From 2b7bd5b579527fe1631cf52bdef728820d6ae20d Mon Sep 17 00:00:00 2001 From: davor Date: Wed, 30 May 2012 17:33:28 +0200 Subject: Adjustment for the Nestle GUI. --- views/feature_table.haml | 6 +++--- views/layout.haml | 12 +++++++----- views/lazar.haml | 6 ++++-- views/lazar_algorithm.haml | 47 ++++------------------------------------------ views/neighbors.haml | 3 ++- views/similarity.haml | 11 ++++++----- 6 files changed, 26 insertions(+), 59 deletions(-) diff --git a/views/feature_table.haml b/views/feature_table.haml index e968b01..daa04a0 100644 --- a/views/feature_table.haml +++ b/views/feature_table.haml @@ -36,13 +36,13 @@ -if features[:deactivating].empty? and features[:activating].empty? and (features[:pc_features].size >= 1) %tr %th - descriptor + Descriptors %th - value + Values - features[:pc_features].sort{|a,b| a[:feature] <=> b[:feature] }.each do |f| %tr %td= f[:feature] - %td= f[:value] + %td= f[:value].uniq.collect{|v| v.to_s + " "} diff --git a/views/layout.haml b/views/layout.haml index eb5f9a5..755ecab 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -35,10 +35,12 @@ %b= session[:username] .notice - This is an experimental version based on - %a{:href => "http://www.opentox.org", :rel => "external"} OpenTox - services. Please report problems and feature requests to our - %a{:href => 'http://github.com/opentox/toxcreate/issues', :rel => "external"} issue tracker. + This is a prediction interface for Nestle based on IST web services. + Please contact us in case of problems: + %a{:href => 'mailto:andreas@maunz.de', :rel => "andreas@maunz.de"} Andreas Maunz + or + %a{:href => 'mailto:david.vorg@googlemail.com', :rel => "david.vorg@googlemail.com"} David Vorgrimmler + - if `hostname`.match(/ot-test/) .notice @@ -55,4 +57,4 @@ .footer © %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology gmbh - 2004-2011 + 2004-2012 diff --git a/views/lazar.haml b/views/lazar.haml index 870fcab..8eab1a9 100644 --- a/views/lazar.haml +++ b/views/lazar.haml @@ -5,7 +5,8 @@ = haml :lazar_algorithm, :layout => false = haml :confidence, :layout => false = haml :similarity, :layout => false - = haml :significant_fragments, :layout => false + -#= haml :significant_fragments, :layout => false + = haml :pc_descriptors, :layout => false = haml :training_data, :layout => false %a{:name => "prediction"} @@ -30,7 +31,8 @@ $("#compound_names").load("#{File.join("/compound",@compound.inchi)}"); $("tr#names").toggle(); }); - %li= toggle_link("#fragments","Significant fragments") + -#%li= toggle_link("#fragments","Significant fragments") + %li= toggle_link("#fragments","Physico chemical descriptors") %tr#names{ :style => "display: none;" } %td{:colspan => '4'} diff --git a/views/lazar_algorithm.haml b/views/lazar_algorithm.haml index 76a993b..62c5ea4 100644 --- a/views/lazar_algorithm.haml +++ b/views/lazar_algorithm.haml @@ -14,51 +14,12 @@ %em (neighbors) and calculates the prediction from their measured activities. %code lazar - calculates predictions using - %ul - %li - a majority vote (weighted by compound similarity) for - %em classification - ( - %a{:href => "http://www.in-silico.de/articles/modi020905.pdf", :rel => "external"} original publication - ) - %li - a local QSAR model based on neighbors for - %em regression - ( - %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf", :rel => "external"} original publication - ) - - %p - = toggle_link "#significant_fragments", "Significant fragments" - are highlighted in the structure display as follows: - - if @value_map.empty? - %ul - %li - .active activating fragments - %li - .inactive deactivating fragments - %li - .inconclusive regions, where activating and deactivating fragments overlap - %li - .other inert parts - - else - %ul - %li - .active= "features that occur predominately in compounds with activity: \"#{@value_map[@value_map.keys.sort.last]}\"" - %li - .inactive= "features that occur predominately in compounds with activity: \"#{@value_map[@value_map.keys.sort.first]}\"" - %li - .inconclusive regions, where fragments from different classes overlap - %li - .other inert parts - - if @value_map.size > 2 - .notice Incomplete implementation of feature highlighting and display of significant fragments. Only features for 2 classes are shown! - - + calculates predictions using a well-established radial basis function (rbf) kernel for SVMs + %em (regression) + %p Please keep in mind that predictions are based on the measured activities of neighbors. - = toggle_link "#significant_fragments", "Significant fragments" + = toggle_link "#pc_descriptors", "Physico chemical descriptors" are solely used to determine = toggle_link "#similarity", "activity specific similarities" of neighbors. diff --git a/views/neighbors.haml b/views/neighbors.haml index 49b72b7..80ef06b 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -25,7 +25,8 @@ $("#compound_names#{neighbor_id}").load("#{File.join("compound",compound.inchi)}"); $("#names#{neighbor_id}").toggle(); }); - %li= toggle_link("#fragments#{neighbor_id}","Significant fragments") + -#%li= toggle_link("#fragments#{neighbor_id}","Significant fragments") + %li= toggle_link("#fragments#{neighbor_id}","Physico chemical descriptors") -#%li Ambit data -# %li %a{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pccompound&term=#{URI.encode('"'+compound.inchi+'"[InChI]')}"} PubChem data diff --git a/views/similarity.haml b/views/similarity.haml index 659eb50..2b65e47 100644 --- a/views/similarity.haml +++ b/views/similarity.haml @@ -8,12 +8,13 @@ %code lazar calculates %em activity specific - similarities based on the presence of statistically - = toggle_link "#significant_fragments", "significant fragments" - This procedure will - %ul + similarities based on the presence of statistically significant + -#= toggle_link "#significant_fragments", "significant fragments" + = toggle_link "#pc_descriptors", "physico chemical descriptors." + -#This procedure will + -#%ul %li consider only those parts of a chemical structure that are relevant for a particular endpoint %li ignore inert parts of the structure %li lead to different similarities, depending on the toxic endpoint - Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored. + -#Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored. -- cgit v1.2.3