<br/>") unless parser.activity_errors.empty?
+    #duplicate_warnings = ''
+    #parser.duplicates.each {|inchi,lines| duplicate_warnings += "<p>#{lines.join('<br/>')}</p>" if lines.size > 1 }
+    #@model.warnings += "<p>Duplicated structures (all structures/activities used for model building, please  make sure, that the results were obtained from <em>independent</em> experiments):</p>" + duplicate_warnings unless duplicate_warnings.empty?
+    @model.update :status => "Completed"
+    lazar.uri
+  end
+  @model.update(:task_uri => task.uri)
+  @model.save
+
+  flash[:notice] = "Model creation and validation started - this may last up to several hours depending on the number and size of the training compounds."
+  redirect url_for('/models')
+
+=begin
+=end
+end
+
+post '/predict/?' do # post chemical name to model
+  @identifier = params[:identifier]
+  unless params[:selection] and params[:identifier] != ''
+    flash[:notice] = "Please enter a compound identifier and select an endpoint from the list."
+    redirect url_for('/predict')
+  end
+  begin
+    @compound = OpenTox::Compound.from_name(params[:identifier])
+  rescue
+    flash[:notice] = "Could not find a structure for '#{@identifier}'. Please try again."
+    redirect url_for('/predict')
+  end
+  @predictions = []
+  params[:selection].keys.each do |id|
+    model = ToxCreateModel.get(id.to_i)
+    #model.process unless model.uri
+    prediction = nil
+    confidence = nil
+    title = nil
+    db_activities = []
+    lazar = OpenTox::Model::Lazar.new model.uri
+    prediction_dataset_uri = lazar.run(:compound_uri => @compound.uri)
+    prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri)
+    if prediction_dataset.metadata[OT.hasSource].match(/dataset/)
+      @predictions << {
+        :title => model.name,
+        :measured_activities => prediction_dataset.measured_activities(@compound)
+      }
+    else
+      predicted_feature = prediction_dataset.metadata[OT.dependentVariables]
+      prediction = OpenTox::Feature.find(predicted_feature)
+      LOGGER.debug prediction.to_yaml
+      if prediction.metadata[OT.error]
+        @predictions << {
+          :title => model.name,
+          :error => prediction.metadata[OT.error]
+          }
+      else
+        @predictions << {
+          :title => model.name,
+          :model_uri => model.uri,
+          :prediction => prediction.metadata[OT.prediction],
+          :confidence => prediction.metadata[OT.confidence]
+          }
+      end
+    end
+    # TODO failed/unavailable predictions
+=begin
+    source = prediction.creator
+    if prediction.data[@compound.uri]
+      if source.to_s.match(/model/) # real prediction
+        prediction = prediction.data[@compound.uri].first.values.first
+        #LOGGER.debug prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#classification")]
+        #LOGGER.debug prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#confidence")]
+        if !prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#classification")].nil?
+          @predictions << {
+            :title => model.name,
+            :model_uri => model.uri,
+            :prediction => prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#classification")],
+            :confidence => prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#confidence")]
+            }
+        elsif !prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#regression")].nil?
+          @predictions << {
+            :title => model.name,
+            :model_uri => model.uri,
+            :prediction => prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#regression")],
+            :confidence => prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#confidence")]
+            }
+        end
+      else # database value
+        prediction = prediction.data[@compound.uri].first.values
+        @predictions << {:title => model.name, :measured_activities => prediction}
+      end
+    else
+      @predictions << {:title => model.name, :prediction => "not available (not enough similar compounds in the training dataset)"}
+    end
+=end
+  end
+  LOGGER.debug @predictions.inspect
+
+  haml :prediction
+end
+
+post "/lazar/?" do # get detailed prediction
+  @page = 0
+  @page = params[:page].to_i if params[:page]
+  @model_uri = params[:model_uri]
+  lazar = OpenTox::Model::Lazar.new @model_uri
+  prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri])
+  @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri)
+  @compound = OpenTox::Compound.new(params[:compound_uri])
+  #@title = prediction.metadata[DC.title]
+  # TODO dataset activity
+  #@activity = prediction.metadata[OT.prediction]
+  #@confidence = prediction.metadata[OT.confidence]
+  #@neighbors = []
+  #@features = []
+#  if @prediction.data[@compound.uri]
+#    if @prediction.creator.to_s.match(/model/) # real prediction
+#      p = @prediction.data[@compound.uri].first.values.first
+#      if !p[File.join(CONFIG[:services]["opentox-model"],"lazar#classification")].nil?
+#        feature = File.join(CONFIG[:services]["opentox-model"],"lazar#classification")
+#      elsif !p[File.join(CONFIG[:services]["opentox-model"],"lazar#regression")].nil?
+#        feature = File.join(CONFIG[:services]["opentox-model"],"lazar#regression")
+#      end
+#      @activity = p[feature]
+#      @confidence = p[File.join(CONFIG[:services]["opentox-model"],"lazar#confidence")]
+#      @neighbors = p[File.join(CONFIG[:services]["opentox-model"],"lazar#neighbors")]
+#      @features = p[File.join(CONFIG[:services]["opentox-model"],"lazar#features")]
+#    else # database value
+#      @measured_activities = @prediction.data[@compound.uri].first.values
+#    end
+#  else
+#    @activity = "not available (no similar compounds in the training dataset)"
+#  end
+  haml :lazar
+end
+
+delete '/model/:id/?' do
+  model = ToxCreateModel.get(params[:id])
+  begin
+    RestClient.delete model.uri if model.uri
+    RestClient.delete model.task_uri if model.task_uri
+    model.destroy
+    flash[:notice] = "#{model.name} model deleted."
+  rescue
+    flash[:notice] = "#{model.name} model delete error."
+  end
+  redirect url_for('/models')
+end
+
+delete '/?' do
+  DataMapper.auto_migrate!
+  response['Content-Type'] = 'text/plain'
+  "All Models deleted."
+end
+
+# SASS stylesheet
+get '/stylesheets/style.css' do
+  headers 'Content-Type' => 'text/css; charset=utf-8'
+  sass :style
+end
diff --git a/config.ru b/config.ru
new file mode 100644
index 0000000..1616a96
--- /dev/null
+++ b/config.ru
@@ -0,0 +1,5 @@
+require 'rubygems'
+require 'opentox-ruby'
+require 'config/config_ru'
+set :app_file, __FILE__ # to get the view path right
+run Sinatra::Application
diff --git a/helper.rb b/helper.rb
new file mode 100644
index 0000000..d691103
--- /dev/null
+++ b/helper.rb
@@ -0,0 +1,50 @@
+helpers do
+
+  def hide_link(destination)
+    @link_id = 0 unless @link_id
+    @link_id += 1
+    haml :js_link, :locals => {:name => "hide", :destination => destination, :method => "hide"}, :layout => false
+  end
+
+  def toggle_link(destination,name)
+    @link_id = 0 unless @link_id
+    @link_id += 1
+    haml :js_link, :locals => {:name => name, :destination => destination, :method => "toggle"}, :layout => false
+  end
+
+  def sort(descriptors)
+    features = {:activating => [], :deactivating => []}
+
+    descriptors.each { |d| LOGGER.debug d.inspect; features[d[OT.effect].to_sym] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} }
+    LOGGER.debug features.to_yaml
+    features
+  end
+
+  def compound_image(compound,descriptors)
+    haml :compound_image, :locals => {:compound => compound, :features => sort(descriptors)}, :layout => false
+  end
+  
+  def activity_markup(activity)
+    case activity.class.to_s
+    when /Float/
+      haml ".other #{sprintf('%.03g', activity)}", :layout => false
+    when /String/
+      haml ".other #{activity.to_s}", :layout => false
+    else
+      if activity #true
+        haml ".active active", :layout => false
+      elsif !activity # false
+        haml ".inactive inactive", :layout => false
+      else
+        haml ".other #{activity.to_s}", :layout => false
+      end
+    end
+  end
+
+  def neighbors_navigation
+    @page = 0 unless @page
+    haml :neighbors_navigation, :layout => false
+  end
+
+end
+
diff --git a/model.rb b/model.rb
new file mode 100644
index 0000000..9929ab0
--- /dev/null
+++ b/model.rb
@@ -0,0 +1,186 @@
+class ToxCreateModel
+
+	include DataMapper::Resource
+
+	property :id, Serial
+	property :name, String, :length => 255
+	property :warnings, Text, :length => 2**32-1 
+	property :error_messages, Text, :length => 2**32-1  # :errors interferes with datamapper validation
+	property :type, String
+  property :status, String, :length => 255
+	property :created_at, DateTime
+
+	property :task_uri, String, :length => 255
+	property :uri, String, :length => 255
+
+	property :training_dataset, String, :length => 255
+	property :feature_dataset, String, :length => 255
+	#property :validation_task_uri, String, :length => 255
+	property :validation_uri, String, :length => 255
+
+	#property :validation_report_task_uri, String, :length => 255
+	property :validation_report_uri, String, :length => 255
+
+	#property :validation_qmrf_task_uri, String, :length => 255
+	property :validation_qmrf_uri, String, :length => 255
+
+	property :nr_compounds, Integer
+	property :nr_predictions, Integer
+	property :true_positives, Integer
+	property :false_positives, Integer
+	property :true_negatives, Integer
+	property :false_negatives, Integer
+	property :correct_predictions, Integer
+	property :weighted_area_under_roc, Float
+	property :sensitivity, Float
+	property :specificity, Float
+	property :r_square, Float
+	property :root_mean_squared_error, Float
+	property :mean_absolute_error, Float
+
+=begin
+def status
+		#begin
+			RestClient.get(File.join(@task_uri, 'hasStatus')).body
+		#rescue
+		#	"Service offline"
+		#end
+	end
+=end
+=begin
+
+	def validation_status
+		begin
+			RestClient.get(File.join(@validation_task_uri, 'hasStatus')).body
+		rescue
+			"Service offline"
+		end
+	end
+
+	def validation_report_status
+		begin
+			RestClient.get(File.join(@validation_report_task_uri, 'hasStatus')).body
+		rescue
+			"Service offline"
+		end
+	end
+
+	def validation_qmrf_status
+		begin
+			RestClient.get(File.join(@validation_qmrf_task_uri, 'hasStatus')).body
+		rescue
+			"Service offline"
+		end
+	end
+
+	def algorithm
+		begin
+			RestClient.get(File.join(@uri, 'algorithm')).body
+		rescue
+			""
+		end
+	end
+
+	def training_dataset
+		begin
+			RestClient.get(File.join(@uri, 'trainingDataset')).body
+		rescue
+			""
+		end
+	end
+
+	def feature_dataset
+		begin
+			RestClient.get(File.join(@uri, 'feature_dataset')).body
+		rescue
+			""
+		end
+	end
+
+  def process
+
+    LOGGER.debug self.to_yaml
+
+    if @uri.nil? and status == "Completed"
+			#update :uri => RestClient.get(File.join(@task_uri, 'resultURI')).body
+			#lazar = YAML.load(RestClient.get(@uri, :accept => "application/x-yaml").body)
+
+		elsif @validation_uri.nil? and validation_status == "Completed"
+			begin
+
+				#update :validation_uri => RestClient.get(File.join(@validation_task_uri, 'resultURI')).body
+				#LOGGER.debug "Validation URI: #{@validation_uri}"
+
+				#update :validation_report_task_uri => RestClient.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"), :validation_uris => @validation_uri).body
+				#LOGGER.debug "Validation Report Task URI: #{@validation_report_task_uri}"
+
+				#update :validation_qmrf_task_uri => RestClient.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), :model_uri => @uri).body
+				#LOGGER.debug "QMRF Report Task URI: #{@validation_qmrf_task_uri}"
+
+        uri = File.join(@validation_uri, 'statistics')
+        yaml = RestClient.get(uri).body
+        v = YAML.load(yaml)
+
+        case type
+        when "classification"
+          tp=0; tn=0; fp=0; fn=0; n=0
+          v[:classification_statistics][:confusion_matrix][:confusion_matrix_cell].each do |cell|
+            if cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "true"
+              tp = cell[:confusion_matrix_value]
+              n += tp
+            elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "false"
+              tn = cell[:confusion_matrix_value]
+              n += tn
+            elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "true"
+              fn = cell[:confusion_matrix_value]
+              n += fn
+            elsif cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "false"
+              fp = cell[:confusion_matrix_value]
+              n += fp
+            end
+          end
+          update :nr_predictions => n
+          update :true_positives => tp
+          update :false_positives => fp
+          update :true_negatives => tn
+          update :false_negatives => fn
+          update :correct_predictions => 100*(tp+tn).to_f/n
+          update :weighted_area_under_roc => v[:classification_statistics][:weighted_area_under_roc].to_f
+          update :sensitivity => tp.to_f/(tp+fn)
+          update :specificity => tn.to_f/(tn+fp)
+        when "regression"
+          update :nr_predictions => v[:num_instances] - v[:num_unpredicted]
+          update :r_square => v[:regression_statistics][:r_square]
+          update :root_mean_squared_error => v[:regression_statistics][:root_mean_squared_error]
+          update :mean_absolute_error => v[:regression_statistics][:mean_absolute_error]
+        end
+			rescue
+				LOGGER.warn "Cannot create Validation Report Task #{@validation_report_task_uri} for  Validation URI #{@validation_uri} from Task #{@validation_task_uri}"
+			end
+
+		else
+
+      if @validation_report_uri.nil? and validation_report_status == "Completed"
+        begin
+          update :validation_report_uri => RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
+        rescue
+          LOGGER.warn "Cannot create Validation Report for  Task URI #{@validation_report_task_uri} "
+        end
+      end
+
+      if @validation_qmrf_uri.nil? and validation_qmrf_status == "Completed"
+        begin
+          update :validation_qmrf_uri => RestClient.get(File.join(@validation_qmrf_task_uri, 'resultURI')).body
+        rescue
+          LOGGER.warn "Cannot create QMRF Report for  Task URI #{@validation_qmrf_task_uri} "
+        end
+      end
+
+    end
+
+  end
+=end
+
+end
+
+DataMapper.auto_upgrade!
diff --git a/public/JME.class b/public/JME.class
new file mode 100644
index 0000000..9efda0e
--- /dev/null
+++ b/public/JME.class
diff --git a/public/JME.jar b/public/JME.jar
new file mode 100644
index 0000000..d571682
--- /dev/null
+++ b/public/JME.jar
diff --git a/public/ToxCreate_rgb_72.png b/public/ToxCreate_rgb_72.png
new file mode 100644
index 0000000..4b96882
--- /dev/null
+++ b/public/ToxCreate_rgb_72.png
diff --git a/public/favicon.ico b/public/favicon.ico
new file mode 100644
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+function(a){var b=this[0];if(a)return this.each(function(e){c.offset.setOffset(this,a,e)});if(!b||!b.ownerDocument)return null;if(b===b.ownerDocument.body)return c.offset.bodyOffset(b);var d=b.getBoundingClientRect(),f=b.ownerDocument;b=f.body;f=f.documentElement;return{top:d.top+(self.pageYOffset||c.support.boxModel&&f.scrollTop||b.scrollTop)-(f.clientTop||b.clientTop||0),left:d.left+(self.pageXOffset||c.support.boxModel&&f.scrollLeft||b.scrollLeft)-(f.clientLeft||b.clientLeft||0)}}:function(a){var b=
+this[0];if(a)return this.each(function(r){c.offset.setOffset(this,a,r)});if(!b||!b.ownerDocument)return null;if(b===b.ownerDocument.body)return c.offset.bodyOffset(b);c.offset.initialize();var d=b.offsetParent,f=b,e=b.ownerDocument,j,i=e.documentElement,o=e.body;f=(e=e.defaultView)?e.getComputedStyle(b,null):b.currentStyle;for(var k=b.offsetTop,n=b.offsetLeft;(b=b.parentNode)&&b!==o&&b!==i;){if(c.offset.supportsFixedPosition&&f.position==="fixed")break;j=e?e.getComputedStyle(b,null):b.currentStyle;
+k-=b.scrollTop;n-=b.scrollLeft;if(b===d){k+=b.offsetTop;n+=b.offsetLeft;if(c.offset.doesNotAddBorder&&!(c.offset.doesAddBorderForTableAndCells&&/^t(able|d|h)$/i.test(b.nodeName))){k+=parseFloat(j.borderTopWidth)||0;n+=parseFloat(j.borderLeftWidth)||0}f=d;d=b.offsetParent}if(c.offset.subtractsBorderForOverflowNotVisible&&j.overflow!=="visible"){k+=parseFloat(j.borderTopWidth)||0;n+=parseFloat(j.borderLeftWidth)||0}f=j}if(f.position==="relative"||f.position==="static"){k+=o.offsetTop;n+=o.offsetLeft}if(c.offset.supportsFixedPosition&&
+f.position==="fixed"){k+=Math.max(i.scrollTop,o.scrollTop);n+=Math.max(i.scrollLeft,o.scrollLeft)}return{top:k,left:n}};c.offset={initialize:function(){var a=s.body,b=s.createElement("div"),d,f,e,j=parseFloat(c.curCSS(a,"marginTop",true))||0;c.extend(b.style,{position:"absolute",top:0,left:0,margin:0,border:0,width:"1px",height:"1px",visibility:"hidden"});b.innerHTML="<div style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;'><div></div></div><table style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;' cellpadding='0' cellspacing='0'><tr><td></td></tr></table>";
+a.insertBefore(b,a.firstChild);d=b.firstChild;f=d.firstChild;e=d.nextSibling.firstChild.firstChild;this.doesNotAddBorder=f.offsetTop!==5;this.doesAddBorderForTableAndCells=e.offsetTop===5;f.style.position="fixed";f.style.top="20px";this.supportsFixedPosition=f.offsetTop===20||f.offsetTop===15;f.style.position=f.style.top="";d.style.overflow="hidden";d.style.position="relative";this.subtractsBorderForOverflowNotVisible=f.offsetTop===-5;this.doesNotIncludeMarginInBodyOffset=a.offsetTop!==j;a.removeChild(b);
+c.offset.initialize=c.noop},bodyOffset:function(a){var b=a.offsetTop,d=a.offsetLeft;c.offset.initialize();if(c.offset.doesNotIncludeMarginInBodyOffset){b+=parseFloat(c.curCSS(a,"marginTop",true))||0;d+=parseFloat(c.curCSS(a,"marginLeft",true))||0}return{top:b,left:d}},setOffset:function(a,b,d){if(/static/.test(c.curCSS(a,"position")))a.style.position="relative";var f=c(a),e=f.offset(),j=parseInt(c.curCSS(a,"top",true),10)||0,i=parseInt(c.curCSS(a,"left",true),10)||0;if(c.isFunction(b))b=b.call(a,
+d,e);d={top:b.top-e.top+j,left:b.left-e.left+i};"using"in b?b.using.call(a,d):f.css(d)}};c.fn.extend({position:function(){if(!this[0])return null;var a=this[0],b=this.offsetParent(),d=this.offset(),f=/^body|html$/i.test(b[0].nodeName)?{top:0,left:0}:b.offset();d.top-=parseFloat(c.curCSS(a,"marginTop",true))||0;d.left-=parseFloat(c.curCSS(a,"marginLeft",true))||0;f.top+=parseFloat(c.curCSS(b[0],"borderTopWidth",true))||0;f.left+=parseFloat(c.curCSS(b[0],"borderLeftWidth",true))||0;return{top:d.top-
+f.top,left:d.left-f.left}},offsetParent:function(){return this.map(function(){for(var a=this.offsetParent||s.body;a&&!/^body|html$/i.test(a.nodeName)&&c.css(a,"position")==="static";)a=a.offsetParent;return a})}});c.each(["Left","Top"],function(a,b){var d="scroll"+b;c.fn[d]=function(f){var e=this[0],j;if(!e)return null;if(f!==w)return this.each(function(){if(j=wa(this))j.scrollTo(!a?f:c(j).scrollLeft(),a?f:c(j).scrollTop());else this[d]=f});else return(j=wa(e))?"pageXOffset"in j?j[a?"pageYOffset":
+"pageXOffset"]:c.support.boxModel&&j.document.documentElement[d]||j.document.body[d]:e[d]}});c.each(["Height","Width"],function(a,b){var d=b.toLowerCase();c.fn["inner"+b]=function(){return this[0]?c.css(this[0],d,false,"padding"):null};c.fn["outer"+b]=function(f){return this[0]?c.css(this[0],d,false,f?"margin":"border"):null};c.fn[d]=function(f){var e=this[0];if(!e)return f==null?null:this;if(c.isFunction(f))return this.each(function(j){var i=c(this);i[d](f.call(this,j,i[d]()))});return"scrollTo"in
+e&&e.document?e.document.compatMode==="CSS1Compat"&&e.document.documentElement["client"+b]||e.document.body["client"+b]:e.nodeType===9?Math.max(e.documentElement["client"+b],e.body["scroll"+b],e.documentElement["scroll"+b],e.body["offset"+b],e.documentElement["offset"+b]):f===w?c.css(e,d):this.css(d,typeof f==="string"?f:f+"px")}});A.jQuery=A.$=c})(window);
diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
new file mode 100755
index 0000000..500b685
--- /dev/null
+++ b/public/javascripts/toxcreate.js
@@ -0,0 +1,121 @@
+$(function() {
+
+  jQuery.fn.toggleWarnings = function(id) {
+    var id = id;
+    this.bind("click", function() {
+      if($("a#show_model_" + id + "_warnings").html()=="show") {
+        $("dd#model_" + id + "_warnings").slideDown("slow");
+        $("a#show_model_" + id + "_warnings").html("hide");
+      }else{
+        $("dd#model_" + id + "_warnings").slideUp("slow");
+        $("a#show_model_" + id + "_warnings").html("show");
+      }
+      return false;
+    });
+  };
+
+  checkStati = function(stati) {
+    stati = stati.split(", ")
+    $("body")
+    var newstati = new Array;
+    $.each(stati, function(){
+      if(checkStatus(this) > 0) newstati.push(this);
+    });  
+    if (newstati.length > 0) var statusCheck = setTimeout('checkStati("' + newstati.join(", ") + '")',10000);
+  };
+  
+  checkStatus = function(id) {
+    if(id == "") return -1; 
+    var opts = {method: 'get', action: 'model/' + id + '/status', id: id};
+    var status_changed = $.ajax({
+      type: opts.method,
+      url: opts.action,
+      async: false,
+      dataType: 'html',
+      data: {
+        '_method': 'get'
+      },
+      success: function(data) {
+        var erg = data.search(/Running/);
+        status_changed = false;
+        if(erg < 0) status_changed = true;        
+        $("span#model_" + id + "_status").animate({"opacity": "0.1"},1000);
+        $("span#model_" + id + "_status").animate({"opacity": "1"},1000);
+        if( status_changed ) {
+          $("span#model_" + id + "_status").html(data);        
+          loadModel(id, 'model');
+          id = -1;
+        }        
+      },
+      error: function(data) {
+        //alert("status check error");
+        id = -1;
+      }
+    });
+    return id;
+  };
+
+  loadModel = function(id, view) {
+    if(id == "") return -1; 
+    var opts = {method: 'get', action: 'model/' + id + '/' + view, view: view };
+    var out = id;
+    $.ajax({
+      type: opts.method,
+      url: opts.action,
+      dataType: 'html',
+      data: {
+        '_method': 'get'
+      },
+      success: function(data) {
+        if (view == "model") $("div#model_" + id).html(data);
+        if (view.match(/validation/)) $("dl#model_validation_" + id).html(data);
+      },
+      error: function(data) {
+        //alert("loadModel error");
+      }
+    });
+    return false;
+  };
+
+  checkValidation = function() {
+    var reload_id = "";
+    $("input.model_validation_report").each(function(){
+        if(!$(this).val().match(/Completed|Error/)) {
+          reload_id = this.id.replace("model_validation_report_","");
+          if(/^\d+$/.test(reload_id)) loadModel(reload_id, 'validation');
+        };
+    });
+    //var validationCheck = setTimeout('checkValidation()',15000);
+    var validationCheck = setTimeout('checkValidation()',5000);
+  }
+});
+
+jQuery.fn.deleteModel = function(type, options) {
+  var defaults = {
+    method: 'post',
+    action: this.attr('href'),
+    confirm_message: 'Are you sure?',
+    trigger_on: 'click'
+  };
+  var opts = $.extend(defaults, options);
+  this.bind(opts.trigger_on, function() {
+    if(confirm(opts.confirm_message)) {
+      $(opts.elem).fadeTo("slow",0.5);
+      $.ajax({
+         type: opts.method,
+         url:  opts.action,
+         dataType: 'html',
+         data: {
+           '_method': 'delete'
+         },
+         success: function(data) {         
+           $(opts.elem).fadeTo("slow",0).slideUp("slow").remove();
+         },
+         error: function(data) {
+           //alert("model delete error!");
+         }
+       });
+     }
+     return false;
+   });
+};
diff --git a/public/jme-200606.jar b/public/jme-200606.jar
new file mode 100644
index 0000000..9cae5e7
--- /dev/null
+++ b/public/jme-200606.jar
diff --git a/public/jme.js b/public/jme.js
new file mode 100644
index 0000000..02a213f
--- /dev/null
+++ b/public/jme.js
@@ -0,0 +1,11 @@
+function getsmiles() {
+  if (document.JME.smiles() != '') {
+    $('smiles').value = document.JME.smiles() ;
+  }
+}
+
+function getsmarts() {
+  if (document.JME.smiles() != '') {
+    $('smarts').value = document.JME.smiles() ;
+  }
+}
diff --git a/public/jme_help.html b/public/jme_help.html
new file mode 100644
index 0000000..ab4942a
--- /dev/null
+++ b/public/jme_help.html
@@ -0,0 +1,195 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html>
+<head>
+  <meta name="generator" content=
+  "HTML Tidy for Linux/x86 (vers 12 April 2005), see www.w3.org">
+  <meta http-equiv="content-type" content=
+  "text/html; charset=us-ascii">
+
+  <title>JME Help</title>
+  <meta name="author" content="Peter Ertl, Novartis Pharma AG">
+  <link rel="stylesheet" href="../style.css" type="text/css">
+<style type="text/css">
+ body {
+  background-color: white;
+ }
+ h2.c3 {text-align: center}
+ p.c2 {font-style: italic; text-align: right}
+ p.c1 {text-align: center}
+</style>
+</head>
+
+<body>
+				<h1>JME Molecular Editor</h1>
+
+        <p class="c2">Written by Peter Ertl, Novartis Pharma
+        AG</p>
+
+        <h2 class="c3">Basic Instructions</h2>
+
+        <p>This editor is intended to be used without any special
+        documentation or training, but there are some tricks which
+        can help you to work with it more efficiently.</p>
+
+        <h3>Menu Buttons</h3>
+
+        <ul>
+          <li><b>D-R</b> deletes functional groups - choose this
+          option and then click on the bond connecting the group
+          with the main skeleton</li>
+
+          <li><b>UDO</b> undo last editing step</li>
+
+          <li><b>QRY</b> (if enabled in the param tag) allows easy
+          specification of atomic queries for substructure
+          searches</li>
+
+          <li><b>Stereo bonds</b> - the type of stereo bond (up,
+          down) may be changed by clicking on the already created
+          stereo bond; this cycles through two / four possible
+          stereo bond types</li>
+
+          <li><b>Atomic charges</b> may be changed by the
+          <b>+/-</b> button. Editor enables modification of charges
+          only in "reasonable" cases. If you are not satisfied with
+          the editor's inteligence (concerning charges and the
+          explicit number of hydrogens) you can force your will by
+          using the <b>X</b> button</li>
+
+          <li><b>"Non-organic" atoms</b> or atoms with nonstandard
+          valence may be entered with help of <b>X</b> button by
+          specifying atomic SMILES (without [ ] brackets, i.e. Si,
+          Fe++, NH3+).</li>
+        </ul>
+
+        <h3>Keyboard Shortcuts</h3>
+
+        <p>Most of the commands may be accessed also by keyboard
+        shortcuts. It is possible to:</p>
+
+        <ul>
+          <li>change <b>atom type</b> by pressing <b>C</b>,
+          <b>N</b>, <b>O</b>, <b>S</b>, <b>F</b>, <b>L</b> (for Cl)
+          <b>B</b> (for Br) <b>I</b>, <b>P</b>, <b>H</b>, <b>X</b>,
+          <b>R</b> and clicking the respective atom</li>
+
+          <li>choose <b>bond order</b>: <b>-</b> for single bond,
+          <b>=</b> for double bond, <b>#</b> for triple bond</li>
+
+          <li>choose <b>ring type</b> by pressing <b>3</b>,
+          <b>4</b>, <b>5</b>, <b>6</b>, <b>7</b>, <b>8</b>,
+          <b>9</b> or <b>1</b> for phenyl, <b>0</b> for furyl</li>
+
+          <li>start <b>delete mode</b> by pressing <b>D</b> or
+          <b>Del</b> and</li>
+
+          <li>return to the <b>standard state</b> (carbon, single
+          bond) with <b>Esc</b></li>
+        </ul>
+
+        <p><b>common functional groups</b> may also be added by
+        keyboard shortcuts. Use <b>t</b> for t-butyl, <b>ft</b> for
+        trifluoromethyl, <b>lt</b> for trichloromethyl, <b>a</b>
+        for COOH, <b>z</b> for SO2Me and <b>y</b> for nitro, and
+        then click the atom where the group should be
+        connected.</p>
+
+        <h3>Moving and Rotation</h3>
+
+        <p>You can move molecule by "dragging free space" with the
+        left mouse button and rotate it by using the left mouse
+        button and <b>Shift</b> key (or left and right mouse
+        buttons together).</p>
+
+        <h3>Adding rings</h3>
+
+        <p>When a ring template is selected and multivalent atom is
+        clicked, a new ring will be created connected by single
+        bond to this atom. When spiro ring is required, the
+        <b>Shift</b> key must be pressed when clicking on the atom.
+        Spiro ring may be added only to atom with 2 single
+        bonds.</p>
+
+        <h3>Multivalent nitrogen groups</h3>
+
+        <p>Multivalent nitrogen groups, such as nitro, azide,
+        N-oxide, nitrile etc, should be drawn with a pentavalent
+        nitrogen as shown below.</p>
+
+        <p class="c1"><img src="images/nitro.gif" alt=
+        "nitro stuff"></p>
+
+        <p>The program automatically converts polar form of these
+        groups into non-polar one with pentavalent nitrogen. If you
+        prefer polar nitro (and similar) groups, use keyword
+        "polarnitro" in the applet param tag.</p>
+
+        <h3>Stereochemistry</h3>
+
+        <p>Stereochemistry at C4 centers, double bonds and allenes
+        is supported. Use the up/down wedge bonds to indicate
+        stereochemistry at the C4 centers. Remember, that only
+        bonds with a "sharp point" towards the atom are considered.
+        When creating SMILES the editor tries to guess missing
+        stereo features, in unresolvable cases an error message is
+        issued and the SMILES without stereo information is
+        created.</p>
+
+        <p>When the autoez keyword is set, SMILES with E,Z
+        stereochemistry on all non-ring double bonds is generated
+        automatically. Without this keyword (or for ring double
+        bonds) you have to mark a double bond as stereo by clicking
+        on it with the stereo bond button selected. The bond color
+        will change to violet.</p>
+
+        <p>Stereochemistry may be completely disabled by the
+        "nostereo" option in the param tag.</p>
+
+        <h3>Input of Multipart Structures</h3>
+
+        <p>By default only non-disconnected structures are allowed.
+        This may be changed by a "multipart" option in the applet
+        param tag. A button <b>NEW</b> appears in the JME menu.
+        Creation of a new molecule may be started only after
+        clicking the <b>NEW</b> button, selecting a proper template
+        (atom, ring, bond) and clicking free space in the drawing
+        area. Without <b>NEW</b> button the click on the free space
+        has the same effect as in the standard mode (i.e moving or
+        rotation of the last touched molecule). In the multipart
+        mode <b>CLR</b> button deletes the last touched
+        molecule.</p>
+
+        <h3>Atom Numbering</h3>
+
+        <p>Atom numbering (marking) is enabled with the option
+        "number" in the applet param tag (for reaction input this
+        is default). Button <b>123</b> appears in the JME menu. To
+        mark an atom press the <b>123</b> button and then the atom.
+        You can mark more atoms with the same number when pressing
+        <b>Shift</b> while clicking the 2nd and further atoms.
+        Second click on the marked atom deletes the number.</p>
+
+        <h3>Reaction Input</h3>
+
+        <p>Reaction input is enabled with the option "reaction" in
+        the applet param tag. Button with an arrow, <b>NEW</b>
+        button and <b>123</b> button appear in the JME menu and
+        arrow appears also in the drawing area. Now simply draw
+        reactant(s), product(s) and modulator(s) (modulators have
+        to be above the arrow) as explained in the description of
+        input of multipart structures. The arrow button enables
+        simplified input of reactions. After clicking it, the
+        reactant will be copied to the product (including atom
+        numbering, if any). When the <b>Shift</b> is pressed during
+        this action all atoms will be automatically numbered.</p>
+
+        <h3>Query Features</h3>
+
+        <p>Query button (when enabled in the option tag) launches a
+        query window which allows creation of SMARTS atom queries
+        by combining various atom attributes. Create a SMARTS query
+        and then click the respective atom in the
+        molecule.</p>
+</body>
+</html>
diff --git a/public/robots.txt b/public/robots.txt
new file mode 100644
index 0000000..1f53798
--- /dev/null
+++ b/public/robots.txt
@@ -0,0 +1,2 @@
+User-agent: *
+Disallow: /
diff --git a/public/snake_transparent.gif b/public/snake_transparent.gif
new file mode 100644
index 0000000..c1eb1c9
--- /dev/null
+++ b/public/snake_transparent.gif
diff --git a/views/classification.haml b/views/classification.haml
new file mode 100644
index 0000000..5c739cf
--- /dev/null
+++ b/views/classification.haml
@@ -0,0 +1,11 @@
+%dl#classification{ :style => "display: none;" }
+  %dt
+    Classification
+    (
+    = hide_link "#classification"
+    )
+  %dd 
+    Prediction of
+    %em qualitative
+    properties, e.g. to distinguish between toxic and non-toxic compounds
+
diff --git a/views/classification_validation.haml b/views/classification_validation.haml
new file mode 100644
index 0000000..94ba8f9
--- /dev/null
+++ b/views/classification_validation.haml
@@ -0,0 +1,33 @@
+%dt Correct predictions:
+%dd
+	= sprintf("%.2f", model.correct_predictions) if model.correct_predictions
+	= '%'
+%dt
+	%a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :target => "_blank"} Weighted area under ROC:
+%dd 
+	= sprintf("%.3f", model.weighted_area_under_roc) if model.weighted_area_under_roc
+%dt
+	%a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Specificity:
+%dd= sprintf("%.3f", model.specificity) if model.specificity
+%dt
+	%a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Sensitivity:
+%dd= sprintf("%.3f", model.sensitivity) if model.sensitivity
+%dt
+	%a{:href => "http://en.wikipedia.org/wiki/Confusion_matrix", :target => "_blank"} Confusion Matrix:
+%dd
+	%table
+		%tr
+			%td{:colspan => 2, :rowspan => 2}
+			%th{:colspan => 2} Measured
+		%tr
+			%th{:bgcolor => "#CCD2DC"} active
+			%th{:bgcolor => "#CCD2DC"} inactive
+		%tr
+			%th{:rowspan => 2} Predicted
+			%th{:bgcolor => "#CCD2DC"} active
+			%td= model.true_positives if model.true_positives
+			%td= model.false_positives if model.false_positives
+		%tr
+			%th{:bgcolor => "#CCD2DC"} inactive
+			%td= model.false_negatives if model.false_negatives
+			%td= model.true_negatives if model.true_negatives
diff --git a/views/compound_image.haml b/views/compound_image.haml
new file mode 100644
index 0000000..18944dc
--- /dev/null
+++ b/views/compound_image.haml
@@ -0,0 +1,2 @@
+%img{:src => compound.matching_smarts_image_uri(features[:activating].collect{|f| f[:smarts]},features[:deactivating].collect{|f| f[:smarts]}), :alt => compound.to_smiles}
+
diff --git a/views/confidence.haml b/views/confidence.haml
new file mode 100644
index 0000000..2b72d63
--- /dev/null
+++ b/views/confidence.haml
@@ -0,0 +1,7 @@
+%dl#confidence{ :style => "display: none;" }
+  %dt
+    Confidence
+    (
+    = hide_link "#confidence"
+    )
+  %dd Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence &gt; 0.025 is a sensible (hard) cutoff to distiguish between reliable and unreliable predictions.
diff --git a/views/create.haml b/views/create.haml
new file mode 100644
index 0000000..6563494
--- /dev/null
+++ b/views/create.haml
@@ -0,0 +1,41 @@
+.input
+
+  %p
+    This service creates 
+    %ul
+      %li
+        = toggle_link("#lazar_description","lazar")
+        %em= toggle_link("#classification","classification")
+        models and
+      %li
+        = toggle_link("#lazar_description","lazar")
+        %em= toggle_link("#regression","regression")
+        models 
+    from your uploaded datasets. Further modelling algorithms will be added in future versions.
+ 
+  %p
+    Please read the 
+    = link_to "instructions for creating training datasets", '/help'
+    before submitting.
+
+  %form{ :action => url_for('/models'), :method => "post", :enctype => "multipart/form-data" }
+    %fieldset
+      -#%label{:for => 'endpoint'} 1. Enter #{toggle_link("#endpoint_description","endpoint")} name and #{toggle_link("#unit","unit")} (for #{toggle_link("#regression","regression")}):
+      -#%input{:type => 'text', :name => 'endpoint', :id => 'endpoint', :size => '50'}
+      -#%br
+      %label{:for => 'file'}
+        Select training dataset in 
+        = link_to "Excel", '/help'
+        or
+        = link_to "CSV", '/help'
+        format:
+      %input{:type => 'file', :name => 'file', :id => 'file', :size => '41'}
+    %input{ :type => "submit", :value => "Create model"}
+    = link_to "Cancel", '/create'
+
+  -# explanations
+  = haml :lazar_description, :layout => false
+  = haml :classification, :layout => false
+  = haml :regression, :layout => false
+  = haml :endpoint, :layout => false
+  = haml :unit, :layout => false
diff --git a/views/endpoint.haml b/views/endpoint.haml
new file mode 100644
index 0000000..af06b80
--- /dev/null
+++ b/views/endpoint.haml
@@ -0,0 +1,12 @@
+%dl#endpoint_description{ :style => "display: none;" }
+  %dt
+    Endpoint
+    (
+    = hide_link "#endpoint_description"
+    )
+  %dd 
+    Toxic effect that constitutes the outcome of an
+    %em in-vitro,
+    or
+    %em in-vivo
+    expriment, clinical trial or epidemiological study
diff --git a/views/feature_table.haml b/views/feature_table.haml
new file mode 100644
index 0000000..4fa927c
--- /dev/null
+++ b/views/feature_table.haml
@@ -0,0 +1,28 @@
+%table
+  - unless features[:activating].empty?
+    %tr
+      %th
+        activating 
+        (
+        %a{:href => "http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html"} SMARTS
+        )
+      %th p value
+    - if features[:activating]
+      - features[:activating].sort{|a,b| b[:p_value] <=> a[:p_value] }.each do |f|
+        %tr
+          %td= f[:smarts]
+          %td= f[:p_value]
+  - unless features[:deactivating].empty?
+    %tr
+      %th
+        deactivating
+        (
+        %a{:href => "http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html"} SMARTS
+        )
+      %th p value
+    - if features[:deactivating]
+      - features[:deactivating].sort{|a,b| b[:p_value] <=> a[:p_value] }.each do |f|
+        %tr
+          %td= f[:smarts]
+          %td= f[:p_value]
+
diff --git a/views/fragment.haml b/views/fragment.haml
new file mode 100644
index 0000000..fa7495d
--- /dev/null
+++ b/views/fragment.haml
@@ -0,0 +1,9 @@
+%form{:name => "form", :action => url_for('/lazar'), :method => "post", :enctype => "multipart/form-data" }
+  %input{:type => :hidden, :name => :compound_uri, :value => compound_uri}
+  %input{:type => :hidden, :name => :model_uri, :value => model_uri}
+  %input{:type => :hidden, :name => :highlight, :value => smarts}
+  - if smarts.nil?
+    %input{ :type => "submit", :value => "Reset"}
+  - else
+    %input{ :type => "submit", :value => smarts}
+
diff --git a/views/help.haml b/views/help.haml
new file mode 100644
index 0000000..eabf978
--- /dev/null
+++ b/views/help.haml
@@ -0,0 +1,104 @@
+= link_to "Back to model creation", '/create'
+%p
+  Input files have two columns. Enter in the first column the chemical structure in
+  %a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification"} SMILES
+  format, in the second column the toxic activity.
+%dl
+  %dt Classification datasets 
+  %dd Please use 1/0, active/inactive or true/false to indicate active/inactive compounds.
+  %dt Regression datasets
+  %dd
+    Enter a quantitative value. For optimal performance you should
+    %ul
+      %li
+        use
+        %a{:href => "http://en.wikipedia.org/wiki/Molar_(concentration)"} molar
+        units
+      %li enter non-logarithmic values (logarithms are taken internally)
+      %li avoid 0 activities (will be ignored)
+%p 
+  Input files are accepted in 
+  %a{:href => "http://en.wikipedia.org/wiki/Microsoft_Excel"} Excel
+  and
+  %a{:href => "en.wikipedia.org/wiki/Comma-separated_values"} CSV
+  formats.
+
+%h3 Excel example
+
+- n = 0
+
+.code
+  %table
+    %tr
+      %td
+      %th A
+      %th B
+    %tr
+      - n += 1
+      %th= n
+      %td CC(=O)Nc1ccc(O)cc1
+      %td 1  
+    %tr
+      - n += 1
+      %th= n
+      %td O=c1[nH]cnc2[nH]ncc12
+      %td 1  
+    %tr
+      - n += 1
+      %th= n
+      %td CCCCNc1cc(cc(c1Oc2ccccc2)S(=O)(=O)N)C(=O)O
+      %td 1  
+    %tr
+      - n += 1
+      %th= n
+      %td CC(C)(C)NCC(O)COc1cccc2NC(=O)CCc12
+      %td 1  
+    %tr
+      - n += 1
+      %th= n
+      %td CN(C)CCCC1(OCc2cc(C#N)ccc21)c3ccc(F)cc3
+      %td 1  
+    %tr
+      - n += 1
+      %th= n
+      %td CCC(CC)CCN1C(=O)CN=C(C2CCCCC2F)c3cc(Cl)ccc13
+      %td 0 
+    %tr
+      - n += 1
+      %th= n
+      %td CCN(CC)CC(=O)Nc1c(C)cccc1C
+      %td 0 
+    %tr
+      - n += 1
+      %th= n
+      %td CC(C)(C)NCC(O)COc1cccc2CC(O)C(O)Cc12
+      %td 0 
+    %tr
+      - n += 1
+      %th= n
+      %td CN1CCCC1c2cccnc2
+      %td 0 
+
+%p
+  Excel example file for download:
+  = link_to "hamster_carcinogenicity.xls", "/hamster_carcinogenicity.xls"
+
+%h3 CSV example
+
+.code
+  %code
+    %br CC(=O)Nc1ccc(O)cc1, 1  
+    %br O=c1[nH]cnc2[nH]ncc12, 1  
+    %br CCCCNc1cc(cc(c1Oc2ccccc2)S(=O)(=O)N)C(=O)O, 1  
+    %br CC(C)(C)NCC(O)COc1cccc2NC(=O)CCc12, 1  
+    %br CN(C)CCCC1(OCc2cc(C#N)ccc21)c3ccc(F)cc3, 1  
+    %br CCC(CC)CCN1C(=O)CN=C(C2CCCCC2F)c3cc(Cl)ccc13, 0 
+    %br CCN(CC)CC(=O)Nc1c(C)cccc1C, 0 
+    %br CC(C)(C)NCC(O)COc1cccc2CC(O)C(O)Cc12, 0 
+    %br CN1CCCC1c2cccnc2, 0 
+
+%p
+  CSV example for download:
+  = link_to "hamster_carcinogenicity.csv", "/hamster_carcinogenicity.csv"
+
+%p You can create CSV files in Excel: Create a sheet with two columns and export them as CSV file with the "Save As" option from the menu, selecting the CSV (comma delimited) format.
diff --git a/views/js_link.haml b/views/js_link.haml
new file mode 100644
index 0000000..7d8cdce
--- /dev/null
+++ b/views/js_link.haml
@@ -0,0 +1,5 @@
+%a{:href => "#{destination}", :id => "js_link#{@link_id}"} #{name}
+:javascript
+  $("a#js_link#{@link_id}").click(function () {
+    $("#{destination}").#{method}();  
+  });
diff --git a/views/layout.haml b/views/layout.haml
new file mode 100644
index 0000000..a3db5e9
--- /dev/null
+++ b/views/layout.haml
@@ -0,0 +1,43 @@
+!!!
+%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"}
+
+  %head
+    %meta{'http-equiv' => 'Content-Type', :content => 'text/html'}
+    %title ToxCreate
+    %script{:type => "text/javascript", :src  => "javascripts/jquery.js"}
+    %script{:type => "text/javascript", :src  => "javascripts/toxcreate.js"}
+    %link{:rel=>'stylesheet', :href=>'stylesheets/style.css', :type => "text/css"}      
+
+  %body
+    .logo
+      = image_tag "/ToxCreate_rgb_72.png", :alt => 'ToxCreate', :align => 'right'
+      %br Create and evaluate models to predict toxicity
+    .index
+      %ul
+        %li{:class => ("selected" if /\/create/ =~ request.path )}
+          = link_to "Create", "/create"
+        %li{:class => ("selected" if /models/ =~ request.path )}
+          = link_to "Inspect", "/models"
+        %li{:class => ("selected" if /predict|lazar/ =~ request.path )}
+          = link_to "Predict", "/predict"
+        %li{:class => ("selected" if /help/ =~ request.path )}
+          = link_to "Help", "/help"
+
+    .content
+      - if `hostname`.match(/ot-test/)
+        .notice 
+          This service is for testing purposes only - once a week all models will be deleted. Please send bug reports and feature requests to our 
+          %a{:href => 'http://github.com/helma/opentox-toxmodel/issues'} issue tracker.
+
+      - if flash[:notice]
+        %p
+        .notice#flashnotice
+          = flash[:notice]
+
+      = yield
+
+    .footer
+      &copy;
+      %a{:href => 'http://www.in-silico.ch'} in silico toxicology
+      2009-2010, powered by
+      %a{:href => 'http://www.opentox.org'} <span style="color:#5D308A;font-family:arial,sans-serif,helvetica;letter-spacing:-1px;">Open</span><span style="color:#000;font-family:arial,sans-serif,helvetica;font-weight:bold;letter-spacing:-1px;position:relative;">Tox</span>
diff --git a/views/lazar.haml b/views/lazar.haml
new file mode 100644
index 0000000..a46f82c
--- /dev/null
+++ b/views/lazar.haml
@@ -0,0 +1,58 @@
+%p= link_to "New prediction", "/predict"
+.lazar-predictions
+
+  -# explanations
+  = haml :lazar_algorithm, :layout => false
+  = haml :confidence, :layout => false
+  = haml :similarity, :layout => false
+  = haml :significant_fragments, :layout => false
+  = haml :training_data, :layout => false
+
+  %a{:name => "prediction"}
+  %table
+    %thead
+      %tr
+        %th= @prediction.title
+        %th= toggle_link("#lazar_algorithm","Prediction")
+        %th= toggle_link("#confidence","Confidence")
+        %th Supporting information
+
+      %tr
+        -# %td
+          %img{:src => @compound.to_image_uri, :alt => @compound.to_smiles}
+        %td.image= compound_image(@compound,@prediction.descriptors(@compound))
+        %td= activity_markup(@prediction.value(@compound))
+        %td= sprintf('%.03g', @prediction.confidence(@compound)) 
+        -#%td= @prediction.confidence(@compound)
+        %td
+          %ul
+            %li
+              %a{:href => "#prediction", :id => "show_names"} Names and synonyms
+              :javascript
+                $("a#show_names").click(function () {
+                  $("#compound_names").load("#{File.join("/compound",@compound.inchi)}");  
+                  $("tr#names").toggle();  
+                });
+            %li= toggle_link("#fragments","Significant fragments")
+            -# This does not work, ask nina/vedrin
+            -# %li
+              %a{:href => "http://ambit.uni-plovdiv.bg:8080/ambit2/query/structure/?search=#{@compound.smiles}"} Ambit data
+            -# %li
+              %a{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pccompound&term=#{URI.encode('"'+@compound.inchi+'"[InChI]')}"}  PubChem data
+              (external)
+            -# %li
+              %a{:href => "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&inchi=#{URI.encode @compound.inchi}"} ToxNet data
+            -#http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&regno=000143157
+
+      %tr#names{ :style => "display: none;" }
+        %td{:colspan => '4'}
+          %a{:name => 'names'}
+          = hide_link('#names')
+          #compound_names
+      %tr#fragments{ :style => "display: none;" }
+        %td{:colspan => '4'}
+          = hide_link('#fragments')
+          = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(@compound))}, :layout => false
+
+    %tbody#neighbors
+      = haml :neighbors, :locals => {:neighbors => @prediction.neighbors(@compound), :page => @page},  :layout => :false
diff --git a/views/lazar_algorithm.haml b/views/lazar_algorithm.haml
new file mode 100644
index 0000000..b83de6b
--- /dev/null
+++ b/views/lazar_algorithm.haml
@@ -0,0 +1,50 @@
+%dl#lazar_algorithm
+  %dt
+    %code lazar
+    prediction
+    (
+    = hide_link "#lazar_algorithm"
+    )
+  %dd 
+    %p
+      %code lazar
+      searches the training dataset for  
+      = toggle_link "#similarity", "similar"
+      compounds 
+      %em (neighbors)
+      and calculates the prediction from their measured activities.
+      %code lazar
+      calculates predictions using
+      %ul
+        %li
+          a majority vote (weighted by compound similarity) for
+          %em classification
+          (
+          %a{:href => "http://www.in-silico.de/articles/modi020905.pdf"} original publication
+          )
+        %li
+          a local QSAR model based on neighbors for
+          %em regression
+          (
+          %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf"} original publication
+          )
+
+    %p
+      = toggle_link "#significant_fragments", "Significant fragments"
+      are highlighted in the structure display as follows:
+      %ul
+        %li
+          .active activating fragments
+        %li
+          .inactive deactivating fragments 
+        %li
+          .inconclusive regions, where activating and deactivating fragments overlap
+        %li
+          .other inert parts
+
+    %p
+      Please keep in mind that predictions are based on the measured activities of neighbors. 
+      = toggle_link "#significant_fragments", "Significant fragments"
+      are solely used to determine 
+      = toggle_link "#similarity", "activity specific similarities"
+      of neighbors.
diff --git a/views/lazar_description.haml b/views/lazar_description.haml
new file mode 100644
index 0000000..d870425
--- /dev/null
+++ b/views/lazar_description.haml
@@ -0,0 +1,29 @@
+%dl#lazar_description{ :style => "display: none;" }
+  %dt
+    %code lazar
+    (
+    = hide_link "#lazar_description"
+    )
+  %dd 
+    %p
+      %code lazar
+      searches the training dataset for  
+      = toggle_link "#similarity", "similar"
+      compounds 
+      %em (neighbors)
+      and calculates the prediction from their measured activities.
+      %code lazar
+      calculates predictions using
+      %ul
+        %li
+          a majority vote (weighted by compound similarity) for
+          %em= toggle_link("#classification","classification")
+          (
+          %a{:href => "http://www.in-silico.de/articles/modi020905.pdf"} original publication
+          )
+        %li
+          a local QSAR model based on neighbors for
+          %em= toggle_link("#regression","regression")
+          (
+          %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf"} original publication
+          )
diff --git a/views/model.haml b/views/model.haml
new file mode 100644
index 0000000..d34079d
--- /dev/null
+++ b/views/model.haml
@@ -0,0 +1,67 @@
+- uri = url_for("/model/#{model.id}", :full)
+- js = "$('#delete_#{model.id}').deleteModel('DELETE', {elem: '#model_#{model.id}'});\n  " + "$('#show_model_#{model.id}_warnings').toggleWarnings('#{model.id}');"
+:javascript
+  $(function() {
+    #{js}
+  });
+  
+%div{:id => "model_#{model.id}"}  
+  %h2
+    = model.name
+  .model
+    %dl
+      %dt Status:
+      %dd
+        %span{:id => "model_#{model.id}_status", :class => model.status}
+          = haml :model_status, :locals=>{:model=>model}, :layout => false 
+        (
+        %a{:href => url_for("/model/#{model.id}"), :id => "delete_#{model.id}", :class => 'delete'} delete
+        )
+      %dt Started:
+      %dd= model.created_at.strftime("%m/%d/%Y - %I:%M:%S%p")
+      - if model.nr_compounds
+        %dt Training compounds:
+        %dd= model.nr_compounds 
+      - if model.error_messages
+        %dt Errors:
+        %dd= model.error_messages
+      - if model.warnings
+        %dt Warnings:
+        %a{:href => "#", :id => "show_model_#{model.id}_warnings"} show
+        %dd{:id => "model_#{model.id}_warnings", :style => "display: none;"}= model.warnings
+      %dt Algorithm:
+      %dd= toggle_link("#lazar_description","lazar")
+      - if model.type
+        %dt Type:
+        %dd= toggle_link("##{model.type}","#{model.type}")
+      %dt Descriptors:
+      %dd
+        %a{:href => 'http://www.maunz.de/libfminer2-bbrc-doc/'} Fminer backbone refinement classes
+      - if model.training_dataset
+        %dt Training dataset:
+        %dd
+          %a{:href => "#{model.training_dataset}.xls"} Excel sheet
+          ,
+          -#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
+          -#%em (experts) ,
+          %a{:href => "#{model.training_dataset}.yaml"} YAML
+          %em  (experts)
+      - if model.feature_dataset
+        %dt Feature dataset:
+        %dd
+          -#%a{:href => "#{model.feature_dataset}.rdf"} RDF/XML
+          -#,
+          %a{:href => "#{model.feature_dataset}.xls"} Excel sheet
+          ,
+          %a{:href => "#{model.feature_dataset}.yaml"} YAML
+          %em  (experts)
+      - if model.uri
+        %dt Model:
+        %dd
+          -#%a{:href => "#{model.uri}.rdf"} RDF/XML
+          -#,
+          - if model.validation_qmrf_uri
+            %a{:href => File.join(model.validation_qmrf_uri,"editor")} QMRF Editor, 
+          %a{:href => "#{model.uri}.yaml"} YAML
+          %em  (experts, models cannot be represented in Excel)
+      = haml :validation, :locals=>{:model=>model}, :layout => false     
diff --git a/views/model_status.haml b/views/model_status.haml
new file mode 100644
index 0000000..897e792
--- /dev/null
+++ b/views/model_status.haml
@@ -0,0 +1,2 @@
+-#= image_tag("/snake_transparent.gif") if model.status.match(/running|started|created/i)
+= model.status
diff --git a/views/models.haml b/views/models.haml
new file mode 100644
index 0000000..17d9c8a
--- /dev/null
+++ b/views/models.haml
@@ -0,0 +1,21 @@
+- stati = @models.map{|m| "#{m.id}" if m.status != "Completed"}.compact
+- stati_to_check = stati.length > 0 ? stati.join(", ") : stati = 0 
+:javascript
+  $(function() {
+    if(#{stati != 0}) { 
+      setTimeout('checkStati("#{stati_to_check}")',1500);
+    }
+    var reload_validation = true;
+    if(reload_validation) setTimeout('checkValidation()',15000);
+  });
+
+-# %p Get an overview about ToxCreate models. This page is refreshed every 15 seconds to update the model status.
+%p Get an overview about ToxCreate models. This page is refreshed every 5 seconds to update the model status.
+
+-# explanations
+= haml :lazar_description, :layout => false
+= haml :classification, :layout => false
+= haml :regression, :layout => false
+
+- @models.each do |model|
+  = haml :model, :locals=>{:model=>model}, :layout => false 
diff --git a/views/neighbors.haml b/views/neighbors.haml
new file mode 100644
index 0000000..87fef13
--- /dev/null
+++ b/views/neighbors.haml
@@ -0,0 +1,44 @@
+%tr
+  %th
+    Neighbors 
+    = neighbors_navigation
+  %th= toggle_link("#training_data","Measured activity")
+  %th= toggle_link("#similarity","Similarity")
+  %th Supporting information
+
+- first = 5*page
+- last = first+4
+- neighbor_id = 0
+-# LOGGER.debug neighbors.to_yaml
+- neighbors.sort{|a,b| b[OT.similarity] <=> a[OT.similarity]}[first..last].each do |neighbor|
+  - neighbor_id += 1
+  - compound = OpenTox::Compound.new(neighbor[OT.compound])
+  %tr
+    %td.image= compound_image(compound,@prediction.descriptors(compound))
+    %td= activity_markup(neighbor[OT.activity])
+    %td= sprintf('%.03g', neighbor[OT.similarity])
+    %td
+      %ul
+        %li
+          %a{:href => "#prediction", :id => "show_names#{neighbor_id}"} Names and synonyms
+          :javascript
+            $("a#show_names#{neighbor_id}").click(function () {
+              $("#compound_names#{neighbor_id}").load("#{File.join("compound",compound.inchi)}");  
+              $("#names#{neighbor_id}").toggle();  
+            });
+        %li= toggle_link("#fragments#{neighbor_id}","Significant fragments")
+        -#%li Ambit data
+        -# %li
+          %a{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pccompound&term=#{URI.encode('"'+compound.inchi+'"[InChI]')}"}  PubChem data
+          (external)
+        -# %li ToxNet data
+
+  %tr{:id => "names#{neighbor_id}", :style => "display: none;" }
+    %td{:colspan => '4'}
+      = hide_link("#names#{neighbor_id}")
+      %div{:id => "compound_names#{neighbor_id}"}
+  %tr{:id => "fragments#{neighbor_id}", :style => "display: none;" }
+    %td{:colspan => '4'}
+      = hide_link("#fragments#{neighbor_id}")
+      = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(compound))}, :layout => false
+
diff --git a/views/neighbors_navigation.haml b/views/neighbors_navigation.haml
new file mode 100644
index 0000000..864a99f
--- /dev/null
+++ b/views/neighbors_navigation.haml
@@ -0,0 +1,22 @@
+.neighbors_navigation
+
+  %form{:name => "nav", :action => url_for('/lazar#prediction'), :method => "post", :enctype => "multipart/form-data", :id => "nav"}
+    %input{:type => :hidden, :name => :compound_uri, :value => @compound.uri}
+    %input{:type => :hidden, :name => :model_uri, :value => @model_uri}
+    %input{:type => :hidden, :name => :page, :id => "page"}
+
+    #prev= "prev" unless @page.to_i == 0
+
+    = "(#{5*@page+1}-#{5*@page+5}/#{@prediction.neighbors(@compound).size})" 
+
+    #next= "next" unless 5*@page.to_i+5 >= @prediction.neighbors(@compound).size
+
+    :javascript
+      $("#prev").click(function() {
+        $("#page").val(#{@page-1});
+        $("#nav").submit();
+      });
+      $("#next").click(function() {
+        $("#page").val(#{@page+1});
+        $("#nav").submit();
+      });
diff --git a/views/predict.haml b/views/predict.haml
new file mode 100644
index 0000000..26c8094
--- /dev/null
+++ b/views/predict.haml
@@ -0,0 +1,34 @@
+:javascript
+  function getsmiles() {
+    if (document.JME.smiles() != '') {
+      document.form.identifier.value = document.JME.smiles() ;
+    }
+  }
+
+.input
+  %p Use this service to obtain predictions from OpenTox models.
+  - unless @models.empty?
+
+    %form{:name => "form", :action => url_for('/predict'), :method => "post", :enctype => "multipart/form-data" }
+      %fieldset
+        %legend Draw a compound
+        %label &nbsp;
+        .jme
+          %applet{:code => "JME.class",  :name => "JME", :archive => "JME.jar", :width => "500", :height => "360"}
+            %param{ :name => "options", :value => "polarnitro"}
+              Please enable Java and JavaScript in your browser to use the JME editor. 
+
+        %label{:for => 'identifier'} or enter a Name, InChI, Smiles, CAS, ...
+        %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
+      %fieldset
+        %legend
+          Choose one or more prediction models
+        - @models.each do |model|
+          %label{:for => model.id}
+            = model.name
+          %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => model.id} 
+          %br
+
+      %input{ :type => "submit", :value => "Predict", :onclick => "getsmiles();"}
+      = link_to 'Cancel', '/predict' 
+
diff --git a/views/prediction.haml b/views/prediction.haml
new file mode 100644
index 0000000..8498abc
--- /dev/null
+++ b/views/prediction.haml
@@ -0,0 +1,50 @@
+%p
+  = link_to "New prediction", "/predict"
+.predictions
+  %table
+    %tr
+      %th{:colspan => @predictions.size+1}
+        = @identifier
+    %tr
+      %td
+        %img{:src => @compound.to_image_uri, :alt => @compound.to_smiles}
+      - @predictions.each do |p|
+        - LOGGER.debug p.to_yaml
+        %td
+          %b
+            = p[:title] + ":"
+          - if p[:measured_activities]
+            %br
+            - p[:measured_activities].each do |a|
+              = activity_markup(a)
+            %br
+              (
+              %a{:href => "#", :id => "linkTrainingData#{p.object_id}"} Measured activity
+              :javascript
+                $("a#linkTrainingData#{p.object_id}").click(function () {
+                  $("dl#training_data").toggle();  
+                });
+              )
+
+          - elsif p[:error]
+            %br= p[:error]
+          - else
+            = activity_markup(p[:prediction])
+            - if p[:confidence]
+              %br
+                (
+                %a{:href => "#", :id => "linkConfidence#{p.object_id}"} Confidence
+                = ": #{sprintf('%.03g', p[:confidence].to_f.abs)}"
+                :javascript
+                  $("a#linkConfidence#{p.object_id}").click(function () {
+                    $("dl#confidence").toggle();  
+                  });
+                )
+            %br
+              %form{:name => "form", :action => url_for('/lazar'), :method => "post", :enctype => "multipart/form-data" }
+                %input{:type => :hidden, :name => :compound_uri, :value => @compound.uri}
+                %input{:type => :hidden, :name => :model_uri, :value => p[:model_uri]}
+                %input{ :type => "submit", :value => "Details"}
+
+= haml :confidence, :layout => false
+= haml :training_data, :layout => false
diff --git a/views/regression.haml b/views/regression.haml
new file mode 100644
index 0000000..4866b08
--- /dev/null
+++ b/views/regression.haml
@@ -0,0 +1,11 @@
+%dl#regression{ :style => "display: none;" }
+  %dt
+    Regression
+    (
+    = hide_link "#regression"
+    )
+  %dd 
+    Prediction of
+    %em quantitative
+    properties, e.g. LC50 values
+
diff --git a/views/regression_validation.haml b/views/regression_validation.haml
new file mode 100644
index 0000000..00267a9
--- /dev/null
+++ b/views/regression_validation.haml
@@ -0,0 +1,9 @@
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/R-squared"} R-squared
+%dd= sprintf '%.03g', model.r_square
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/Root_mean_square_deviation"} Root Mean Square Error
+%dd= sprintf '%.03g', model.root_mean_squared_error
+%dt
+  %a{:href => "http://en.wikipedia.org/wiki/Mean_absolute_error"} Mean Absolute Error
+%dd= sprintf '%.03g', model.mean_absolute_error
diff --git a/views/significant_fragments.haml b/views/significant_fragments.haml
new file mode 100644
index 0000000..87cb113
--- /dev/null
+++ b/views/significant_fragments.haml
@@ -0,0 +1,10 @@
+%dl#significant_fragments{ :style => "display: none;" }
+  %dt
+    Significant fragments
+    (
+    = hide_link "#significant_fragments"
+    )
+  %dd 
+    Substructures that occur (statistically significant) more frequently in active or inactive compounds. Substuctures can take any shape (without cycles) and are determined with the 
+    %a{:href => "http://www.maunz.de/libfminer2-bbrc-doc/"} fminer
+    algorithm.
diff --git a/views/similarity.haml b/views/similarity.haml
new file mode 100644
index 0000000..659eb50
--- /dev/null
+++ b/views/similarity.haml
@@ -0,0 +1,19 @@
+%dl#similarity{ :style => "display: none;" }
+  %dt
+    Similarity
+    (
+    = hide_link "#similarity"
+    )
+  %dd 
+    %code lazar
+    calculates 
+    %em activity specific
+    similarities based on the presence of statistically 
+    = toggle_link "#significant_fragments", "significant fragments"
+    This procedure will
+    %ul
+      %li consider only those parts of a chemical structure that are relevant for a particular endpoint
+      %li ignore inert parts of the structure
+      %li lead to different similarities, depending on the toxic endpoint
+    Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.
+    
diff --git a/views/style.sass b/views/style.sass
new file mode 100644
index 0000000..5f362a3
--- /dev/null
+++ b/views/style.sass
@@ -0,0 +1,239 @@
+$bg_color: #b9dcff
+$bg_color2: #e5e7eb
+$fg_color: #424345
+$ot_purple: #5d308a
+$body_color: white
+$text_color: black
+$notice_border: black
+
+body
+  min-width: 30em
+  font-family: verdana, arial, helvetica, sans-serif
+  background-color: $body_color
+  color: $text_color
+  padding: 1em
+  a
+    text-decoration: none
+    font-weight: bold
+    color: $ot_purple
+  a:hover
+    color: black
+
+  .headline
+    .logo
+      float: right
+
+  .index
+    clear: both
+    ul
+      margin: 0 0 2px 0
+      padding: 0
+      white-space: nowrap
+      list-style-type: none
+    li
+      margin: 0
+      padding: 2px
+      display: inline
+      border-right: 1px solid
+        color: $body_color
+      border-top: 1px solid
+        color: $body_color
+      background-color: $fg_color
+      padding-left: 0.5em
+      padding-right: 0.5em
+      font-weight: bold
+      a
+        text-decoration: none
+        color: $bg_color
+        &:hover
+          color: $body_color
+    li.selected
+      font-weight: bold
+      background-color: $bg_color
+      border: 1px solid
+        color: $fg_color
+      border-bottom: 1px solid
+        color: $bg_color
+      a
+        color: $text_color
+
+  .content
+    background-color: $bg_color
+    height: 100%
+    padding: 1em
+    border: 1px solid
+      color: $fg_color
+    h2
+      margin: 20px 3px 2px 3px
+    .notice
+      padding: 1em
+      background-color: $body_color
+      border: 1px solid
+      border-color: $notice_border
+    .input
+      text-align: left
+      form
+        padding: 1em
+        background-color: $bg_color2
+        border: 1px solid
+          color: $fg_color
+        fieldset
+          margin: 0
+          padding: 0
+          border: 0
+        legend
+          font-weight: bold
+          color: $fg_color
+        label
+          width: 28em
+          display: block
+          float: left
+        br
+          clear: both
+    .code
+      border: 1px solid black
+      padding: 1%
+      background-color: white
+      table
+        display: inline-table
+        border-collapse: collapse
+        th
+          padding: 0.5em
+          border: 1px solid
+          background-color: #ccd2dc
+        td
+          padding: 0.5em
+          border: 1px solid
+
+    .predictions
+      text-align: center
+      overflow: auto
+      table
+        border-spacing: 0
+        border-collapse: collapse
+        margin: 0
+        th
+          color: $body_color
+          background-color: $fg_color
+          border: 1px solid
+          margin: 0.5em
+        td
+          border: 1px solid
+          background-color: $bg_color2
+          padding: 0.5em
+        img
+          padding: 0
+          height: 100%
+
+    .lazar-predictions
+      clear: both
+      margin-top: 2%
+      .neighbors_navigation
+        font-size: x-small
+        #prev
+          @extend a
+          display: inline
+          cursor: pointer
+        #next
+          @extend a
+          display: inline
+          cursor: pointer
+        
+      dt
+        font-weight: bold
+      table
+        width: 100%
+        //height: 100%
+        background-color: $bg_color2
+        border-spacing: 0
+        border-collapse: collapse
+        margin: 0
+        tbody
+          //height: 10em
+        th
+          text-align: center
+          border: 1px solid
+          color: $body_color
+          background-color: $fg_color
+          margin: 0.5em
+          a
+            text-decoration: underline
+            font-weight: bold
+            color: $bg_color
+
+          a:hover
+            color: $bg_color2
+        td
+          border: 1px solid
+          overflow: auto
+          ul
+            list-style-type: none
+        td.image
+          padding: 0
+          width: 150px
+          height: 150px
+
+          table
+            font-size: x-small
+            td
+              border: none
+            td.selected
+              background-color: blue
+          //overflow-y: scroll;
+
+  .model
+    padding: 0em 1em
+    background-color: $bg_color2
+    border: 1px solid
+    margin-top: 0.6em
+    dl
+      dt
+        width: 15em
+        font-weight: bold
+        float: left
+        clear: both
+      dd
+        clear: right
+        margin: 0.2em 0em
+        dl
+          clear: both
+          padding: 0em
+          background-color: $bg_color2
+          border: 0
+          dt
+            white-space: nowrap
+            width: 16em
+            font-weight: bold
+            float: left
+            clear: right
+          
+  .footer
+    margin: 0.5em
+    padding: 0.5em
+
+.active
+  color: red
+
+.inactive
+  color: green
+
+.inconclusive
+  color: yellow
+
+.other
+  color: black
+
+dl
+  dd
+    td
+      border: 1px dotted white
+      text-align: right
+      padding: 0.2em
+      .blank
+        border: 0
+    th
+      border-bottom: 1px dotted white
+      text-align: center
+      padding: 0.3em
+    table
+      border-collapse: collapse
diff --git a/views/training_data.haml b/views/training_data.haml
new file mode 100644
index 0000000..0593776
--- /dev/null
+++ b/views/training_data.haml
@@ -0,0 +1,7 @@
+%dl#training_data{ :style => "display: none;" }
+  %dt
+    Measured activity
+    (
+    = hide_link "#training_data"
+    )
+  %dd Experimental result(s) from the training dataset. 
diff --git a/views/unit.haml b/views/unit.haml
new file mode 100644
index 0000000..a352599
--- /dev/null
+++ b/views/unit.haml
@@ -0,0 +1,10 @@
+%dl#unit{ :style => "display: none;" }
+  %dt
+    Unit
+    (
+    = hide_link "#unit"
+    )
+  %dd 
+    Unit of measurement, e.g. mmol or mmol/kg-bodyweight.  For optimal performance you should use 
+    %a{:href => "http://en.wikipedia.org/wiki/Molar_(concentration)"} molar
+    units.
diff --git a/views/validation.haml b/views/validation.haml
new file mode 100644
index 0000000..5fc7371
--- /dev/null
+++ b/views/validation.haml
@@ -0,0 +1,23 @@
+- if model.validation_uri
+  %dl{:id => "model_validation_#{model.id}"}
+    %dt
+      Validation:
+      -# %input{ :id => "model_validation_report_#{model.id}", :type => "hidden", :value => "#{model.validation_report_status}", :class => "model_validation_report" }
+    %dd
+      %dl
+        - if model.validation_report_uri
+          %dt Detailed report:
+          %dd
+            %a{:href => model.validation_report_uri, :target => "_blank"} show
+        %dt Number of predictions
+        %dd= model.nr_predictions
+        - case model.type
+        - when "classification"
+          = haml :classification_validation, :locals=>{:model=>model}, :layout => false if model.correct_predictions
+        - when "regression"
+          = haml :regression_validation, :locals=>{:model=>model}, :layout => false     
+-# else
+  = image_tag("/snake_transparent.gif") if model.validation_status == "Running"
+  %a{:href => model.validation_task_uri} #{model.validation_status}
+            
+