lazar details implemented

18 files changed, 379 insertions, 256 deletions

diff --git a/application.rb b/application.rb
index cd4cb54..7bbbafb 100644
--- a/application.rb
+++ b/application.rb
@@ -28,11 +28,11 @@ delete '/model/:id/?' do
 	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
-	model.destroy!
-	flash[:notice] = "#{model.name} model deleted."
 	redirect url_for('/models')
 end
 
@@ -122,14 +122,20 @@ post '/upload' do # create a new model
 		redirect url_for('/create')
 	end
 
-	validation_task_uri = OpenTox::Validation.crossvalidation(
-		:algorithm_uri => OpenTox::Algorithm::Lazar.uri,
-		:dataset_uri => parser.dataset_uri,
-		:prediction_feature => feature_uri,
-		:algorithm_params => "feature_generation_uri=#{OpenTox::Algorithm::Fminer.uri}"
-	).uri
-	LOGGER.debug "Validation task: " + validation_task_uri
-	@model.validation_task_uri = validation_task_uri
+=begin
+  begin
+    validation_task_uri = OpenTox::Validation.crossvalidation(
+      :algorithm_uri => OpenTox::Algorithm::Lazar.uri,
+      :dataset_uri => parser.dataset_uri,
+      :prediction_feature => feature_uri,
+      :algorithm_params => "feature_generation_uri=#{OpenTox::Algorithm::Fminer.uri}"
+    ).uri
+    LOGGER.debug "Validation task: " + validation_task_uri
+    @model.validation_task_uri = validation_task_uri
+	rescue
+		flash[:notice] = "Model validation failed."
+  end
+=end
 
 =begin
 	if parser.nr_compounds < 10
@@ -170,7 +176,6 @@ post '/predict/?' do # post chemical name to model
 	params[:selection].keys.each do |id|
 		model = ToxCreateModel.get(id.to_i)
 		model.process unless model.uri
-		LOGGER.debug model.to_yaml
 		prediction = nil
 		confidence = nil
 		title = nil
@@ -178,12 +183,13 @@ post '/predict/?' do # post chemical name to model
 		#LOGGER.debug "curl -X POST -d 'compound_uri=#{@compound.uri}' -H 'Accept:application/x-yaml' #{model.uri}"
 		prediction = YAML.load(`curl -X POST -d 'compound_uri=#{@compound.uri}' -H 'Accept:application/x-yaml' #{model.uri}`)
     #prediction = YAML.load(OpenTox::Model::Lazar.predict(params[:compound_uri],params[:model_uri]))
+    LOGGER.debug prediction.to_yaml
 		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")]
+				#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,
@@ -215,7 +221,7 @@ end
 post "/lazar/?" do
   @page = 0
   @page = params[:page].to_i if params[:page]
-  @highlight = params[:highlight]
+  #@highlight = params[:highlight]
   @model_uri = params[:model_uri]
   @prediction = YAML.load(OpenTox::Model::Lazar.predict(params[:compound_uri],params[:model_uri]))
   @compound = OpenTox::Compound.new(:uri => params[:compound_uri])
@@ -230,8 +236,7 @@ post "/lazar/?" do
       end
       @activity = p[feature]
       @confidence = p[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]
-      @neighbors = p[File.join(@@config[:services]["opentox-model"],"lazar#neighbors")]#.sort{|a,b| b.last[:similarity] <=> a.last[:similarity]}
-      #@training_activities = p[File.join(@@config[:services]["opentox-model"],"lazar#activities")]
+      @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
@@ -242,6 +247,22 @@ post "/lazar/?" do
   haml :lazar
 end
 
+# proxy to get data from compound service
+# (jQuery load does not work with external URIs)
+get %r{/compound/(.*)} do |inchi|
+  OpenTox::Compound.new(:inchi => inchi).names.gsub(/\n/,', ')
+end
+
+=begin
+post "/neighbors" do
+  @neighbors = params[:neighbors]
+  @page = params[:page].to_i
+  LOGGER.debug @neighbors
+  LOGGER.debug @page
+  haml :neighbors
+end
+=end
+
 delete '/?' do
   ToxCreateModel.auto_migrate!
 	response['Content-Type'] = 'text/plain'
diff --git a/helper.rb b/helper.rb
index 4a5f739..9c4b04c 100644
--- a/helper.rb
+++ b/helper.rb
@@ -1,14 +1,40 @@
 helpers do
-	def activity(a)
-		case a.to_s
-		when "true"
-			act = "active"
-		when "false"
-			act = "inactive"
-		else
-			act = "not available"
-		end
-		act
-	end
+
+  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 compound_image(compound,features)
+    haml :compound_image, :locals => {:compound => compound, :features => features}, :layout => false
+  end
+  
+  def activity_markup(activity)
+    case activity.class.to_s
+    when /Float/
+      haml ".other #{sprintf('%.03g', activity)}", :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/views/compound_image.haml b/views/compound_image.haml
new file mode 100644
index 0000000..c6f962a
--- /dev/null
+++ b/views/compound_image.haml
@@ -0,0 +1,2 @@
+%img{:src => compound.display_smarts_uri(features[:activating].collect{|f| f[:smarts]},@features[:deactivating].collect{|f| f[:smarts]}), :alt => compound.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/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/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 () {
+    $("#{destination}").#{method}();  
+  });
diff --git a/views/layout.haml b/views/layout.haml
index a301358..6c9202b 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -16,7 +16,7 @@
           = link_to "Create", "/create"
         %li{:class => ("selected" if /models/ =~ request.path )}
           = link_to "Inspect", "/models"
-        %li{:class => ("selected" if /predict/ =~ request.path )}
+        %li{:class => ("selected" if /predict|lazar/ =~ request.path )}
           = link_to "Predict", "/predict"
         %li{:class => ("selected" if /help/ =~ request.path )}
           = link_to "Help", "/help"
diff --git a/views/lazar.haml b/views/lazar.haml
index 057b1cd..59d5396 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -1,163 +1,55 @@
+%p= link_to "New prediction", "/predict"
 .lazar-predictions
-  %table
-    %tr
-      %th= @title.gsub(/_lazar_.*$/,' ').capitalize
-      %th Prediction
-      %th 
-        %a{:href => "#", :id => "linkConfidence#{p.object_id}"} Confidence
-        :javascript
-          $("a#linkConfidence#{p.object_id}").click(function () {
-            $("dl#confidence").toggle();  
-          });
-      -#%th
-        Significant fragments
-        = haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => nil}, :layout => false
-      -#%th Additional data
 
-    %tr
-      %td
-        %img{:src => @compound.display_smarts_uri(@features[:activating].keys,@features[:deactivating].keys, params[:highlight]), :alt => @compound.smiles}
-        %td
-          - if @measured_activities
-            %br
-            - @measured_activities.each do |a|
-              - if activity(a) == 'active'
-                .active
-                  = activity(a)
-              - elsif activity(a) == 'inactive'
-                .inactive
-                  = activity(a)
-              - else
-                = a
-            %br
-              (
-              %a{:href => "#", :id => "linkTrainingData#{p.object_id}"} Training data
-              :javascript
-                $("a#linkTrainingData#{p.object_id}").click(function () {
-                  $("dl#training_data").toggle();  
-                });
-              )
+  -# explanations
+  = haml :lazar_algorithm, :layout => false
+  = haml :confidence, :layout => false
+  = haml :similarity, :layout => false
+  = haml :significant_fragments, :layout => false
+  = haml :training_data, :layout => false
 
-          - else
-            - if activity(@activity) == 'active'
-              .active
-                = activity(@activity)
-            - elsif activity(@activity) == 'inactive'
-              .inactive
-                = activity(@activity)
-            - elsif @activity.is_a?(Float)
-              .other
-                = sprintf('%.03g', @activity)
-            - else
-              .other
-                %em= @activity.to_s
-        %td= sprintf('%.03g', @confidence.to_f.abs) if @confidence
-        -#%td
-          %table
-            - unless @features[:activating].empty?
-              %tr
-                %th activating
-                %th p value
-              - if @features[:activating]
-                - @features[:activating].sort{|a,b| b.last <=> a.last }.each do |f|
-                  %tr
-                  - if @highlight == f[0]
-                    %td.selected= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[0]}, :layout => false
-                    %td.selected= f[1]
-                  - else
-                    %td= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[0]}, :layout => false
-                    %td= f[1]
-            - unless @features[:deactivating].empty?
-              %tr
-                %th deactivating
-                %th p value
-              - if @features[:deactivating]
-                - @features[:deactivating].sort{|a,b| b.last <=> a.last }.each do |f|
-                  %tr
-                  - if @highlight == f[0]
-                    %td.selected= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[0]}, :layout => false
-                    %td.selected= f[1]
-                  - else
-                    %td= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[0]}, :layout => false
-                    %td= f[1]
-        -#%td
+  %a{:name => "prediction"}
+  %table
+    %thead
+      %tr
+        %th= @title.gsub(/_lazar_.*$/,' ').capitalize
+        %th= toggle_link("#lazar_algorithm","Prediction")
+        %th= toggle_link("#confidence","Confidence")
+        %th Supporting information
 
-    %tr
-      %th
-        Neighbors 
-        = haml :prev, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => @highlight, :page => @page, :size => @neighbors.size}, :layout => false
-        = "(#{5*@page+1}-#{5*@page+5}/#{@neighbors.size})"
-        = haml :next, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => @highlight, :page => @page, :size => @neighbors.size}, :layout => false
-      %th Activity
-      %th Similarity (activity specific)
-      -#%th
-        Significant fragemnts
-        = haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => nil}, :layout => false
-      -#%th Additional data
-      -#%th Exclude
-    - first = 5*@page
-    - last = first+4
-    - @neighbors.sort{|a,b| b.last[:similarity] <=> a.last[:similarity]}[first..last].each do |uri,data|
-      - c = OpenTox::Compound.new(:uri => uri)
       %tr
-        %td 
-          -#%br
-            %a{:href => c.display_smarts_uri(data[:features][:activating].collect{|f| f[:smarts]}, data[:features][:deactivating].collect{|f| f[:smarts]}, params[:highlight])} #{c.smiles}
-          %br
-            %img{:src => c.display_smarts_uri(data[:features][:activating].collect{|f| f[:smarts]}, data[:features][:deactivating].collect{|f| f[:smarts]}, params[:highlight]), :alt => c.smiles}
-        %td
-          - data[:activities].each do |act|
-            - if activity(act) == 'active'
-              .active
-                = activity(act)
-            - elsif activity(act) == 'inactive'
-              .inactive
-                = activity(act)
-            - elsif act.is_a?(Float)
-              .other
-                = sprintf('%.03g', act)
-            - else
-              .other
-                %em= act.to_s
+        %td.image= compound_image(@compound,@features)
+        %td= activity_markup(@activity)
+        %td= sprintf('%.03g', @confidence.to_f.abs) if @confidence
         %td
-          = sprintf('%.03g', data[:similarity])
-        -#%td
-          %table
-            - unless data[:features][:activating].empty?
-              %tr
-                %th activating
-                %th p value
-              - data[:features][:activating].sort{|a,b| b[:p_value] <=> a[:p_value] }.each do |f|
-                %tr
-                  - if @highlight == f[:smarts]
-                    %td.selected= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[:smarts]}, :layout => false
-                    %td.selected= f[:p_value]
-                  - else
-                    %td= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[:smarts]}, :layout => false
-                    %td= f[:p_value]
-            - unless data[:features][:deactivating].empty?
-              %tr
-                %th deactivating
-                %th p value
-              - data[:features][:deactivating].sort{|a,b| b[:p_value] <=> a[:p_value] }.each do |f|
-                %tr
-                  - if @highlight == f[:smarts]
-                    %td.selected= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[:smarts]}, :layout => false
-                    %td.selected= f[:p_value]
-                  - else
-                    %td= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[:smarts]}, :layout => false
-                    %td= f[:p_value]
-        -#%td 
-        -#%td 
-
-
-%dl#confidence{ :style => "display: none;" }
-  %dt 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.
-
-
-%dl#training_data{ :style => "display: none;" }
-  %dt Training data:
-  %dd Experimental result(s) from the training dataset are displayed here. 
-
-
+          %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 => @features}, :layout => false
+
+    %tbody#neighbors
+      = haml :neighbors, :locals => {:neighbors => @neighbors, :page => @page},  :layout => :false
diff --git a/views/lazar_algorithm.haml b/views/lazar_algorithm.haml
new file mode 100644
index 0000000..6322b17
--- /dev/null
+++ b/views/lazar_algorithm.haml
@@ -0,0 +1,44 @@
+%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
+        %li
+          a local QSAR model based on neighbors for
+          %em regression
+
+    %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/neighbors.haml b/views/neighbors.haml
new file mode 100644
index 0000000..82fafd2
--- /dev/null
+++ b/views/neighbors.haml
@@ -0,0 +1,45 @@
+%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
+- neighbors.sort{|a,b| b.last[:similarity] <=> a.last[:similarity]}[first..last].each do |uri,data|
+  - neighbor_id += 1
+  - compound = OpenTox::Compound.new(:uri => uri)
+  %tr
+    %td.image= compound_image(compound,data[:features])
+    %td
+      - data[:activities].each do |act|
+        = activity_markup(act)
+    %td= sprintf('%.03g', data[: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 => data[:features]}, :layout => false
+
diff --git a/views/neighbors_navigation.haml b/views/neighbors_navigation.haml
new file mode 100644
index 0000000..43ec3ed
--- /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}/#{@neighbors.size})" 
+
+    #next= "next" unless 5*@page.to_i+5 >= @neighbors.size
+
+    :javascript
+      $("#prev").click(function() {
+        $("#page").val(#{@page-1});
+        $("#nav").submit();
+      });
+      $("#next").click(function() {
+        $("#page").val(#{@page+1});
+        $("#nav").submit();
+      });
diff --git a/views/next.haml b/views/next.haml
deleted file mode 100644
index b7a2b3a..0000000
--- a/views/next.haml
+++ /dev/null
@@ -1,7 +0,0 @@
-- unless 5*page.to_i+5 >= size
-  %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}
-    %input{:type => :hidden, :name => :page, :value => page.to_i+1}
-    %input{ :type => "submit", :value => "&gt;&gt;"}
diff --git a/views/prediction.haml b/views/prediction.haml
index 94d7987..dd7d155 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -15,17 +15,10 @@
           - if p[:measured_activities]
             %br
             - p[:measured_activities].each do |a|
-              - if activity(a) == 'active'
-                .active
-                  = activity(a)
-              - elsif activity(a) == 'inactive'
-                .inactive
-                  = activity(a)
-              - else
-                = a
+              = activity_markup(a)
             %br
               (
-              %a{:href => "#", :id => "linkTrainingData#{p.object_id}"} Training data
+              %a{:href => "#", :id => "linkTrainingData#{p.object_id}"} Measured activity
               :javascript
                 $("a#linkTrainingData#{p.object_id}").click(function () {
                   $("dl#training_data").toggle();  
@@ -33,18 +26,7 @@
               )
 
           - else
-            - if activity(p[:prediction]) == 'active'
-              .active
-                = activity(p[:prediction])
-            - elsif activity(p[:prediction]) == 'inactive'
-              .inactive
-                = activity(p[:prediction])
-            - elsif p[:prediction].is_a?(Float)
-              .other
-                = sprintf('%.03g', p[:prediction])
-            - else
-              .other
-                %em= p[:prediction].to_s
+            = activity_markup(p[:prediction])
             - if p[:confidence]
               %br
                 (
@@ -61,13 +43,5 @@
                 %input{:type => :hidden, :name => :model_uri, :value => p[:model_uri]}
                 %input{ :type => "submit", :value => "Details"}
 
-%dl#confidence{ :style => "display: none;" }
-  %dt 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.
-
-
-%dl#training_data{ :style => "display: none;" }
-  %dt Training data:
-  %dd Experimental result(s) from the training dataset are displayed here. 
-
-
+= haml :confidence, :layout => false
+= haml :training_data, :layout => false
diff --git a/views/prev.haml b/views/prev.haml
deleted file mode 100644
index 9a00579..0000000
--- a/views/prev.haml
+++ /dev/null
@@ -1,8 +0,0 @@
-- unless page.to_i == 0
-  %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}
-    %input{:type => :hidden, :name => :page, :value => page.to_i-1}
-    %input{ :type => "submit", :value => "&lt;&lt;"}
-
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
index b64b919..4977da1 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -18,6 +18,7 @@ body
     color: $ot_purple
   a:hover
     color: black
+
   .headline
     .logo
       float: right
@@ -55,6 +56,7 @@ body
         color: $bg_color
       a
         color: $text_color
+
   .content
     background-color: $bg_color
     height: 100%
@@ -102,6 +104,7 @@ body
         td
           padding: 0.5em
           border: 1px solid
+
     .predictions
       text-align: center
       overflow: auto
@@ -121,57 +124,87 @@ body
         img
           padding: 0
           height: 100%
+
     .lazar-predictions
       clear: both
       margin-top: 2%
+      .neighbors_navigation
+        font-size: x-small
+        #prev
+          @extend a
+          display: inline
+        #next
+          @extend a
+          display: inline
+        
+      dt
+        font-weight: bold
       table
+        width: 100%
+        //height: 100%
+        background-color: $bg_color2
         border-spacing: 0
         border-collapse: collapse
         margin: 0
+        tbody
+          height: 10em
+          overflow: scroll
         th
+          text-align: center
           border: 1px solid
           color: $body_color
           background-color: $fg_color
-          //border: 1px solid
           margin: 0.5em
+          a
+            text-decoration: underline
+            font-weight: bold
+            color: $bg_color
+
+          a:hover
+            color: $bg_color2
         td
           border: 1px solid
-          background-color: $bg_color2
-          padding: 0.5em
+          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
-        //img
-          padding: 0
-          //height: 100%
+          //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
+    dl
+      dt
+        width: 15em
+        font-weight: bold
+        float: left
         clear: both
-        padding: 0em
-        background-color: $bg_color2
-        border: 0
-        dt
-          white-space: nowrap
-          width: 16em
-          font-weight: bold
-          float: left
-          clear: right
+      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
@@ -183,6 +216,9 @@ body
 .inactive
   color: green
 
+.inconclusive
+  color: yellow
+
 .other
   color: black
 
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.