From ddbe5c5478c7dd71d9c851008340e28a61d5ba33 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Tue, 27 Oct 2015 12:24:58 +0000
Subject: enabled batch

---
 views/predict.haml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'views')

diff --git a/views/predict.haml b/views/predict.haml
index 9863cd9..0dc767b 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -125,12 +125,11 @@
       %br
       %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
       %p
-      // disable for public version
       %label{:for=>"fileselect"}
         or upload a CSV file for batch predictions (disabled in public version)
       %br
       %span.btn.btn-default.btn-file
-        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
+        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv"}
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
-- 
cgit v1.2.3


From 41f948d58ba99a635ae7e04573bd368d9ab34d99 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Tue, 27 Oct 2015 12:26:14 +0000
Subject: enabled batch

---
 views/predict.haml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'views')

diff --git a/views/predict.haml b/views/predict.haml
index 0dc767b..a4fa080 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -126,7 +126,7 @@
       %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
       %p
       %label{:for=>"fileselect"}
-        or upload a CSV file for batch predictions (disabled in public version)
+        or upload a CSV file for batch predictions
       %br
       %span.btn.btn-default.btn-file
         %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv"}
-- 
cgit v1.2.3


From d2d8db1e59e830b1a24e9b8d270a3b393d746b6c Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 28 Oct 2015 13:58:45 +0000
Subject: consisten use of brackets for units; collect measured activity for
 equal neighbors

---
 views/batch.haml     | 3 +--
 views/neighbors.haml | 4 ++--
 2 files changed, 3 insertions(+), 4 deletions(-)

(limited to 'views')

diff --git a/views/batch.haml b/views/batch.haml
index 8389651..ec987c4 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -44,7 +44,7 @@
                 %br
                 %b Prediction:
                 / TODO scientific notation
-                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit}" : prediction[:value]
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value]
                 %br
                 / TODO probability
                 %b Confidence:
@@ -53,4 +53,3 @@
               - else
                 %p
                   = "Not enough similar compounds </br>in training dataset."
-              %p
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 21b4b35..a741b45 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -58,7 +58,7 @@
                     / %td
                 %tbody
                   - type = @model_types[j]
-                - prediction[:neighbors].each_with_index do |neighbor,count|
+                - prediction[:neighbors].uniq.each_with_index do |neighbor,count|
                   %tr
                     / Compound
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"}
@@ -67,7 +67,7 @@
                       %p= Compound.find(neighbor[0]).smiles
                     / Measured Activity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join(", ") : neighbor[2].join(", ")
+                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("</br>") : neighbor[2].join(", ")
                     / Similarity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
-- 
cgit v1.2.3


From b452a81e9c0a470bf9aa51f0192378f5fba5177a Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 29 Oct 2015 09:54:15 +0000
Subject: trim and log SMILES input

---
 views/predict.haml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'views')

diff --git a/views/predict.haml b/views/predict.haml
index a4fa080..7f19071 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -24,7 +24,7 @@
   });  
   
   function getInput(){
-    identifier = document.getElementById("identifier").value;
+    identifier = document.getElementById("identifier").value.trim();
     fileselect = document.getElementById("fileselect").value;
     if (fileselect != ""){
       return 1;
-- 
cgit v1.2.3


From efd241beab11fbfc200f0c32ffb9e198ed406c83 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 29 Oct 2015 18:20:39 +0000
Subject: added mg/kg_bw/day

---
 views/batch.haml      | 5 +++--
 views/neighbors.haml  | 6 ++++--
 views/prediction.haml | 6 +++---
 3 files changed, 10 insertions(+), 7 deletions(-)

(limited to 'views')

diff --git a/views/batch.haml b/views/batch.haml
index ec987c4..f593188 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -18,6 +18,7 @@
       / key = compound, values = array of arrays with model, prediction
       - @batch.each do |key, values|
         - compound = key
+        - mw = compound.molecular_weight
         %tr
           %td{:style=>"vertical-align:top;"}
             %p= compound.svg
@@ -34,7 +35,7 @@
                 %p
                 / TODO fix scientific notation from database
                 %b Measured activity:
-                = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value]
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 %p Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
@@ -44,7 +45,7 @@
                 %br
                 %b Prediction:
                 / TODO scientific notation
-                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value]
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 %br
                 / TODO probability
                 %b Confidence:
diff --git a/views/neighbors.haml b/views/neighbors.haml
index a741b45..4a1f3ea 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -65,9 +65,11 @@
                       /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}}
                       %p= Compound.find(neighbor[0]).svg
                       %p= Compound.find(neighbor[0]).smiles
+                    - c = Compound.find(neighbor[0])
+                    - mw = c.molecular_weight
                     / Measured Activity
-                    %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("</br>") : neighbor[2].join(", ")
+                    %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
+                      = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n, mw); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : neighbor[2].join(", ")
                     / Similarity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
diff --git a/views/prediction.haml b/views/prediction.haml
index ef0c5db..11d542e 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,6 +18,7 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
+          - mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -32,7 +33,7 @@
                 %p
                 / TODO fix scientific notation from database
                 %b Measured activity:
-                = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit})" : prediction[:value]
+                = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 %p Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
@@ -41,8 +42,7 @@
                 = type
                 %br
                 %b Prediction:
-                / TODO scientific notation
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit})" : prediction[:value]
+                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 / TODO update description
                 / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
                 %br
-- 
cgit v1.2.3


From a348f222c0b32bbb308083bb03127fe55b1563dc Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Fri, 30 Oct 2015 08:26:04 +0000
Subject: fixed weight for multiple database hits in prediction

---
 views/batch.haml      | 12 +++++++-----
 views/prediction.haml | 10 +++++++---
 2 files changed, 14 insertions(+), 8 deletions(-)

(limited to 'views')

diff --git a/views/batch.haml b/views/batch.haml
index f593188..9bfa67e 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -33,10 +33,13 @@
               %p
               - if prediction[:confidence] == "measured"
                 %p
-                / TODO fix scientific notation from database
-                %b Measured activity:
-                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
-                %p Compound is part of the training dataset
+                  %b Measured activity:
+                - if prediction[:value].is_a?(Array)
+                  = prediction[:value][0].numeric? ? prediction[:value].collect{|v| weight = compound.mmol_to_mg(v, mw); '%.2e' % v + " (#{model.unit})"+" | #{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
+                - else
+                  = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
+                %p 
+                %b Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
@@ -44,7 +47,6 @@
                 = model.model.class.to_s.match("Classification") ? "Classification" : "Regression"
                 %br
                 %b Prediction:
-                / TODO scientific notation
                 = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 %br
                 / TODO probability
diff --git a/views/prediction.haml b/views/prediction.haml
index 11d542e..a74b95a 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -31,10 +31,14 @@
               - if prediction[:confidence] == "measured"
                 - @dbhit[i] = true
                 %p
-                / TODO fix scientific notation from database
                 %b Measured activity:
-                = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
-                %p Compound is part of the training dataset
+                - p prediction[:value] 
+                - if prediction[:value].is_a?(Array)
+                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v, mw); '%.2e' % v + " (#{@models[i].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
+                - else
+                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
+                %p 
+                  %b Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
-- 
cgit v1.2.3


From f7680842ee830af78d860b3a0a09b654368df90a Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 14 Jan 2016 09:37:39 +0000
Subject: changed weight method for lazar v8-nestec release

---
 views/neighbors.haml  | 4 ++--
 views/prediction.haml | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

(limited to 'views')

diff --git a/views/neighbors.haml b/views/neighbors.haml
index 4a1f3ea..a69f38b 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -66,10 +66,10 @@
                       %p= Compound.find(neighbor[0]).svg
                       %p= Compound.find(neighbor[0]).smiles
                     - c = Compound.find(neighbor[0])
-                    - mw = c.molecular_weight
+                    //- mw = c.molecular_weight
                     / Measured Activity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
-                      = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n, mw); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : neighbor[2].join(", ")
+                      = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : neighbor[2].join(", ")
                     / Similarity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
diff --git a/views/prediction.haml b/views/prediction.haml
index a74b95a..8d7e3d0 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,7 +18,7 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
-          - mw = @compound.molecular_weight
+          -#- mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -34,9 +34,9 @@
                 %b Measured activity:
                 - p prediction[:value] 
                 - if prediction[:value].is_a?(Array)
-                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v, mw); '%.2e' % v + " (#{@models[i].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
+                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{@models[i].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
                 - else
-                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
+                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value]
                 %p 
                   %b Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
@@ -46,7 +46,7 @@
                 = type
                 %br
                 %b Prediction:
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
+                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value]
                 / TODO update description
                 / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
                 %br
-- 
cgit v1.2.3


From f0588c7e072ea3e22f26916d669e9baaa8fa3197 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Tue, 26 Jan 2016 11:45:30 +0000
Subject: enabled sticky headers for neighbors table

---
 views/neighbors.haml | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

(limited to 'views')

diff --git a/views/neighbors.haml b/views/neighbors.haml
index a69f38b..6001605 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -29,7 +29,20 @@
                 debug: false,
                 theme: "bootstrap",
                 headerTemplate: '{content} {icon}',
-                widgets: ['zebra', 'columns', 'uitheme'],
+                widgets: ['zebra', 'columns', 'uitheme', 'stickyHeaders'],
+                widgetOptions: {
+                  stickyHeaders_attachTo : '.tab-content',
+                  stickyHeaders : '',
+                  stickyHeaders_offset : 0,
+                  stickyHeaders_cloneId : '-sticky',
+                  stickyHeaders_addResizeEvent : true,
+                  stickyHeaders_includeCaption : true,
+                  stickyHeaders_zIndex : 2,
+                  stickyHeaders_attachTo : null,
+                  stickyHeaders_xScroll : null,
+                  stickyHeaders_yScroll : null,
+                  stickyHeaders_filteredToTop: true
+                },
                 headers: {0: {sorter: false}, 3: {sorter: false}},
                 sortList: [[2,1]],
                 widthFixed: false
-- 
cgit v1.2.3


From f86c084311282036ffa7b4588c0fa0d5b59af95b Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 24 Nov 2016 16:03:09 +0000
Subject: several fixes; works with lazar tree
 e111369ce5564f159b3f5f85c92afdd22352eaa1

---
 views/details.haml       |   2 +-
 views/layout.haml        |  18 ++++---
 views/license.haml       |   1 +
 views/model_details.haml | 134 +++++++++++++++++++++++++++--------------------
 views/neighbors.haml     |  13 +++--
 views/predict.haml       |   1 +
 views/prediction.haml    |  35 ++++++++-----
 views/style.scss         |  14 +++--
 views/validation.haml    |  16 ------
 9 files changed, 127 insertions(+), 107 deletions(-)
 create mode 100644 views/license.haml
 delete mode 100644 views/validation.haml

(limited to 'views')

diff --git a/views/details.haml b/views/details.haml
index 8a57440..bb8250d 100644
--- a/views/details.haml
+++ b/views/details.haml
@@ -19,6 +19,6 @@
   %hr
   %p{:style=>"padding-left:0.5em;"}
     / pubchem link
-    %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :target=>"_blank"} PubChem read across 
+    %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :rel=>"external"} PubChem read across 
     %i (experimental)
   %br
diff --git a/views/layout.haml b/views/layout.haml
index a40b68c..dddf854 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -15,7 +15,7 @@
     %script{:src=>"/javascripts/bootstrap.min.js"}
     %script{:src=>"/javascripts/jquery.tablesorter.min.js"}
     %script{:src=>"/javascripts/jquery.tablesorter.widgets.js"}
-    %script{ :src=>"/javascripts/lazar-gui.js"}
+    %script{:src=>"/javascripts/lazar-gui.js"}
   %body
     %noscript
       %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
@@ -26,7 +26,7 @@
           %a{:href=> to("/predict")}
             %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"150px", :heigth=>"150px", :style=>"margin:0 3em 0 2em;"}
         %div.col-md-8
-          %h1.media-heading{:style=>"margin: 0 0 0 2em;"}
+          %h1.media-heading
             lazar toxicity predictions
         %div.col-md-2
           %h1.media-heading
@@ -55,7 +55,7 @@
               %img.share{:src=>"/images/Facebook.png"}
         %div.row
         Previous version:
-        %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old
+        %a{:href=>"http://lazar-old.in-silico.ch", :rel => "external"} lazar-old
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
@@ -79,15 +79,17 @@
             %p.text-muted
               &copy; 
               %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
+              |
+              %a{:href => to("/license"), :rel => "external"} GPL3 License
           %supporters.col-md-12
-            %p Financial support:
-            %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"}
+            %p Financial support by
+            %a{:href=>"http://www.bfr.bund.de/de/start.html", :rel=>"external"}
               %img{:src=>"/images/bfr_logo.gif"}
-            %a{:href=>"http://www.opentox.org/", :target=>"_blank"}
+            %a{:href=>"http://www.opentox.org/", :rel=>"external"}
               %img{:src=>"/images/ot_logo.png"}
-            %a{:href=>"https://enanomapper.net/", :target=>"_blank"}
+            %a{:href=>"https://enanomapper.net/", :rel=>"external"}
               %img{:src=>"/images/enm_logo.png"}
-            %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"}
+            %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :rel=>"external"}
               %img{:src=>"/images/nestec.jpg"}
     
 
diff --git a/views/license.haml b/views/license.haml
new file mode 100644
index 0000000..2813220
--- /dev/null
+++ b/views/license.haml
@@ -0,0 +1 @@
+= @license
diff --git a/views/model_details.haml b/views/model_details.haml
index 1be75e7..7646471 100644
--- a/views/model_details.haml
+++ b/views/model_details.haml
@@ -1,26 +1,39 @@
 %b Model:
 %br
 Source:
-%a{:href=>model.source, :target=>"external"}
+%a{:href=>model.source, :rel=>"external"}
   = model.source
 %br
 - model.classification? ? type = "Classification" : type = "Regression"
 = "Type:\t"
 = type
 %br
-- training_dataset = OpenTox::Dataset.find model.training_dataset.id
+- training_dataset = OpenTox::Dataset.find model.model.training_dataset_id
 = "Training compounds:\t"
 = training_dataset.compounds.size
-
+%br
+%b Algorithms:
+%br
+Similarity:
+%a{:href=> "http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["similarity"]["method"].sub("::", "%2F")}", :rel=>"external"}
+  = model.model.algorithms["similarity"]["method"]
+= ", min: #{model.model.algorithms["similarity"]["min"]}"
+%br
+Prediction:
+%a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"}
+  = model.model.algorithms["prediction"]["method"]
+%br
+Descriptors:
+= model.model.algorithms["descriptors"]["method"]+","
+= model.model.algorithms["descriptors"]["type"]
 %p
 - if type == "Classification"
   %b Independent crossvalidations:
 - else
   %b Independent crossvalidations (-log10 transformed):
 %div.row{:id=>"validations#{model.id}", :style=>"background-color:#f5f5f5;"}
-  - model.crossvalidations.each do |crossvalidation|
+  - crossvalidations.each do |cv|
     %span.col-xs-4.col-sm-4.col-md-4.col-lg-4
-      - cv = OpenTox::CrossValidation.find crossvalidation.id
       = "Num folds:\t"
       = cv.folds
       %br
@@ -34,76 +47,81 @@ Source:
         = "Accuracy:\t"
         = cv.accuracy.round(3) if cv.accuracy
         %br
+        = "Weighted accuracy:\t"
+        = cv.weighted_accuracy.round(3) if cv.weighted_accuracy
+        %br
         = "True positive rate:\t"
-        = cv.true_rate["active"].round(3) if cv.true_rate["active"]
+        = cv.true_rate["active"].round(3) if cv.true_rate
         %br
         = "True negative rate:\t"
-        = cv.true_rate["inactive"].round(3) if cv.true_rate["inactive"]
+        = cv.true_rate["inactive"].round(3) if cv.true_rate
         %br 
         = "Positive predictive value:\t"
-        = cv.predictivity["active"].round(3) if cv.predictivity["active"]
+        = cv.predictivity["active"].round(3) if cv.predictivity
         %br
         = "Negative predictive value:\t"
-        = cv.predictivity["inactive"].round(3) if cv.predictivity["inactive"]
+        = cv.predictivity["inactive"].round(3) if cv.predictivity
         %p
-        %b Confusion Matrix:
-        %table.table.table-condensed.table-borderless{:style=>"width:20%;"}
-          %tbody
-            %tr
-              %td
-              %td
-              %td 
-                %b actual
-              %td
-              %td
-            %tr
-              %td
-              %td
-              %td active
-              %td inactive
-              -#%td total
-            %tr
-              %td 
-                %b predicted
-              %td active
-              %td 
-                =cv.confusion_matrix[0][0]
-              %td 
-                =cv.confusion_matrix[0][1]
-              -#%td 
-                =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1]
-            %tr
-              %td
-              %td inactive
-              %td 
-                =cv.confusion_matrix[1][0]
-              %td 
-                =cv.confusion_matrix[1][1]
-              -#%td 
-                =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1]
-            -#%tr
-              %td
-              %td total
-              %td
-                =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0]
-              %td
-                =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1]
-              %td
-                -#= "Confusion Matrix:\t"
-                -#= cv.confusion_matrix
+        - ["confusion_matrix", "weighted_confusion_matrix"].each_with_index do |matrix,idx|
+          %b= (idx == 0 ? "Confusion Matrix" : "Weighted Confusion Matrix")
+          %table.table.table-condensed.table-borderless{:style=>"width:20%;"}
+            %tbody
+              %tr
+                %td
+                %td
+                %td 
+                  %b actual
+                %td
+                %td
+              %tr
+                %td
+                %td
+                %td active
+                %td inactive
+                -#%td total
+              %tr
+                %td 
+                  %b predicted
+                %td active
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[0][0].round(3) : cv.send(matrix)[0][0])
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[0][1].round(3) : cv.send(matrix)[0][1])
+                -#%td 
+                  =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1]
+              %tr
+                %td
+                %td inactive
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[1][0].round(3) : cv.send(matrix)[1][0])
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[1][1].round(3) : cv.send(matrix)[1][1])
+                -#%td 
+                  =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1]
+              -#%tr
+                %td
+                %td total
+                %td
+                  =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0]
+                %td
+                  =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1]
+                %td
+                  -#= "Confusion Matrix:\t"
+                  -#= cv.confusion_matrix
+              %br
         %br
         /= "Confidence plot:"
         /%p.plot
         /  %img{:src=>"confp#{cv.id}.svg"}
       - if model.regression?
         %br
-        = "Root mean squared error:\t"
+        %a.ht5{:href=>"https://en.wikipedia.org/wiki/Root-mean-square_deviation", :rel=>"external"} RMSE:
         = cv.rmse.round(3) if cv.rmse
         %br
-        = "Mean absolute error:\t"
+        %a.ht5{:href=>"https://en.wikipedia.org/wiki/Mean_absolute_error", :rel=>"external"} MAE:
         = cv.mae.round(3) if cv.mae
         %br 
-        = "R square:\t"
+        %a.ht5{:href=>"https://en.wikipedia.org/wiki/Coefficient_of_determination", :rel=>"external"}= "R"+"<sup>2</sup>"+":"
         = cv.r_squared.round(3) if cv.r_squared
         %br
         /= "Confidence plot:"
@@ -113,5 +131,5 @@ Source:
         /= "Correlation plot"
         /%p.plot
         /  %img{:src=>"/corrp#{cv.id}.svg"}
-        
+          
 %br
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 096e432..d9f2796 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -79,20 +79,19 @@
                 - prediction[:neighbors].uniq.each_with_index do |neighbor,count|
                   %tr
                     / Compound
-                    - c = Compound.find(neighbor["_id"])
+                    - c = Compound.find(neighbor)
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"}
                       /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor["_id"])}/details"), :id=>"link#{j+1}#{count}"}}
                       %p= c.svg
                       %p= c.smiles
-                    - mw = c.molecular_weight
-                    / Measured Activity = compound.features
+                    / Measured Activity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
-                      - features = c.features.collect{|k,v| v if k == predictionFeature[j]["id"] }.compact.flatten
-                      = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" , #{'%.2e' % weight} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : features.join("</br>")
+                      = (type == "Regression" ? "#{neighbor[:measurement].delog10}" + " (#{unit})" : neighbor[:measurement])
+                      %br
+                      = "#{c.mmol_to_mg(neighbor[:measurement].delog10)}" + " (#{(unit =~ /\b(mol\/L)\b/) ? "mg/L" : "mg/kg_bw/day"})" if type == "Regression"
                     / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
-                      = neighbor[:tanimoto] != nil ? neighbor[:tanimoto].to_f.round(3) : "Not enough similar compounds </br>in training dataset."
+                      = neighbor[:similarity].round(3)
 
           - else
             %span.btn.btn-default.disabled
diff --git a/views/predict.haml b/views/predict.haml
index 010ed12..8ae5684 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -162,6 +162,7 @@
                     document.getElementById("details#{model.id}").appendChild(details);
                     $(button).show();
                     $(image).hide();
+                    addExternalLinks();
                   });
                 }
               }
diff --git a/views/prediction.haml b/views/prediction.haml
index 0f3d57b..1aefe06 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,7 +18,6 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
-          - mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -29,17 +28,20 @@
               %b{:class => "title"}
                 = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})"
               %p
-              - if prediction[:confidence] == "measured"
+              - if prediction[:warning] =~ /\b(identical)\b/i
                 - @dbhit[i] = true
                 %p
+                /TODO combine with regular view, if prediction value is present
                 %b Measured activity:
                 - p prediction[:value]
                 - if prediction[:value].is_a?(Array)
-                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{unit})"+", #{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
+                  = (type == "Regression") ? prediction[:value].collect{|value| "#{value} (#{unit}) , #{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
                 - else
-                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                  = (type == "Regression") ? "#{prediction[:value]} (#{unit}), #{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 %p
                   %b Compound is part of the training dataset
+                  / warning popover
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"#{prediction[:warning]}"}}
               - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
@@ -47,23 +49,30 @@
                 = type
                 %br
                 %b Prediction:
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) , #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
-                / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
                 / prediction popover
                 %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
                 %br
+                = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
+                %br
                 - if type == "Regression"
                   %b 95% Prediction interval:
-                  - interval = prediction[:prediction_interval].nil? ? " - - " : prediction[:prediction_interval].collect{|i| i.round(2)}
-                  %br
-                  = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"
+                  - interval = (prediction[:prediction_interval].nil? ? ["- -","- -"] : prediction[:prediction_interval])
                   / prediction intervall popover
                   %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
+                  %br
+                  = "#{interval[0].delog10} - #{interval[1].delog10} (#{unit})"
+                  %br
+                  = "#{@compound.mmol_to_mg(interval[0].delog10)} - #{@compound.mmol_to_mg(interval[1].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
                 - else
-                  %b Confidence:
-                  = prediction[:confidence].round(2) unless prediction[:confidence].nil?
-                  / confidence popover
-                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"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 distinguish between reliable and unreliable predictions."}}
+                  %b Probability:
+                  - unless prediction[:probabilities].nil?
+                    %br
+                    = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}"
+                    %br
+                    = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}"
+                  / probability popover
+                  -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"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 distinguish between reliable and unreliable predictions."}}
                 %p
                 /TODO add tooltip for significant ftagments and descriptors
                 / - if @model_type[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
diff --git a/views/style.scss b/views/style.scss
index 49e03ab..2c84781 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -51,10 +51,12 @@ ul.share-buttons{
   padding: 0 2px 1px 2px !important;
 }
 .page-header{
-  margin:20px 0 20px;
-  text-align:justify;
+  background-color: #fff;
+  padding:20px 0 20px 0;
+  margin: 0;
+  text-align:center;
   display:inline-block;
-  width:98.5%;
+  width:100%;
 }
 .share{
   width: 30px;
@@ -62,9 +64,13 @@ ul.share-buttons{
 }
 supporters{
   background-color: white;
-
+  text-align:center;
   img{
     width: 200px;
     margin-right: 1em;
   }
 }
+
+.footer{
+  margin-top:3em;
+}
diff --git a/views/validation.haml b/views/validation.haml
deleted file mode 100644
index fd63ea6..0000000
--- a/views/validation.haml
+++ /dev/null
@@ -1,16 +0,0 @@
-- case @model_type
-- when "classification"
-  - prediction = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numCorrect"] + @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numIncorrect"]
-  %p= "Number of predictions: #{prediction}"
-  - percent = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#percentCorrect"]
-  %p= "Correct predictions: #{percent.round(2)} %"
-- when "regression"
-  - prediction = @cv.metadata["http://www.opentox.org/api/1.2#numInstances"].to_i - @cv.metadata["http://www.opentox.org/api/1.2#numUnpredicted"].to_i
-  %p= "Number of predictions: #{prediction}"
-  - rSquare = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rSquare"]
-  %p= "R-squared: #{rSquare.round(2)} %"
-  - rootMeanSquaredError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rootMeanSquaredError"]
-  %p= "Root Mean Square Error: #{rootMeanSquaredError.round(2)} %"
-  - meanAbsoluteError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#meanAbsoluteError"]
-  %p= "Mean Absolute Error: #{meanAbsoluteError.round(2)} %"
-
-- 
cgit v1.2.3


From c5ca09fb039e38abd89005d49ef373cf18b79039 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 28 Nov 2016 14:13:18 +0000
Subject: bumped version;training dataset download;show warnings for batch;csv
 info and upload catch;code cleanup

---
 views/batch.haml         | 106 +++++++++++++++++++++++++++++++++--------------
 views/layout.haml        |  38 +----------------
 views/model_details.haml |   4 ++
 views/neighbors.haml     |  13 +++---
 views/predict.haml       |   1 +
 views/prediction.haml    | 103 +++++++++++++++++++++++----------------------
 6 files changed, 142 insertions(+), 123 deletions(-)

(limited to 'views')

diff --git a/views/batch.haml b/views/batch.haml
index 9bfa67e..6c37a2b 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -2,57 +2,99 @@
   %a.btn.btn-warning{:href => to('/predict')}
     %span.glyphicon.glyphicon-menu-left{:aria=>{:hidden=>"true"}}
     New Prediction
-  / displays all prediction result in first table
+  %a.btn.btn-success{:href=>"#{to("/predict/#{@filename}")}", :title=>"download"}
+    %span.glyphicon.glyphicon-download-alt
+    download CSV
+
+  / show processed file name
+  %topline
+    %div.row
+      %div.col-md-4
+        %h3 Batch Prediction Results:
+      %div.col-md-8
+        %h3= @filename
+  
+  / displays all prediction result in one table
   %div.table-responsive
     %table.table.table-bordered{:id=>"batch", :style=>"background-color:white;"}
-      %thead
-        %tr
-          %h3.col-md-4{:style=>"padding-left:0;"} Batch Prediction Results:
-          %h3.col-md-8= @filename
-        %tr
-          %span.btn.btn-default
-            %a{:href=>"#{to("/predict/#{@filename}")}", :title=>"download"}
-              %span.glyphicon.glyphicon-download-alt{:aria=>{:hidden=>"true"}}
-                CSV
       %tbody
-      / key = compound, values = array of arrays with model, prediction
+      - if @warnings
+        - @warnings.each do |warning|
+          %tr
+            %td
+              %b Warning
+            %td
+              = warning.sub(/\b(tmp\/)\b/,"")
+      / key = compound, values = [model,prediction]
       - @batch.each do |key, values|
         - compound = key
-        - mw = compound.molecular_weight
         %tr
           %td{:style=>"vertical-align:top;"}
             %p= compound.svg
             %p= compound.smiles
-          / array = single prediction [endpoint, result]
+          
+          / array[0] = model, array[1] = prediction
           - values.each_with_index do |array,i|
             %td{:style=>"vertical-align:top;white-space:nowrap;"}
               - model = array[0]
+              / model type (classification|regression)
+              - model.model.class.to_s.match("Classification") ? type = "Classification" : type = "Regression"
+              - unit = model.unit
               - prediction = array[1]
+              
               %b{:class => "title"}
                 = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
-              %p
-              - if prediction[:confidence] == "measured"
+                  
+              / check for prediction
+              - if prediction[:neighbors].size > 0
                 %p
-                  %b Measured activity:
-                - if prediction[:value].is_a?(Array)
-                  = prediction[:value][0].numeric? ? prediction[:value].collect{|v| weight = compound.mmol_to_mg(v, mw); '%.2e' % v + " (#{model.unit})"+" | #{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
-                - else
-                  = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
+                / show model type (classification|regression)
+                %b Type:
+                = type
                 %p 
-                %b Compound is part of the training dataset
-              - elsif prediction[:neighbors].size > 0
+                / check for database hit
+                - if prediction[:warning] =~ /\b(identical)\b/i
+                  
+                  / show message about dbhit and measurements
+                  %p
+                    %b Compound is part of the training dataset
+                    %p
+                    %b Measured activity:
+                    %br
+                    - if prediction[:measurements].is_a?(Array)
+                      = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10} (#{unit})</br>#{compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ")
+                    - else
+                      = (type == "Regression") ? "#{prediction[:measurements].delog10} (#{unit})</br>#{compound.mmol_to_mg(prediction[:measurements].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements]
+                
+                
+                / show prediction
                 %p
-                / model type (classification|regression)
-                %b Type:
-                = model.model.class.to_s.match("Classification") ? "Classification" : "Regression"
-                %br
-                %b Prediction:
-                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
-                %br
-                / TODO probability
-                %b Confidence:
-                = prediction[:confidence].round(3)
+                  %b Prediction:
+                  %br
+                  = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                  
+                  / show prediction interval or probability
+                  %p
+                  - if type == "Regression"
+                    %b 95% Prediction interval:
+                    - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval])
+                    %br
+                    = interval.nil? ? "--" : "#{interval[1].delog10} - #{interval[0].delog10} (#{unit})"
+                    %br
+                    = "#{compound.mmol_to_mg(interval[1].delog10)} - #{compound.mmol_to_mg(interval[0].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
+                  - else
+                    %b Probability:
+                    - unless prediction[:probabilities].nil?
+                      %br
+                      = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}"
+                      %br
+                / show warnings
                 %p
+                - if !prediction[:warning].nil?
+                  %b Warnings:
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"#{prediction[:warning]}"}}
+                    
+                / no prediction  
               - else
                 %p
                   = "Not enough similar compounds </br>in training dataset."
diff --git a/views/layout.haml b/views/layout.haml
index dddf854..5ed63e8 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -29,33 +29,11 @@
           %h1.media-heading
             lazar toxicity predictions
         %div.col-md-2
-          %h1.media-heading
+          %h5
             %small
-              %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar
+              [version: #{@version}]
 
     %div.container-fluid
-      %topline
-        %div.row
-          %div.col-md-8
-            Problems, bugs, ideas for improvements ? Please report at our
-            %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker
-            or send us an email
-            %a{ :href=>"mailto:info@in-silico.ch", :target=>"_top"}
-              %img.share{:src=>"/images/Email.png"}
-            (version #{@version}).
-          %div.col-md-2
-          %div.col-md-2
-            %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"}
-              %img.share{:src=>"/images/Twitter.png"}
-            %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"}
-              %img.share{:src=>"/images/Google+.png"}
-            %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"}
-              %img.share{:src=>"/images/LinkedIn.png"}
-            %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Facebook"}
-              %img.share{:src=>"/images/Facebook.png"}
-        %div.row
-        Previous version:
-        %a{:href=>"http://lazar-old.in-silico.ch", :rel => "external"} lazar-old
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
@@ -79,18 +57,6 @@
             %p.text-muted
               &copy; 
               %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
-              |
-              %a{:href => to("/license"), :rel => "external"} GPL3 License
-          %supporters.col-md-12
-            %p Financial support by
-            %a{:href=>"http://www.bfr.bund.de/de/start.html", :rel=>"external"}
-              %img{:src=>"/images/bfr_logo.gif"}
-            %a{:href=>"http://www.opentox.org/", :rel=>"external"}
-              %img{:src=>"/images/ot_logo.png"}
-            %a{:href=>"https://enanomapper.net/", :rel=>"external"}
-              %img{:src=>"/images/enm_logo.png"}
-            %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :rel=>"external"}
-              %img{:src=>"/images/nestec.jpg"}
     
 
     #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"}
diff --git a/views/model_details.haml b/views/model_details.haml
index 7646471..3fa8c8b 100644
--- a/views/model_details.haml
+++ b/views/model_details.haml
@@ -12,6 +12,10 @@ Source:
 = "Training compounds:\t"
 = training_dataset.compounds.size
 %br
+= "Training dataset:\t"
+%a{:href=>"#{to("/predict/dataset/#{training_dataset.name}")}"}
+  = training_dataset.name
+%br
 %b Algorithms:
 %br
 Similarity:
diff --git a/views/neighbors.haml b/views/neighbors.haml
index d9f2796..32b8389 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -67,10 +67,10 @@
                       Compound
                     %th.sorter-false{:style =>"vertical-align:middle;"}
                       Measured Activity
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
                     %th.sorter-false{:style =>"vertical-align:middle;"}
                       Similarity
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
                     / %th{:style =>"vertical-align:middle;"}
                     / Supporting Information
                 %tbody
@@ -84,11 +84,14 @@
                       /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor["_id"])}/details"), :id=>"link#{j+1}#{count}"}}
                       %p= c.svg
                       %p= c.smiles
+                    
                     / Measured Activity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
-                      = (type == "Regression" ? "#{neighbor[:measurement].delog10}" + " (#{unit})" : neighbor[:measurement])
-                      %br
-                      = "#{c.mmol_to_mg(neighbor[:measurement].delog10)}" + " (#{(unit =~ /\b(mol\/L)\b/) ? "mg/L" : "mg/kg_bw/day"})" if type == "Regression"
+                      - if neighbor[:measurement].is_a?(Array)
+                        = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10} (#{unit})</br>#{c.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : neighbor[:measurement].join(", ")
+                      - else
+                        = (type == "Regression") ? "#{neighbor[:measurement].delog10} (#{unit})</br>#{c.mmol_to_mg(neighbor[:measurement].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement]
+                    
                     / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       = neighbor[:similarity].round(3)
diff --git a/views/predict.haml b/views/predict.haml
index 66006d4..9a7d0d4 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -127,6 +127,7 @@
       %p
       %label{:for=>"fileselect"}
         or upload a CSV file for batch predictions
+      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}}
       %br
       %span.btn.btn-default.btn-file
         %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv"}
diff --git a/views/prediction.haml b/views/prediction.haml
index 2454aca..b090be5 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,7 +18,6 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
-          -#- mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -28,62 +27,66 @@
             %td{:style=>"vertical-align:top;white-space:nowrap;"}
               %b{:class => "title"}
                 = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})"
-              %p
-              - if prediction[:warning] =~ /\b(identical)\b/i
-                - @dbhit[i] = true
+              
+              / check for prediction
+              - if prediction[:neighbors].size > 0
                 %p
-                /TODO combine with regular view, if prediction value is present
-                %b Measured activity:
-                - p prediction[:value]
-                - if prediction[:value].is_a?(Array)
-                  = (type == "Regression") ? prediction[:value].collect{|value| "#{value} (#{unit}) , #{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
-                - else
-                  = (type == "Regression") ? "#{prediction[:value]} (#{unit}), #{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
-                %p
-                  %b Compound is part of the training dataset
-                  / warning popover
-                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"#{prediction[:warning]}"}}
-              - elsif prediction[:neighbors].size > 0
-                %p
-                / model type (classification|regression)
+                / show model type (classification|regression)
                 %b Type:
                 = type
-                %br
-                %b Prediction:
-                / prediction popover
-                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
-                %br
-                = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
-                / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
-                %br
-                - if type == "Regression"
-                  %b 95% Prediction interval:
-                  - interval = (prediction[:prediction_interval].nil? ? ["- -","- -"] : prediction[:prediction_interval])
-                  / prediction intervall popover
-                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
-                  %br
-                  = "#{interval[0].delog10} - #{interval[1].delog10} (#{unit})"
-                  %br
-                  = "#{@compound.mmol_to_mg(interval[0].delog10)} - #{@compound.mmol_to_mg(interval[1].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
+                %p 
+                / check for database hit
+                - if prediction[:warning] =~ /\b(identical)\b/i
+                  - @dbhit[i] = true
+                  
+                  / show message about dbhit and measurements
+                  %p
+                    %b Compound is part of the training dataset
+                    %p
+                    %b Measured activity:
+                    %br
+                    - if prediction[:measurements].is_a?(Array)
+                      = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10} (#{unit})</br>#{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ")
+                    - else
+                      = (type == "Regression") ? "#{prediction[:measurements].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:measurements].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements]
+                
                 - else
-                  %b Probability:
-                  - unless prediction[:probabilities].nil?
+                  - @dbhit[i] = false
+                
+                / show prediction
+                %p
+                  %b Prediction:
+                  / prediction popover
+                  -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
+                  %br
+                  = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                  
+                  / show prediction interval or probability
+                  %p
+                  - if type == "Regression"
+                    %b 95% Prediction interval:
+                    - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval])
+                    / prediction interval popover
+                    -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
                     %br
-                    = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}"
+                    = interval.nil? ? "--" : "#{interval[1].delog10} - #{interval[0].delog10} (#{unit})"
                     %br
-                    = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}"
-                  / probability popover
-                  -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"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 distinguish between reliable and unreliable predictions."}}
-                %p
-                /TODO add tooltip for significant ftagments and descriptors
-                / - if @model_type[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
-                / Significant fragments:
-                / %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments
-                / - if @model_type[i] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
-                / Descriptors
-                / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors
-                / %p
+                    = "#{@compound.mmol_to_mg(interval[1].delog10)} - #{@compound.mmol_to_mg(interval[0].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
+                  - else
+                    %b Probability:
+                    - unless prediction[:probabilities].nil?
+                      %br
+                      = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}"
+                      %br
+                      = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}"
+                    / probability popover
+                    -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"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 distinguish between reliable and unreliable predictions."}}
+                
+                / show warnings
                 %p
+                - if !prediction[:warning].nil?
+                  %b Warnings:
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"#{prediction[:warning]}"}}
               - else
                 - @dbhit[i] = false
                 %p
-- 
cgit v1.2.3


From 55bf06381a42c9bb1e1e991e990f5d6e90c8e33e Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 7 Dec 2016 12:07:13 +0000
Subject: rebuild code for public release;prepared to work with lazar
 v1.0.0;reintroduced compound details

---
 views/details.haml    |  6 +++++-
 views/layout.haml     | 37 ++++++++++++++++++++++++++++++++++---
 views/neighbors.haml  |  4 ++--
 views/predict.haml    | 12 ++++++------
 views/prediction.haml | 22 ++++++++++------------
 5 files changed, 57 insertions(+), 24 deletions(-)

(limited to 'views')

diff --git a/views/details.haml b/views/details.haml
index bb8250d..be4948a 100644
--- a/views/details.haml
+++ b/views/details.haml
@@ -1,8 +1,12 @@
+:javascript
+  $(document).ready(function(){
+    addExternalLinks();
+  });
 %div.modal-body{:style=>"padding:10px;"}
   %button.close{ :type=>" button", data: { dismiss:"modal"}} &times;
   %h3
     Names and synonyms:
-  %img.img-responsive{:src=>"#{@compound.uri}/image", :alt=>"Compound image not available", :width=>"300px", :heigth=>"300px", :style=>"float:left;"}
+  %p= @compound.svg
   %p
   %b="SMILES:"
   %p= @smiles
diff --git a/views/layout.haml b/views/layout.haml
index 5ed63e8..62a224b 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -29,11 +29,30 @@
           %h1.media-heading
             lazar toxicity predictions
         %div.col-md-2
-          %h5
+          %h1.media-heading
             %small
-              [version: #{@version}]
+              %a{:href=>"https://nano-lazar.in-silico.ch", :rel=>"external"} nano-lazar
 
     %div.container-fluid
+      %topline
+        %div.row
+          %div.col-md-8
+            Problems, bugs, ideas for improvements ? Please report at our
+            %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker
+            or send us an email.
+            %a{ :href=>"mailto:info@in-silico.ch", :target=>"_top"}
+              %img.share{:src=>"/images/Email.png"}
+            [version: #{@version}]
+          %div.col-md-2
+          %div.col-md-2
+            %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Tweet"}
+              %img.share{:src=>"/images/Twitter.png"}
+            %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Google+"}
+              %img.share{:src=>"/images/Google+.png"}
+            %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on LinkedIn"}
+              %img.share{:src=>"/images/LinkedIn.png"}
+            %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Facebook"}
+              %img.share{:src=>"/images/Facebook.png"}
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
@@ -57,7 +76,19 @@
             %p.text-muted
               &copy; 
               %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
-    
+              |
+              %a{:href => to("/license"), :rel => "external"} GPL3 License
+          %supporters.col-md-12
+            %p Financial support by
+            %a{:href=>"http://www.bfr.bund.de/de/start.html", :rel=>"external"}
+              %img{:src=>"/images/bfr_logo.gif"}
+            %a{:href=>"http://www.opentox.org/", :rel=>"external"}
+              %img{:src=>"/images/ot_logo.png"}
+            %a{:href=>"https://enanomapper.net/", :rel=>"external"}
+              %img{:src=>"/images/enm_logo.png"}
+            %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :rel=>"external"}
+              %img{:src=>"/images/nestec.jpg"}
+ 
 
     #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"}
       %a{:href => "", :style=>"text:decoration:none;color:#ccc;"}
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 32b8389..a608c4d 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -81,8 +81,8 @@
                     / Compound
                     - c = Compound.find(neighbor)
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"}
-                      /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor["_id"])}/details"), :id=>"link#{j+1}#{count}"}}
-                      %p= c.svg
+                      %a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(c.id.to_s)}/details"), :id=>"link#{j+1}#{count}"}}
+                        = c.svg
                       %p= c.smiles
                     
                     / Measured Activity
diff --git a/views/predict.haml b/views/predict.haml
index 9a7d0d4..b7a4087 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -125,12 +125,12 @@
       %br
       %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
       %p
-      %label{:for=>"fileselect"}
-        or upload a CSV file for batch predictions
-      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}}
-      %br
-      %span.btn.btn-default.btn-file
-        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv"}
+      -#%label{:for=>"fileselect"}
+        or upload a CSV file for batch predictions (disabled in public version)
+      -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}}
+      -#%br
+      -#%span.btn.btn-default.btn-file
+        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
diff --git a/views/prediction.haml b/views/prediction.haml
index b090be5..362f006 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -1,10 +1,3 @@
-:javascript
-  $(document).ready(function(){
-    $('[data-toggle="popover"]').popover();
-    $('.modal').on('hidden.bs.modal', function () {
-      $(this).removeData('bs.modal');
-    });
-  });
 %div.well
   %a.btn.btn-warning{:href => to('/predict')}
     %i.glyphicon.glyphicon-menu-left
@@ -16,7 +9,8 @@
       %tbody
         %tr
           %td{:id=>"compound", :style=>"vertical-align:top;"}
-            %p= @compound.svg
+            %a.btn.btn-link{:href => "#details0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@compound.id.to_s)}/details"), :id=>"link01"}}
+              = @compound.svg
             %p= @compound.smiles
           - @model_types = {}
           - @dbhit = {}
@@ -57,7 +51,7 @@
                 %p
                   %b Prediction:
                   / prediction popover
-                  -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
                   %br
                   = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                   
@@ -67,20 +61,20 @@
                     %b 95% Prediction interval:
                     - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval])
                     / prediction interval popover
-                    -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
+                    %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
                     %br
                     = interval.nil? ? "--" : "#{interval[1].delog10} - #{interval[0].delog10} (#{unit})"
                     %br
                     = "#{@compound.mmol_to_mg(interval[1].delog10)} - #{@compound.mmol_to_mg(interval[0].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
                   - else
                     %b Probability:
+                    / probability popover
+                    %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"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 distinguish between reliable and unreliable predictions."}}
                     - unless prediction[:probabilities].nil?
                       %br
                       = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}"
                       %br
                       = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}"
-                    / probability popover
-                    -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"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 distinguish between reliable and unreliable predictions."}}
                 
                 / show warnings
                 %p
@@ -94,4 +88,8 @@
 
   / always show the neighbors table, message is given there  
   = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit
+    
+%div.modal.fade{:id=>"details0", :role=>"dialog"}
+  %div.modal-dialog.modal-lg
+    %div.modal-content
 
-- 
cgit v1.2.3


From cb2ad5835eae10c85ee426102b2a9bf165c5c848 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Tue, 20 Dec 2016 16:25:27 +0000
Subject: result values round by signif(n);set dependent lazar gem version

---
 views/model_details.haml | 30 ++++++++++++++++--------------
 views/neighbors.haml     |  4 ++--
 views/prediction.haml    | 16 ++++++++--------
 3 files changed, 26 insertions(+), 24 deletions(-)

(limited to 'views')

diff --git a/views/model_details.haml b/views/model_details.haml
index 3fa8c8b..5c3aa4f 100644
--- a/views/model_details.haml
+++ b/views/model_details.haml
@@ -10,7 +10,7 @@ Source:
 %br
 - training_dataset = OpenTox::Dataset.find model.model.training_dataset_id
 = "Training compounds:\t"
-= training_dataset.compounds.size
+= training_dataset.data_entries.size
 %br
 = "Training dataset:\t"
 %a{:href=>"#{to("/predict/dataset/#{training_dataset.name}")}"}
@@ -53,18 +53,20 @@ Descriptors:
         %br
         = "Weighted accuracy:\t"
         = cv.weighted_accuracy.round(3) if cv.weighted_accuracy
-        %br
-        = "True positive rate:\t"
-        = cv.true_rate["active"].round(3) if cv.true_rate
-        %br
-        = "True negative rate:\t"
-        = cv.true_rate["inactive"].round(3) if cv.true_rate
-        %br 
-        = "Positive predictive value:\t"
-        = cv.predictivity["active"].round(3) if cv.predictivity
-        %br
-        = "Negative predictive value:\t"
-        = cv.predictivity["inactive"].round(3) if cv.predictivity
+        - if cv.true_rate
+          %br
+          = "True positive rate:\t"
+          = cv.true_rate[cv.accept_values[0]].round(3)
+          %br
+          = "True negative rate:\t"
+          = cv.true_rate[cv.accept_values[1]].round(3)
+        - if cv.predictivity
+          %br 
+          = "Positive predictive value:\t"
+          = cv.predictivity[cv.accept_values[0]].round(3)
+          %br
+          = "Negative predictive value:\t"
+          = cv.predictivity[cv.accept_values[1]].round(3)
         %p
         - ["confusion_matrix", "weighted_confusion_matrix"].each_with_index do |matrix,idx|
           %b= (idx == 0 ? "Confusion Matrix" : "Weighted Confusion Matrix")
@@ -136,4 +138,4 @@ Descriptors:
         /%p.plot
         /  %img{:src=>"/corrp#{cv.id}.svg"}
           
-%br
+%br 
diff --git a/views/neighbors.haml b/views/neighbors.haml
index a608c4d..2f0b3d7 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -88,9 +88,9 @@
                     / Measured Activity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
                       - if neighbor[:measurement].is_a?(Array)
-                        = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10} (#{unit})</br>#{c.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : neighbor[:measurement].join(", ")
+                        = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : neighbor[:measurement].join(", ")
                       - else
-                        = (type == "Regression") ? "#{neighbor[:measurement].delog10} (#{unit})</br>#{c.mmol_to_mg(neighbor[:measurement].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement]
+                        = (type == "Regression") ? "#{neighbor[:measurement].delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(neighbor[:measurement].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement]
                     
                     / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
diff --git a/views/prediction.haml b/views/prediction.haml
index 362f006..1b8d38d 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -40,9 +40,9 @@
                     %b Measured activity:
                     %br
                     - if prediction[:measurements].is_a?(Array)
-                      = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10} (#{unit})</br>#{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ")
+                      = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ")
                     - else
-                      = (type == "Regression") ? "#{prediction[:measurements].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:measurements].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements]
+                      = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements]
                 
                 - else
                   - @dbhit[i] = false
@@ -53,7 +53,7 @@
                   / prediction popover
                   %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
                   %br
-                  = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                  = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                   
                   / show prediction interval or probability
                   %p
@@ -63,18 +63,18 @@
                     / prediction interval popover
                     %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
                     %br
-                    = interval.nil? ? "--" : "#{interval[1].delog10} - #{interval[0].delog10} (#{unit})"
+                    = interval.nil? ? "--" : "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)} (#{unit})"
                     %br
-                    = "#{@compound.mmol_to_mg(interval[1].delog10)} - #{@compound.mmol_to_mg(interval[0].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
+                    = "#{@compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{@compound.mmol_to_mg(interval[0].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
                   - else
                     %b Probability:
                     / probability popover
-                    %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"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 distinguish between reliable and unreliable predictions."}}
+                    %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Pobability", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Probability that the prediction belongs to one of the given classes."}}
                     - unless prediction[:probabilities].nil?
                       %br
-                      = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}"
+                      = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0].signif(3)}"
                       %br
-                      = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}"
+                      = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1].signif(3)}"
                 
                 / show warnings
                 %p
-- 
cgit v1.2.3


From e6b8488b757f1d6036fd74b75f44d8c75ed3779f Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 16 Jan 2017 16:53:13 +0000
Subject: issue fixes;added faq

---
 views/faq_layout.haml | 67 ---------------------------------------------------
 views/layout.haml     | 11 +++++----
 views/neighbors.haml  |  8 +++++-
 views/predict.haml    |  5 ++--
 4 files changed, 16 insertions(+), 75 deletions(-)
 delete mode 100644 views/faq_layout.haml

(limited to 'views')

diff --git a/views/faq_layout.haml b/views/faq_layout.haml
deleted file mode 100644
index a9b6664..0000000
--- a/views/faq_layout.haml
+++ /dev/null
@@ -1,67 +0,0 @@
-!!!
-%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"}
-  %head
-    %meta{'charset'=>"utf-8"}
-    %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"}
-    %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"}
-    %title Lazar GUI FAQ
-    %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'}
-    %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"}
-    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"}
-    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.bootstrap.min.css'}"}
-    %link{ :href=>"/style.css", :rel=>"stylesheet"}
-    %link{ :href=>"/stylesheets/jquery-ui.css", :rel=>"stylesheet"}
-    %script{:src=>"/javascripts/jquery-1.11.2.min.js"}
-    %script{:src=>"/javascripts/bootstrap.min.js"}
-    %script{ :src=>"/javascripts/lazar-gui.js"}
-  %body
-    %noscript
-      %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
-      Your web browser must have JavaScript enabled in order for this application to display correctly.
-    %header.page-header
-      %div.row
-        %div.col-md-2
-          %a{:href=> to("/predict")}
-            %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"}
-        %div.col-md-10
-          %h1.media-heading{:style=>"margin: 0 0 0 1em;display:inline;"} Lazar GUI
-          A Graphical User Interface for the <a href="http://github.com/opentox/lazar">Lazar</a> framework
-    
-    %div.container-fluid
-      :javascript
-        $(document).ready(function(){
-          $("#back-top").hide();
-          $(".blind").error(function(){
-            $(this).attr('src', '/images/blind.png');
-          });
-        });
-          
-      = yield
-    
-    %footer.footer
-      %div.container-fluid
-        %p.text-muted
-          &copy; 
-          %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
-
-    #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"}
-      %a{:href => "", :style=>"text:decoration:none;color:#ccc;"}
-        %span.glyphicon.glyphicon-circle-arrow-up{:style => "font-size:3em;color:black;"}
-    :javascript
-      $("#back-top").hide();
-      $(function () {
-        $(window).scroll(function () {
-          if ($(this).scrollTop() > 600) {
-            $('#back-top').fadeIn();
-          } else {
-            $('#back-top').fadeOut();
-          }
-        });
-        // scroll body to 0px on click
-        $('#back-top a').click(function () {
-          $('body,html').animate({
-            scrollTop: 0
-          }, 500);
-          return false;
-        });
-      });
diff --git a/views/layout.haml b/views/layout.haml
index 62a224b..dc83956 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -36,15 +36,16 @@
     %div.container-fluid
       %topline
         %div.row
-          %div.col-md-8
+          %div.col-md-10
             Problems, bugs, ideas for improvements ? Please report at our
             %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker
-            or send us an email.
-            %a{ :href=>"mailto:info@in-silico.ch", :target=>"_top"}
+            , check out the 
+            %a{:href=> to("/faq"), :rel => "external"} FAQ
+            page or send us an email.
+            %a{ :href=>"mailto:info@in-silico.ch?subject=[lazar v#{@version}]", :target=>"_top"}
               %img.share{:src=>"/images/Email.png"}
             [version: #{@version}]
-          %div.col-md-2
-          %div.col-md-2
+          %div.col-md-2{:style=>"text-align:right;"}
             %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Tweet"}
               %img.share{:src=>"/images/Twitter.png"}
             %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Google+"}
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 2f0b3d7..18c23f8 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -3,6 +3,11 @@
 / align single prediction to endpoint ;
 / display preordered in table view ;
 
+:javascript
+  $(document).ready(function(){
+    addExternalLinks();
+  });
+
 %div.results
   %h3 Neighbors:
   / tabs div
@@ -35,6 +40,7 @@
           / presort by similarity ;
           :javascript
             $(document).ready(function(){
+              addExternalLinks();
               $("table##{j+1}").tablesorter({
                 debug: false,
                 theme: "bootstrap",
@@ -70,7 +76,7 @@
                       %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
                     %th.sorter-false{:style =>"vertical-align:middle;"}
                       Similarity
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"<a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
                     / %th{:style =>"vertical-align:middle;"}
                     / Supporting Information
                 %tbody
diff --git a/views/predict.haml b/views/predict.haml
index b7a4087..59630d0 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -111,7 +111,7 @@
   };
 
 // whole site content needs to be in one form. Input and checkboxes are proofed by js functions. 
-%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return  !!(showcircle())" }
+%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return !!(showcircle())" }
   %fieldset#top.well
     %h2 1. Draw a chemical structure
     #insert
@@ -130,7 +130,8 @@
       -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}}
       -#%br
       -#%span.btn.btn-default.btn-file
-        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
+        -#%input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
+      %input{:type=>"hidden", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"}
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
-- 
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