merge with helma/development

29 files changed, 1000 insertions, 0 deletions

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 > 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}
+            
+