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authorgebele <gebele@in-silico.ch>2017-01-16 16:53:13 +0000
committergebele <gebele@in-silico.ch>2017-01-16 16:53:13 +0000
commite6b8488b757f1d6036fd74b75f44d8c75ed3779f (patch)
treefa8016e17063ad448b5f0a219a31743064c4d89f
parentcb2ad5835eae10c85ee426102b2a9bf165c5c848 (diff)
issue fixes;added faq
-rw-r--r--FAQ.md39
-rw-r--r--VERSION2
-rw-r--r--application.rb5
-rw-r--r--views/faq_layout.haml67
-rw-r--r--views/layout.haml11
-rw-r--r--views/neighbors.haml8
-rw-r--r--views/predict.haml5
7 files changed, 36 insertions, 101 deletions
diff --git a/FAQ.md b/FAQ.md
index 73fec91..2530968 100644
--- a/FAQ.md
+++ b/FAQ.md
@@ -1,29 +1,18 @@
-Frequently Asked Questions
-==========================
-<br>
-####How does this prediction works?
->
+## lazar Frequently Asked Questions
-####You talk about significant fragments. Where can I find them?
-> We will show up those significant fragments in a further version.
+####The LAZAR program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version, I would consider a confidence value higher than 0.025 as reliable. But now, there is no such parameter in the prediction results. How can I consider a prediction as presenting high or low confidence?
-####What is endpoint details about?
-> You get the source from where we took compounds for the endpoint. The type and the number of compounds we used.
+In the past many users had problems to interpret the confidence level,
+for this reason we provide now the probabilities that the prediction
+belongs to one of the two classes. In contrast to the confidence level,
+these numbers can be interpreted as real probabilities ranging from 0 to
+1.
-####What is three times independent validation about?
->
+Reliable prediction have a high probability for the predicted class and
+a low probability for the other one. Unreliable predictions have similar
+values for both classes, and are caused by a lot of contradictory
+activities of similar compounds.
-####Do you consider providing plots for the validation results?
-> In a further version we will show up confidence and correlation plots.
-
-####What does 'Not enough similar compounds in training dataset' mean?
-> Lazar uses neighbors from the training dataset of the endpoint to predict your compound. If there are not enough neighbors for Lazar it is not possible to make a prediction.
-
-####Is there a minimum number of necessary neighbors to make a prediction?
->
-
-####How can I activate the 'batch prediction' option?
-> Please contact us directly via [mail](mailto:support@in-silico.ch).
-
-####Not the right answers for me. Is there a way to contact you or report problems.
-> You can always ask your questions via [mail](mailto:support@in-silico.ch). If you run into problems with the GUI please post your issue [here](https://github.com/opentox/lazar-gui/issues). If you would like to post any other issue e.g. about an expected prediction result please use this [form](https://github.com/opentox/lazar/issues).
+Probabilities are calculated from the activities and similarities of
+neighbors, please make sure to inspect the neighbors list for any
+inconsistencies that might affect the prediction.
diff --git a/VERSION b/VERSION
index 9084fa2..524cb55 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.1.0
+1.1.1
diff --git a/application.rb b/application.rb
index 4eb4a36..fa5df0a 100644
--- a/application.rb
+++ b/application.rb
@@ -175,6 +175,11 @@ get '/license' do
haml :license, :layout => false
end
+get '/faq' do
+ @faq = RDiscount.new(File.read("FAQ.md")).to_html
+ haml :faq, :layout => false
+end
+
get '/style.css' do
headers 'Content-Type' => 'text/css; charset=utf-8'
scss :style
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