nano-lazar 1.1.0

data/VERSION

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+1.1.0

data/application.rb

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+require 'qsar-report'
+require 'rdiscount'
+require File.join './npo.rb'
+$ambit_search = "http://data.enanomapper.net/substance?type=name&search="
+
+include OpenTox
+
+# collect nanoparticles from training dataset (Au + Ag)
+dataset = Dataset.find_by(:name=> "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles")
+$nanoparticles = dataset.nanoparticles
+$coating_list = $nanoparticles.collect{|n| n if !n.coating[0].smiles.nil?}.compact.uniq
+
+configure :development do
+  #$logger = Logger.new(STDOUT)
+end
+
+before do
+  @version = File.read("VERSION").chomp
+end
+
+get '/?' do
+  redirect to('/predict') 
+end
+#=begin
+get '/qmrf-report/:id' do
+  prediction_model = OpenTox::Model::Validation.find(params[:id])
+  if prediction_model
+    model = prediction_model.model
+		model_type = "regression"
+    report = QMRFReport.new
+		if File.directory?("#{File.dirname(__FILE__)}/../../lazar")
+    	lazar_commit = `cd #{File.dirname(__FILE__)}/../../lazar; git rev-parse HEAD`.strip
+    	lazar_commit = "https://github.com/opentox/lazar/tree/#{lazar_commit}"
+  	else
+    	lazar_commit = "https://github.com/opentox/lazar/releases/tag/v#{Gem.loaded_specs["lazar"].version}"
+		end
+    report.value "QSAR_title", "Model for #{prediction_model.species} #{prediction_model.endpoint}"
+    report.change_catalog :software_catalog, :firstsoftware, {:name => "nano-lazar", :description => "nano-lazar toxicity predictions", :number => "1", :url => "https://nano-lazar.in-silico.ch", :contact => "helma@in-silico.ch"}
+    report.ref_catalog :QSAR_software, :software_catalog, :firstsoftware
+    report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}"
+    report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstrasse 41, CH-4057 Basel, Switzerland", :email => "helma@in-silico.ch", :number => "1", :url => "http://in-silico.ch"}
+    report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor
+    report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstrasse 41, CH-4057 Basel, Switzerland", :email => "helma@in-silico.ch", :number => "1", :url => "http://in-silico.ch"}
+    report.ref_catalog :model_authors, :authors_catalog, :modelauthor
+    report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}"
+    report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Helma, Rautenberg and Gebele (2013), Validation of read across predictions for nanoparticle toxicities ", :url => "in preparation"}
+    report.ref_catalog :references, :publications_catalog, :publications_catalog_1
+    report.value "model_species", prediction_model.species
+    report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""}
+    report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1
+    report.value "endpoint_units", "#{prediction_model.unit}"
+    report.value "algorithm_type", "#{model.class.to_s.gsub('Model::Lazar','')}"
+    #TODO add updated algorithms
+		#report.change_catalog :algorithms_catalog, :algorithms_catalog_1, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Neighbor algorithm: #{model.neighbor_algorithm.gsub('_',' ').titleize}#{(model.neighbor_algorithm_parameters[:min_sim] ? ' with similarity > ' + model.neighbor_algorithm_parameters[:min_sim].to_s : '')}"}
+		#report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1
+		#report.change_catalog :algorithms_catalog, :algorithms_catalog_3, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "modified k-nearest neighbor #{model_type}"}
+		#report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_3
+		#if model.prediction_algorithm_parameters
+		#	pred_algorithm_params = (model.prediction_algorithm_parameters[:method] == "rf" ? "random forest" : model.prediction_algorithm_parameters[:method])
+		#end
+		#report.change_catalog :algorithms_catalog, :algorithms_catalog_2, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Prediction algorithm: #{model.prediction_algorithm.gsub('Algorithm::','').gsub('_',' ').gsub('.', ' with ')} #{(pred_algorithm_params ? pred_algorithm_params : '')}"}
+		#report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_2
+
+		# Descriptors in the model 4.3
+		#if model.neighbor_algorithm_parameters[:type]
+		#	report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.neighbor_algorithm_parameters[:type]}", :publication_ref => "", :units => ""}
+		#	report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1
+		#end
+
+		# Descriptor selection 4.4
+		#report.value "descriptors_selection", "#{model.feature_selection_algorithm.gsub('_',' ')} #{model.feature_selection_algorithm_parameters.collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.feature_selection_algorithm  
+    
+    response['Content-Type'] = "application/xml"
+    return report.to_xml
+  else
+    bad_request_error "model with id: #{params[:id]} does not exist."
+  end
+end
+#=end
+get '/predict/?' do
+  @prediction_models = []
+  models = OpenTox::Model::Validation.all
+  prediction_models = models.delete_if{|m| m.model.name !~ /\b(Net cell association)\b/}
+ 
+  # sort and collect prediction models
+  @prediction_models[0] = prediction_models.find{|m| m.model[:algorithms]["descriptors"]["method"] == "fingerprint"}
+  @prediction_models[1] = prediction_models.delete_if{|m| m.model[:algorithms]["descriptors"]["method"] == "fingerprint"}.find{|m| m.model[:algorithms]["descriptors"]["categories"][0] =~ /P-CHEM/}
+  @prediction_models[2] = prediction_models.find{|m| m.model[:algorithms]["descriptors"]["categories"][0] == "Proteomics"}
+
+  # define type (fingerprint,physchem,proteomics)
+  @prediction_models[0]["type"] = "fingerprint"
+  @prediction_models[1]["type"] = "physchem"
+  @prediction_models[2]["type"] = "proteomics"
+  
+  # select relevant features for each model
+  @fingerprint_relevant_features = @prediction_models[0].model.substance_ids.collect{|id| Substance.find(id)}
+  fingerprint = $coating_list.sample
+  #fingerprint.properties.delete_if{|id,v| !@fingerprint_relevant_features.include?(Feature.find(id))}
+  @example_fingerprint = fingerprint
+  
+  @physchem_relevant_features = @prediction_models[1].model.descriptor_ids.collect{|id, v| Feature.find(id)}
+  physchem = $nanoparticles.sample
+  # only Ag for testing
+  #physchem = $nanoparticles.find{|n| c = Substance.find(n.core_id); c.name == "Ag"}
+  physchem.properties.delete_if{|id,v| !@physchem_relevant_features.include?(Feature.find(id))}
+  @example_physchem = physchem
+  
+  @proteomics_relevant_features = @prediction_models[2].model.descriptor_ids.collect{|id, v| Feature.find(id)}
+  proteomics = $nanoparticles.sample
+  proteomics.properties.delete_if{|id,v| !@proteomics_relevant_features.include?(Feature.find(id))}
+  @example_proteomics = proteomics
+  
+
+  haml :predict
+end
+
+get '/license' do
+  @license = RDiscount.new(File.read("LICENSE.md")).to_html
+  haml :license, :layout => false
+end
+
+post '/predict/?' do
+  # select the prediction model
+  prediction_model = OpenTox::Model::Validation.find(params[:prediction_model])
+  size = params[:size].to_i
+  @type = params[:type]
+
+  example_core = params[:example_core]
+  example_coating = params.collect{|k,v| v if k =~ /example_coating_/}.compact
+  
+  input_core = params[:input_core]
+  input_coating = params.collect{|k,v| v if k =~ /input_coating_/}.compact
+
+  example_pc = eval(params[:example_pc])
+  input_pc = {}
+  if @type =~ /physchem|proteomics/
+    (1..size).each{|i| input_pc["#{params["input_key_#{i}"]}"] = [params["input_value_#{i}"].to_f] unless params["input_value_#{i}"].blank?}
+  end
+  
+  if @type == "fingerprint"
+    # search for database hit
+    dbhit = $coating_list.find{|nano| nano.core.name == input_core && (nano.coating.collect{|co| co.name}) == input_coating }
+    if !dbhit.nil?
+      @match = true
+      nanoparticle = dbhit
+      @nanoparticle = dbhit
+      @name = @nanoparticle.name
+    else
+      # no database hit => create nanoparticle
+      nanoparticle = Nanoparticle.new
+      nanoparticle.core_id = Compound.find_by(:name=>input_core).id.to_s
+      input_coating.each{|ic| nanoparticle.coating_ids << Compound.find_by(:name=>ic).id.to_s}
+      @match = false
+      @nanoparticle = nanoparticle
+    end
+  end
+
+  if @type =~ /physchem|proteomics/
+    (@type == "physchem") ? (@physchem_relevant_features = input_pc.collect{|id,v| Feature.find(id)}.compact) : (@physchem_relevant_features = [])
+    (@type == "proteomics") ? (@proteomics_relevant_features = input_pc.collect{|id,v| Feature.find(id)}.compact) : (@proteomics_relevant_features = [])
+    
+    if input_pc == example_pc && input_core == example_core #&& input_coating == example_coating
+      # unchanged input = database hit
+      nanoparticle = Nanoparticle.find_by(:id => params[:example_id])
+      nanoparticle.properties = input_pc
+      @match = true
+      @nanoparticle = nanoparticle
+      @name = nanoparticle.name
+    else
+      # changed input = create nanoparticle to predict
+      nanoparticle = Nanoparticle.new
+      nanoparticle.core_id = Compound.find_by(:name=>input_core).id.to_s
+      #nanoparticle.coating_ids = [Compound.find_by(:name=>input_coating).id.to_s] if input_coating
+      nanoparticle.properties = input_pc
+      @match = false
+      @nanoparticle = nanoparticle
+    end
+  end
+
+
+  # prediction output
+  @input = input_pc
+  @prediction = prediction_model.model.predict nanoparticle
+  haml :prediction
+end

data/bin/nano-lazar-start

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+#!/usr/bin/env ruby
+bin_dir = File.expand_path(File.dirname(__FILE__))
+shell_script_path = File.join(bin_dir, 'nano-lazar-start.sh')
+app_dir = File.expand_path('..')
+unicorn_conf = File.join(app_dir, 'unicorn.rb')
+
+`#{shell_script_path}`
+`#{unicorn_conf}`

data/bin/nano-lazar-start.sh

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+#!/bin/bash
+sudo mongod &
+R CMD Rserve
+GEMPATH=$(gem path nano-lazar)
+cd $GEMPATH
+unicorn -c unicorn.rb -E production -D
+
+exit 0

data/bin/nano-lazar-stop

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+#!/usr/bin/env ruby
+bin_dir = File.expand_path(File.dirname(__FILE__))
+shell_script_path = File.join(bin_dir, 'nano-lazar-stop.sh')
+
+`#{shell_script_path}`

data/bin/nano-lazar-stop.sh

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+#!/bin/bash
+grep_nano_lazar=`ps aux | grep -v grep | grep nano-lazar-start`
+grep_mongo=`ps aux | grep -v grep | grep mongod`
+grep_rserve=`ps aux | grep -v grep | grep Rserve`
+grep_unicorn=`ps aux | grep -v grep | grep unicorn`
+
+# lazar
+if [ ${#grep_lazar} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep nano-lazar-start | awk '{ print $1 }'`
+  for i in "${PID}"
+  do
+    `kill $i`
+  done
+else
+  echo "nano-lazar is stopped."
+fi
+
+# mongod
+if [ ${#grep_mongo} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep mongod | awk '{ print $1 }'`
+  for i in "${PID}"
+  do 
+    `sudo kill $i`
+  done
+else
+  echo "MongoDB is not running."
+fi
+
+# rserve
+if [ ${#grep_rserve} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep Rserve | awk '{ print $1 }'`
+  for i in "${PID}"
+  do 
+    `kill $i`
+  done
+else
+  echo "Rserve is not running."
+fi
+
+# unicorn
+if [ ${#grep_unicorn} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep unicorn | awk '{ print $1 }'`
+  `kill ${PID[0]}`
+else
+  echo "Unicorn is not running."
+fi
+
+exit 0

data/config.ru

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+ENV["LAZAR_ENV"] = "development"
+SERVICE = "nano-lazar-gui"
+require 'bundler'
+Bundler.require
+require File.expand_path './application.rb'
+require "sinatra/reloader" if development?
+
+FileUtils.mkdir_p 'log' unless File.exists?('log')
+log = File.new("log/nano-lazar.log", "a")
+#$stdout.reopen(log)
+#$stderr.reopen(log)
+
+run Sinatra::Application

data/feature-filter.rb

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+require 'rserve'
+require 'json'
+require 'yaml'
+require 'csv'
+
+R = Rserve::Connection.new
+ENDPOINT = "Cell.association (Net cell association [mL/ug(Mg)])"
+
+def feature_filter
+  data = JSON.parse(File.read("./data.json"))
+  features = data["G15.AC"]["physchem"].keys
+  R.assign "tox", data.collect{|id,cats| cats["tox"][ENDPOINT]}
+  filtered_features = {}
+  features.each do |feature|
+    R.assign "feature", data.collect{|id,cats| cats["physchem"][feature]}
+    begin
+      #R.eval "cor <- cor.test(-log(tox),-log(feature),use='complete')"
+      R.eval "cor <- cor.test(tox,feature,method = 'pearson',use='complete')"
+      pvalue = R.eval("cor$p.value").to_ruby
+      if pvalue <= 0.05
+        r = R.eval("cor$estimate").to_ruby
+        filtered_features[feature] = {}
+        filtered_features[feature]["pvalue"] = pvalue
+        filtered_features[feature]["r"] = r
+      end
+    rescue
+      f = data.collect{|id,cats| cats["physchem"][feature]}
+      f = R.eval("feature").to_ruby
+      p f.collect{|f| p f; Math.log f}
+      p R.eval("log(feature)").to_ruby
+    end
+  end
+  filtered_features.sort{|a,b| a[1]["pvalue"] <=> b[1]["pvalue"]}.to_h
+end
+
+puts feature_filter.to_json

data/helper.rb

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+

data/nano-lazar.gemspec

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+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name        = "nano-lazar"
+  s.version     = File.read("./VERSION")
+  s.authors     = ["Christoph Helma","Micha Rautenberg","Denis Gebele"]
+  s.email       = ["helma@in-silico.ch","rautenberg@in-silico.ch","gebele@in-silico.ch"]
+  s.homepage    = "http://github.com/enanomapper/nano-lazar"
+  s.summary     = %q{nano-lazar}
+  s.description = %q{Graphical user interface for nano-lazar toxicology predictions}
+  s.license     = 'GPL-3.0'
+  s.executables = ["nano-lazar-start", "nano-lazar-stop"]
+  s.rubyforge_project = "nano-lazar"
+
+  s.files       = `git ls-files`.split("\n")
+  s.required_ruby_version = '>= 2.0.0'
+
+  s.add_runtime_dependency "lazar"
+  s.add_runtime_dependency "sinatra"
+  s.add_runtime_dependency "rdiscount"
+  s.add_runtime_dependency "haml"
+  s.add_runtime_dependency "unicorn"
+  s.add_runtime_dependency "gem-path"
+
+  s.post_install_message = %q{
+    How to build nano-lazar prediction models described over here: https://github.com/opentox/lazar-public-data .  
+    Service commands:
+      nano-lazar-start
+      nano-lazar-stop
+  }
+end

data/npo.rb

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+$npo = {
+  "Localized Surface Plasmon Resonance (LSPR) index" => "http://bioportal.bioontology.org/ontologies/OBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0001136",
+  "ZETA POTENTIAL" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1302",
+  "Total protein (BCA assay)" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOAE_0001659",
+  "Core size" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.enanomapper.org%2Fonto%2FENM_8000039",
+  "Z-Average Hydrodynamic Diameter" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1915",
+  "Volume Mean Hydrodynamic Diameter" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1915",
+  "Intensity Mean Hydrodynamic Diameter" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1915",
+  "Autot (ICP-AES)" => "http://bioportal.bioontology.org/ontologies/ERO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FERO_0001675",
+  "Polydispersity index" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1155"
+}