Adjustment for the Nestle GUI.

views/feature_table.haml

@@ -36,13 +36,13 @@
   -if features[:deactivating].empty? and features[:activating].empty? and (features[:pc_features].size >= 1)
     %tr
       %th
-        descriptor
+        Descriptors
       %th
-        value
+        Values
     - features[:pc_features].sort{|a,b| a[:feature] <=> b[:feature] }.each do |f|
       %tr
         %td= f[:feature]
-        %td= f[:value]
+        %td= f[:value].uniq.collect{|v| v.to_s  + " "}
 
 
 

views/layout.haml

@@ -35,10 +35,12 @@
           %b= session[:username]
 
       .notice
-        This is an experimental version based on
-        %a{:href => "http://www.opentox.org", :rel => "external"} OpenTox
-        services. Please report problems and feature requests to our 
-        %a{:href => 'http://github.com/opentox/toxcreate/issues', :rel => "external"} issue tracker.
+        This is a prediction interface for Nestle based on IST web services. 
+        Please contact us in case of problems: 
+        %a{:href => 'mailto:andreas@maunz.de', :rel => "andreas@maunz.de"} Andreas Maunz
+        or
+        %a{:href => 'mailto:david.vorg@googlemail.com', :rel => "david.vorg@googlemail.com"} David Vorgrimmler
+
 
       - if `hostname`.match(/ot-test/)
         .notice 
@@ -55,4 +57,4 @@
     .footer
       © 
       %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology gmbh
-      2004-2011
+      2004-2012

views/lazar.haml

@@ -5,7 +5,8 @@
   = haml :lazar_algorithm, :layout => false
   = haml :confidence, :layout => false
   = haml :similarity, :layout => false
-  = haml :significant_fragments, :layout => false
+  -#= haml :significant_fragments, :layout => false
+  = haml :pc_descriptors, :layout => false
   = haml :training_data, :layout => false
 
   %a{:name => "prediction"}
@@ -30,7 +31,8 @@
                   $("#compound_names").load("#{File.join("/compound",@compound.inchi)}");  
                   $("tr#names").toggle();  
                 });
-            %li= toggle_link("#fragments","Significant fragments")
+            -#%li= toggle_link("#fragments","Significant fragments")
+            %li= toggle_link("#fragments","Physico chemical descriptors")
 
       %tr#names{ :style => "display: none;" }
         %td{:colspan => '4'}

views/lazar_algorithm.haml

@@ -14,51 +14,12 @@
       %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", :rel => "external"} original publication
-          )
-        %li
-          a local QSAR model based on neighbors for
-          %em regression
-          (
-          %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf", :rel => "external"} original publication
-          )
-
-    %p
-      = toggle_link "#significant_fragments", "Significant fragments"
-      are highlighted in the structure display as follows:
-      - if @value_map.empty?
-        %ul
-          %li
-            .active activating fragments
-          %li
-            .inactive deactivating fragments 
-          %li
-            .inconclusive regions, where activating and deactivating fragments overlap
-          %li
-            .other inert parts
-      - else
-        %ul
-          %li
-            .active= "features that occur predominately in compounds with activity: \"#{@value_map[@value_map.keys.sort.last]}\""
-          %li
-            .inactive= "features that occur predominately in compounds with activity: \"#{@value_map[@value_map.keys.sort.first]}\""
-          %li
-            .inconclusive regions, where fragments from different classes overlap
-          %li
-            .other inert parts
-      - if @value_map.size > 2
-        .notice Incomplete implementation of feature highlighting and display of significant fragments. Only features for 2 classes are shown!
-
-
+      calculates predictions using a well-established radial basis function (rbf) kernel for SVMs
+      %em (regression)
+
     %p
       Please keep in mind that predictions are based on the measured activities of neighbors. 
-      = toggle_link "#significant_fragments", "Significant fragments"
+      = toggle_link "#pc_descriptors", "Physico chemical descriptors"
       are solely used to determine 
       = toggle_link "#similarity", "activity specific similarities"
       of neighbors.

views/neighbors.haml

@@ -25,7 +25,8 @@
               $("#compound_names#{neighbor_id}").load("#{File.join("compound",compound.inchi)}");  
               $("#names#{neighbor_id}").toggle();  
             });
-        %li= toggle_link("#fragments#{neighbor_id}","Significant fragments")
+        -#%li= toggle_link("#fragments#{neighbor_id}","Significant fragments")
+        %li= toggle_link("#fragments#{neighbor_id}","Physico chemical descriptors")
         -#%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

views/similarity.haml

@@ -8,12 +8,13 @@
     %code lazar
     calculates 
     %em activity specific
-    similarities based on the presence of statistically 
-    = toggle_link "#significant_fragments", "significant fragments"
-    This procedure will
-    %ul
+    similarities based on the presence of statistically significant 
+    -#= toggle_link "#significant_fragments", "significant fragments"
+    = toggle_link "#pc_descriptors", "physico chemical descriptors."
+    -#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.
+    -#Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.