From e6b8488b757f1d6036fd74b75f44d8c75ed3779f Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 16 Jan 2017 16:53:13 +0000 Subject: issue fixes;added faq --- FAQ.md | 39 +++++++++++------------------- VERSION | 2 +- application.rb | 5 ++++ views/faq_layout.haml | 67 --------------------------------------------------- views/layout.haml | 11 +++++---- views/neighbors.haml | 8 +++++- views/predict.haml | 5 ++-- 7 files changed, 36 insertions(+), 101 deletions(-) delete mode 100644 views/faq_layout.haml 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 -========================== -
-####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 Lazar 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 - © - %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico 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:"Tanimoto/Jaccard similarity based on Molprint2D 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:"Tanimoto/Jaccard similarity based on Molprint2D 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 -- cgit v1.2.3