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-rw-r--r--data.json1
-rw-r--r--data/marina.json3282
-rw-r--r--data/multi-walled-nano-tubes.json430
-rw-r--r--data/nanowiki.json30302
-rw-r--r--data/protein-corona.json20614
-rw-r--r--diff-features.json18
-rw-r--r--nanoparticles.rb182
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-rw-r--r--query-features.json15
-rw-r--r--relevant-features.json1
-rw-r--r--test/predict.rb11
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+{"G15.AC":{"composition":{"Core composition":"[Au]","Surface modifier1":"N-Acetyl-L-cysteine","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.02751},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":22.36,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":57.53,"Z-Average Hydrodynamic Diameter Change":35.1667,"Volume Mean Hydrodynamic Diameter [nm]":21.94,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":21.75,"Volume Mean Hydrodynamic Diameter Change":-0.1854,"Number Mean Hydrodynamic Diameter [nm]":23.49,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":18.38,"Number Mean Hydrodynamic Diameter Change":-5.117,"Intensity Mean Hydrodynamic Diameter [nm]":23.49,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":70.97,"Intensity Mean Hydrodynamic Diameter Change":47.4778,"Polydispersity 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(Net cell association [mL/ug(Mg)])":0.49705},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":30.95,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":90.06,"Z-Average Hydrodynamic Diameter Change":59.1089,"Volume Mean Hydrodynamic Diameter [nm]":11.76,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":67.79,"Volume Mean Hydrodynamic Diameter Change":56.032,"Number Mean Hydrodynamic Diameter [nm]":47.5,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":53.87,"Number Mean Hydrodynamic Diameter Change":6.3667,"Intensity Mean Hydrodynamic Diameter [nm]":47.5,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":106.7,"Intensity Mean Hydrodynamic Diameter Change":59.2033,"Polydispersity index [nm]":0.399,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.215,"Polydispersity index Change":-0.1837,"ZETA POTENTIAL [mV]":15.22,"ZETA POTENTIAL Human serum 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[nm]":21.22,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":74.66,"Volume Mean Hydrodynamic Diameter Change":53.4389,"Number Mean Hydrodynamic Diameter [nm]":23.04,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":31.4,"Number Mean Hydrodynamic Diameter Change":8.3653,"Intensity Mean Hydrodynamic Diameter [nm]":23.04,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":68.92,"Intensity Mean Hydrodynamic Diameter Change":45.8817,"Polydispersity index [nm]":0.15,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.207,"Polydispersity index Change":0.0568,"ZETA POTENTIAL [mV]":-20.27,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-8.29,"ZETA POTENTIAL Change":11.975,"Localized Surface Plasmon Resonance (LSPR) index":0.273619886,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.327264445,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0536,"LSPR peak position (nm) [nm]":518.57,"Total 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[ug/cm^2]":0.049275338}},"G15.CIT":{"composition":{"Core composition":"[Au]","Surface modifier1":"Citrate","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.02336},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":18.65,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":54.03,"Z-Average Hydrodynamic Diameter Change":35.3825,"Volume Mean Hydrodynamic Diameter [nm]":19.47,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":38.58,"Volume Mean Hydrodynamic Diameter Change":19.1137,"Number Mean Hydrodynamic Diameter [nm]":28.3,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":32.35,"Number Mean Hydrodynamic Diameter Change":4.0509,"Intensity Mean Hydrodynamic Diameter [nm]":28.3,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":64.47,"Intensity Mean Hydrodynamic Diameter 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[mV]":-5.91,"ZETA POTENTIAL Change":0.4133,"Localized Surface Plasmon Resonance (LSPR) index":0.211466307,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.263698153,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0522,"LSPR peak position (nm) [nm]":519.07,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":1.67,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":258.6099131,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.008213753}},"G15.CTAB":{"composition":{"Core composition":"[Au]","Surface modifier1":"Hexadecyltrimethylammonium bromide","Surface modifier2":null,"Classification":"Cationic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.01719},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":15.6,"Z-Average 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Diameter [nm]":22.84,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":175.14,"Volume Mean Hydrodynamic Diameter Change":152.2956,"Number Mean Hydrodynamic Diameter [nm]":27.78,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":23.34,"Number Mean Hydrodynamic Diameter Change":-4.4378,"Intensity Mean Hydrodynamic Diameter [nm]":27.78,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":140.15,"Intensity Mean Hydrodynamic Diameter Change":112.3656,"Polydispersity index [nm]":0.187,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.336,"Polydispersity index Change":0.1494,"ZETA POTENTIAL [mV]":13.49,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-9.7,"ZETA POTENTIAL Change":-23.1917,"Localized Surface Plasmon Resonance (LSPR) index":0.266578823,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.317133738,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0506,"LSPR peak position (nm) 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diff --git a/data/marina.json b/data/marina.json
new file mode 100644
index 0000000..a615f42
--- /dev/null
+++ b/data/marina.json
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index 0000000..0902a72
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new file mode 100644
index 0000000..93d623d
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diff --git a/data/protein-corona.json b/data/protein-corona.json
new file mode 100644
index 0000000..ac2215c
--- /dev/null
+++ b/data/protein-corona.json
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+}
diff --git a/diff-features.json b/diff-features.json
new file mode 100644
index 0000000..eced440
--- /dev/null
+++ b/diff-features.json
@@ -0,0 +1,18 @@
+{
+ "ZETA POTENTIAL Change": [
+ "ZETA POTENTIAL [mV]",
+ "ZETA POTENTIAL Human serum (Sigma #H4522) [mV]"
+ ],
+ "Localized Surface Plasmon Resonance (LSPR) index Change": [
+ "Localized Surface Plasmon Resonance (LSPR) index",
+ "Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)"
+ ],
+ "Polydispersity index Change": [
+ "Polydispersity index [nm]",
+ "Polydispersity index Human serum (Sigma #H4522) [nm]"
+ ],
+ "Volume Mean Hydrodynamic Diameter Change": [
+ "Volume Mean Hydrodynamic Diameter [nm]",
+ "Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]"
+ ]
+}
diff --git a/nanoparticles.rb b/nanoparticles.rb
new file mode 100644
index 0000000..d3399e9
--- /dev/null
+++ b/nanoparticles.rb
@@ -0,0 +1,182 @@
+require 'rserve'
+require 'json'
+require 'yaml'
+require 'csv'
+
+ENDPOINT = "Cell.association (Net cell association [mL/ug(Mg)])"
+
+def query_features
+ relevant_features = JSON.parse(File.read("./relevant-features.json"))
+end
+
+def predict params
+ # calculate difference parameters
+ diff_features = JSON.parse(File.read("./diff-features.json"))
+ diff_features.each do |feature,originals|
+ params[feature] = params[originals[1]]-params[originals[0]] # causes rounding errors!
+ end
+ neighbors = []
+ sim_sum = 0
+ weighted_sum = 0
+ match = nil
+ relevant_features = JSON.parse(File.read("./relevant-features.json"))
+ weights = relevant_features.values.collect{|v| v["r"]}
+ JSON.parse(File.read("./data.json")).each do |id,categories|
+ query_values = []
+ neighbor_values = []
+ relevant_features.keys.each do |f|
+ query_values << params[f]
+ neighbor_values << categories["physchem"][f]
+ end
+ sim = weighted_cosine_similarity(query_values,neighbor_values,weights)
+ if sim > 0.9999 # no exact match because of rounding errors
+ match = {id => categories}
+ elsif sim > 0.95
+ neighbor = categories
+ neighbor["similarity"] = sim
+ neighbor["sim"] = cosine_similarity(query_values,neighbor_values)
+ neighbor["id"] = id
+ sim_sum += sim
+ weighted_sum += sim*Math.log10(categories["tox"][ENDPOINT])
+ #weighted_sum += sim*categories["tox"][ENDPOINT]
+ neighbors << neighbor
+ end
+ end
+ neighbors.sort!{|a,b| b["similarity"] <=> a["similarity"]}
+ sim_sum == 0 ? prediction = nil : prediction = 10**(weighted_sum/sim_sum)
+ {
+ :query => params,
+ :match => match,
+ :prediction => {ENDPOINT => prediction},
+ :neighbors => neighbors
+ }
+end
+
+class Object
+ def numeric?
+ true if Float(self) rescue false
+ end
+end
+
+def euclidean_distance(a, b)
+ sq = a.zip(b).map{|a,b| (a - b) ** 2}
+ Math.sqrt(sq.inject(0) {|s,c| s + c})
+end
+
+def dot_product(a, b)
+ products = a.zip(b).map{|a, b| a * b}
+ products.inject(0) {|s,p| s + p}
+end
+
+def magnitude(point)
+ squares = point.map{|x| x ** 2}
+ Math.sqrt(squares.inject(0) {|s, c| s + c})
+end
+
+# http://stackoverflow.com/questions/1838806/euclidean-distance-vs-pearson-correlation-vs-cosine-similarity
+def cosine_similarity(a, b)
+ dot_product(a, b) / (magnitude(a) * magnitude(b))
+end
+
+def weighted_cosine_similarity(a, b, w)
+ dot_product = 0
+ magnitude_a = 0
+ magnitude_b = 0
+ (0..a.size-1).each do |i|
+ dot_product += w[i].abs*a[i]*b[i]
+ magnitude_a += w[i].abs*a[i]**2
+ magnitude_b += w[i].abs*b[i]**2
+ end
+ dot_product/Math.sqrt(magnitude_a*magnitude_b)
+
+end
+
+#@endpoint = @data.collect{|r| r[5]}
+
+def neighbors query
+end
+
+def csv2json
+ csv = CSV.read("data/MergedSheets_edit.csv")
+ csv.collect!{|row| row[0..36].collect{|c| c.numeric? ? c.to_f : c } }.compact
+ feature_names = [
+ "ID",
+ csv[0][1],
+ csv[0][2],
+ csv[0][3],
+ csv[6][4],
+ "#{csv[0][5]} (#{csv[6][5]} [#{csv[11][5]}])", # endpoint
+ "#{csv[0][6]} (#{csv[6][6]})", # endpoint
+ "#{csv[6][7]} [#{csv[11][7]}]",
+ "#{csv[6][8]} [#{csv[11][8]}]",
+ "#{csv[6][9]} [#{csv[11][9]}]",
+ ]
+ (10..10+5*3).step(3) do |i|
+ feature_names += [
+ "#{csv[6][i]} [#{csv[11][i]}]",
+ "#{csv[6][i+1]} #{csv[8][i+1]} [#{csv[11][i+1]}]",
+ "#{csv[6][i+2]} #{csv[8][i+2]}",
+ ]
+ end
+ feature_names += [
+ "#{csv[6][28]}",
+ "#{csv[6][29]} #{csv[8][29]}",
+ "#{csv[6][30]} #{csv[8][30]}",
+ ]
+ (31..34).each do |i|
+ feature_names << "#{csv[6][i]} #{csv[8][i]} [#{csv[11][i]}]"
+ end
+ (35..36).each do |i|
+ feature_names << "#{csv[6][i]} #{csv[8][i]} #{csv[10][i]} [#{csv[11][i]}]"
+ end
+ data = {}
+ csv.drop(12).each do |row|
+ id = row.first
+ if id.match /^G/ # skip Ag, too many missing values
+ data[id] = {}
+ row.each_with_index do |col,i|
+ if i == 0
+ data[id][:composition] = {}
+ elsif i < 5
+ data[id][:composition][feature_names[i]] = col
+ elsif i == 5
+ data[id][:tox] ||= {}
+ data[id][:tox][feature_names[i]] = col
+ elsif i > 6
+ data[id][:physchem] ||= {}
+ data[id][:physchem][feature_names[i]] = col
+ end
+ end
+ end
+ end
+ File.open("data.json","w+"){|f| f.puts data.to_json}
+ data
+end
+
+#puts data.to_yaml
+=begin
+R.assign "endpoint", endpoint
+(0..data[0].size).each do |c|
+ if data.collect{|r| r[c]}.uniq.size > 1
+ begin
+ R.assign "feature", data.collect{|r| r[c]}
+ R.eval "r <- cor(-log(endpoint),-log(feature),use='complete')"
+ r = R.eval("r").to_ruby
+ p "#{c}: #{r}" if r > 0.3 or r < -0.3
+ rescue
+ end
+ end
+end
+
+
+csv[0..13].each do |row|
+ row.each_with_index do |col,i|
+ features[i] = features[i].to_s+", "+col.to_s
+ end
+end
+
+puts features.select{|f| f.match(/Mean/)}.to_yaml
+
+ #n+=1
+ #p n,row.first unless row.first.match /^[G|S]/
+=end
diff --git a/presentation/enm-workshop.html b/presentation/enm-workshop.html
new file mode 100644
index 0000000..f0c6781
--- /dev/null
+++ b/presentation/enm-workshop.html
@@ -0,0 +1,445 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.12: http://docutils.sourceforge.net/" />
+<meta name="version" content="S5 1.1" />
+<title>Read across toxicity predictions with nano-lazar</title>
+<style type="text/css">
+
+/*
+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 7614 2013-02-21 15:55:51Z milde $
+:Copyright: This stylesheet has been placed in the public domain.
+
+Default cascading style sheet for the HTML output of Docutils.
+
+See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
+customize this style sheet.
+*/
+
+/* used to remove borders from tables and images */
+.borderless, table.borderless td, table.borderless th {
+ border: 0 }
+
+table.borderless td, table.borderless th {
+ /* Override padding for "table.docutils td" with "! important".
+ The right padding separates the table cells. */
+ padding: 0 0.5em 0 0 ! important }
+
+.first {
+ /* Override more specific margin styles with "! important". */
+ margin-top: 0 ! important }
+
+.last, .with-subtitle {
+ margin-bottom: 0 ! important }
+
+.hidden {
+ display: none }
+
+a.toc-backref {
+ text-decoration: none ;
+ color: black }
+
+blockquote.epigraph {
+ margin: 2em 5em ; }
+
+dl.docutils dd {
+ margin-bottom: 0.5em }
+
+object[type="image/svg+xml"], object[type="application/x-shockwave-flash"] {
+ overflow: hidden;
+}
+
+/* Uncomment (and remove this text!) to get bold-faced definition list terms
+dl.docutils dt {
+ font-weight: bold }
+*/
+
+div.abstract {
+ margin: 2em 5em }
+
+div.abstract p.topic-title {
+ font-weight: bold ;
+ text-align: center }
+
+div.admonition, div.attention, div.caution, div.danger, div.error,
+div.hint, div.important, div.note, div.tip, div.warning {
+ margin: 2em ;
+ border: medium outset ;
+ padding: 1em }
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+div.admonition p.admonition-title, div.hint p.admonition-title,
+div.important p.admonition-title, div.note p.admonition-title,
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+ font-weight: bold ;
+ font-family: sans-serif }
+
+div.attention p.admonition-title, div.caution p.admonition-title,
+div.danger p.admonition-title, div.error p.admonition-title,
+div.warning p.admonition-title, .code .error {
+ color: red ;
+ font-weight: bold ;
+ font-family: sans-serif }
+
+/* Uncomment (and remove this text!) to get reduced vertical space in
+ compound paragraphs.
+div.compound .compound-first, div.compound .compound-middle {
+ margin-bottom: 0.5em }
+
+div.compound .compound-last, div.compound .compound-middle {
+ margin-top: 0.5em }
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+ margin: 2em 5em ;
+ text-align: center ;
+ font-style: italic }
+
+div.dedication p.topic-title {
+ font-weight: bold ;
+ font-style: normal }
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+div.figure {
+ margin-left: 2em ;
+ margin-right: 2em }
+
+div.footer, div.header {
+ clear: both;
+ font-size: smaller }
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+ display: block ;
+ margin-top: 1em ;
+ margin-bottom: 1em }
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+div.sidebar {
+ margin: 0 0 0.5em 1em ;
+ border: medium outset ;
+ padding: 1em ;
+ background-color: #ffffee ;
+ width: 40% ;
+ float: right ;
+ clear: right }
+
+div.sidebar p.rubric {
+ font-family: sans-serif ;
+ font-size: medium }
+
+div.system-messages {
+ margin: 5em }
+
+div.system-messages h1 {
+ color: red }
+
+div.system-message {
+ border: medium outset ;
+ padding: 1em }
+
+div.system-message p.system-message-title {
+ color: red ;
+ font-weight: bold }
+
+div.topic {
+ margin: 2em }
+
+h1.section-subtitle, h2.section-subtitle, h3.section-subtitle,
+h4.section-subtitle, h5.section-subtitle, h6.section-subtitle {
+ margin-top: 0.4em }
+
+h1.title {
+ text-align: center }
+
+h2.subtitle {
+ text-align: center }
+
+hr.docutils {
+ width: 75% }
+
+img.align-left, .figure.align-left, object.align-left {
+ clear: left ;
+ float: left ;
+ margin-right: 1em }
+
+img.align-right, .figure.align-right, object.align-right {
+ clear: right ;
+ float: right ;
+ margin-left: 1em }
+
+img.align-center, .figure.align-center, object.align-center {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+.align-left {
+ text-align: left }
+
+.align-center {
+ clear: both ;
+ text-align: center }
+
+.align-right {
+ text-align: right }
+
+/* reset inner alignment in figures */
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+ text-align: inherit }
+
+/* div.align-center * { */
+/* text-align: left } */
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+ol.simple, ul.simple {
+ margin-bottom: 1em }
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+p.attribution {
+ text-align: right ;
+ margin-left: 50% }
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+ font-style: italic }
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+ font-style: italic ;
+ font-size: smaller }
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+ font-weight: bold ;
+ font-size: larger ;
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+ font-weight: bold ;
+ font-size: larger }
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+p.sidebar-subtitle {
+ font-family: sans-serif ;
+ font-weight: bold }
+
+p.topic-title {
+ font-weight: bold }
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+pre.address {
+ margin-bottom: 0 ;
+ margin-top: 0 ;
+ font: inherit }
+
+pre.literal-block, pre.doctest-block, pre.math, pre.code {
+ margin-left: 2em ;
+ margin-right: 2em }
+
+pre.code .ln { color: grey; } /* line numbers */
+pre.code, code { background-color: #eeeeee }
+pre.code .comment, code .comment { color: #5C6576 }
+pre.code .keyword, code .keyword { color: #3B0D06; font-weight: bold }
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+pre.code .name.builtin, code .name.builtin { color: #352B84 }
+pre.code .deleted, code .deleted { background-color: #DEB0A1}
+pre.code .inserted, code .inserted { background-color: #A3D289}
+
+span.classifier {
+ font-family: sans-serif ;
+ font-style: oblique }
+
+span.classifier-delimiter {
+ font-family: sans-serif ;
+ font-weight: bold }
+
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+ font-family: sans-serif }
+
+span.option {
+ white-space: nowrap }
+
+span.pre {
+ white-space: pre }
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+span.problematic {
+ color: red }
+
+span.section-subtitle {
+ /* font-size relative to parent (h1..h6 element) */
+ font-size: 80% }
+
+table.citation {
+ border-left: solid 1px gray;
+ margin-left: 1px }
+
+table.docinfo {
+ margin: 2em 4em }
+
+table.docutils {
+ margin-top: 0.5em ;
+ margin-bottom: 0.5em }
+
+table.footnote {
+ border-left: solid 1px black;
+ margin-left: 1px }
+
+table.docutils td, table.docutils th,
+table.docinfo td, table.docinfo th {
+ padding-left: 0.5em ;
+ padding-right: 0.5em ;
+ vertical-align: top }
+
+table.docutils th.field-name, table.docinfo th.docinfo-name {
+ font-weight: bold ;
+ text-align: left ;
+ white-space: nowrap ;
+ padding-left: 0 }
+
+/* "booktabs" style (no vertical lines) */
+table.docutils.booktabs {
+ border: 0px;
+ border-top: 2px solid;
+ border-bottom: 2px solid;
+ border-collapse: collapse;
+}
+table.docutils.booktabs * {
+ border: 0px;
+}
+table.docutils.booktabs th {
+ border-bottom: thin solid;
+ text-align: left;
+}
+
+h1 tt.docutils, h2 tt.docutils, h3 tt.docutils,
+h4 tt.docutils, h5 tt.docutils, h6 tt.docutils {
+ font-size: 100% }
+
+ul.auto-toc {
+ list-style-type: none }
+
+</style>
+<!-- configuration parameters -->
+<meta name="defaultView" content="slideshow" />
+<meta name="controlVis" content="hidden" />
+<!-- style sheet links -->
+<script src="ui/small-white/slides.js" type="text/javascript"></script>
+<link rel="stylesheet" href="ui/small-white/slides.css"
+ type="text/css" media="projection" id="slideProj" />
+<link rel="stylesheet" href="ui/small-white/outline.css"
+ type="text/css" media="screen" id="outlineStyle" />
+<link rel="stylesheet" href="ui/small-white/print.css"
+ type="text/css" media="print" id="slidePrint" />
+<link rel="stylesheet" href="ui/small-white/opera.css"
+ type="text/css" media="projection" id="operaFix" />
+
+<style type="text/css">
+#currentSlide {display: none;}
+</style>
+</head>
+<body>
+<div class="layout">
+<div id="controls"></div>
+<div id="currentSlide"></div>
+<div id="header">
+
+</div>
+<div id="footer">
+<h1>Read across toxicity predictions with nano-lazar</h1>
+
+</div>
+</div>
+<div class="presentation">
+<div class="slide" id="slide0">
+<h1 class="title">Read across toxicity predictions with nano-lazar</h1>
+
+<p class="center">Christoph Helma</p>
+<p class="center">in silico toxicology gmbh</p>
+<img alt="http://www.enanomapper.net/sites/all/themes/theme807/logo.png" class="center align-center" src="http://www.enanomapper.net/sites/all/themes/theme807/logo.png" />
+
+</div>
+<div class="slide" id="requirements">
+<h1>Requirements</h1>
+<ul class="simple">
+<li>Nanoparticle characterisation</li>
+<li>Toxicity measurements</li>
+</ul>
+</div>
+<div class="slide" id="enanomapper-data-import">
+<h1>eNanoMapper data import</h1>
+<ul class="incremental simple">
+<li>Nanoparticles imported: 464</li>
+<li>Nanoparticles with particle characterisation: 394</li>
+<li>Nanoparticles with toxicity data: 167</li>
+<li>Nanoparticles with toxicity data and particle characterisation: 160</li>
+</ul>
+</div>
+<div class="slide" id="enanomapper-toxicity-endpoints">
+<h1>eNanoMapper toxicity endpoints</h1>
+<ul class="incremental simple">
+<li>Toxicity endpoints: 41</li>
+<li>Toxicity endpoints with more than one measurement value: 22</li>
+<li>Toxicity endpoints with more than 10 measurements: 2</li>
+</ul>
+</div>
+<div class="slide" id="selected-data">
+<h1>Selected data</h1>
+<p>Protein corona dataset Au particles (106 particles)
+Toxicity endpoint:</p>
+</div>
+<div class="slide" id="read-across-procedure">
+<h1>Read across procedure</h1>
+<ul class="incremental simple">
+<li>Identify relevant fragments (significant correlation with toxicity)
+TODO list of fragments, number</li>
+<li>Calculate similarities (weighted cosine similarity, correlation coefficients = weights)</li>
+<li>Identify neighbors (particles with more than 0.95 similarity)</li>
+<li>Calculate prediction (weighted average from neighbors, similarities = weights)</li>
+</ul>
+</div>
+<div class="slide" id="future-development">
+<h1>Future development</h1>
+<ul class="simple">
+<li>Validation of predictions</li>
+<li>Applicability domain/reliability of predictions</li>
+<li>Accuracy improvements:
+- additional data
+- feature selection
+- similarity calculation
+- predictions (local regression models)</li>
+<li>Usability improvements:
+- additional data (extension of applicability domain, additional endpoints and chemistries)
+- inclusion of ontologies
+- descriptor calculation directly from core and coating chemistries</li>
+</ul>
+</div>
+<div class="slide" id="webinterface">
+<h1>Webinterface</h1>
+<p><a class="reference external" href="https://nano-lazar.in-silico.ch/predict">https://nano-lazar.in-silico.ch/predict</a></p>
+<p>Your recommendations?</p>
+</div>
+<div class="slide" id="source-code">
+<h1>Source code</h1>
+<p><a class="reference external" href="https://github.com/opentox/nano-lazar">https://github.com/opentox/nano-lazar</a></p>
+</div>
+</div>
+</body>
+</html>
diff --git a/presentation/enm-workshop.rst b/presentation/enm-workshop.rst
new file mode 100644
index 0000000..26a3524
--- /dev/null
+++ b/presentation/enm-workshop.rst
@@ -0,0 +1,89 @@
+.. |date| date::
+
+
+
+=============================================================
+Read across toxicity predictions with nano-lazar
+=============================================================
+
+.. class:: center
+
+ Christoph Helma
+
+ in silico toxicology gmbh
+
+ .. image:: http://www.enanomapper.net/sites/all/themes/theme807/logo.png
+ :align: center
+
+Requirements
+============
+
+- Nanoparticle characterisation
+- Toxicity measurements
+
+
+eNanoMapper data import
+=======================
+
+.. class:: incremental
+
+ - Nanoparticles imported: 464
+ - Nanoparticles with particle characterisation: 394
+ - Nanoparticles with toxicity data: 167
+ - Nanoparticles with toxicity data and particle characterisation: 160
+
+
+eNanoMapper toxicity endpoints
+==============================
+
+.. class:: incremental
+
+- Toxicity endpoints: 41
+- Toxicity endpoints with more than one measurement value: 22
+- Toxicity endpoints with more than 10 measurements: 2
+
+Selected data
+=============
+
+Protein corona dataset Au particles (106 particles)
+Toxicity endpoint:
+
+Read across procedure
+=====================
+
+.. class:: incremental
+
+- Identify relevant fragments (significant correlation with toxicity)
+ TODO list of fragments, number
+- Calculate similarities (weighted cosine similarity, correlation coefficients = weights)
+- Identify neighbors (particles with more than 0.95 similarity)
+- Calculate prediction (weighted average from neighbors, similarities = weights)
+
+Future development
+==================
+
+- Validation of predictions
+- Applicability domain/reliability of predictions
+
+- Accuracy improvements:
+ - additional data
+ - feature selection
+ - similarity calculation
+ - predictions (local regression models)
+
+- Usability improvements:
+ - additional data (extension of applicability domain, additional endpoints and chemistries)
+ - inclusion of ontologies
+ - descriptor calculation directly from core and coating chemistries
+
+Webinterface
+============
+
+https://nano-lazar.in-silico.ch/predict
+
+Your recommendations?
+
+Source code
+===========
+
+https://github.com/opentox/nano-lazar
diff --git a/presentation/ui/small-white/blank.gif b/presentation/ui/small-white/blank.gif
new file mode 100644
index 0000000..75b945d
--- /dev/null
+++ b/presentation/ui/small-white/blank.gif
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diff --git a/presentation/ui/small-white/framing.css b/presentation/ui/small-white/framing.css
new file mode 100644
index 0000000..70287dd
--- /dev/null
+++ b/presentation/ui/small-white/framing.css
@@ -0,0 +1,24 @@
+/* This file has been placed in the public domain. */
+/* The following styles size, place, and layer the slide components.
+ Edit these if you want to change the overall slide layout.
+ The commented lines can be uncommented (and modified, if necessary)
+ to help you with the rearrangement process. */
+
+/* target = 1024x768 */
+
+div#header, div#footer, .slide {width: 100%; top: 0; left: 0;}
+div#footer {top: auto; bottom: 0; height: 2.5em; z-index: 5;}
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+div#controls {left: 50%; bottom: 0; width: 50%; z-index: 100;}
+div#controls form {position: absolute; bottom: 0; right: 0; width: 100%;
+ margin: 0;}
+#currentSlide {position: absolute; width: 10%; left: 45%; bottom: 1em;
+ z-index: 10;}
+html>body #currentSlide {position: fixed;}
+
+/*
+div#header {background: #FCC;}
+div#footer {background: #CCF;}
+div#controls {background: #BBD;}
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diff --git a/presentation/ui/small-white/iepngfix.htc b/presentation/ui/small-white/iepngfix.htc
new file mode 100644
index 0000000..2a44681
--- /dev/null
+++ b/presentation/ui/small-white/iepngfix.htc
@@ -0,0 +1,42 @@
+<public:component>
+<public:attach event="onpropertychange" onevent="doFix()" />
+
+<script>
+
+// IE5.5+ PNG Alpha Fix v1.0 by Angus Turnbull http://www.twinhelix.com
+// Free usage permitted as long as this notice remains intact.
+
+// This must be a path to a blank image. That's all the configuration you need here.
+var blankImg = 'ui/small-white/blank.gif';
+
+var f = 'DXImageTransform.Microsoft.AlphaImageLoader';
+
+function filt(s, m) {
+ if (filters[f]) {
+ filters[f].enabled = s ? true : false;
+ if (s) with (filters[f]) { src = s; sizingMethod = m }
+ } else if (s) style.filter = 'progid:'+f+'(src="'+s+'",sizingMethod="'+m+'")';
+}
+
+function doFix() {
+ if ((parseFloat(navigator.userAgent.match(/MSIE (\S+)/)[1]) < 5.5) ||
+ (event && !/(background|src)/.test(event.propertyName))) return;
+
+ if (tagName == 'IMG') {
+ if ((/\.png$/i).test(src)) {
+ filt(src, 'image'); // was 'scale'
+ src = blankImg;
+ } else if (src.indexOf(blankImg) < 0) filt();
+ } else if (style.backgroundImage) {
+ if (style.backgroundImage.match(/^url[("']+(.*\.png)[)"']+$/i)) {
+ var s = RegExp.$1;
+ style.backgroundImage = '';
+ filt(s, 'crop');
+ } else filt();
+ }
+}
+
+doFix();
+
+</script>
+</public:component> \ No newline at end of file
diff --git a/presentation/ui/small-white/opera.css b/presentation/ui/small-white/opera.css
new file mode 100644
index 0000000..c9d1148
--- /dev/null
+++ b/presentation/ui/small-white/opera.css
@@ -0,0 +1,8 @@
+/* This file has been placed in the public domain. */
+/* DO NOT CHANGE THESE unless you really want to break Opera Show */
+.slide {
+ visibility: visible !important;
+ position: static !important;
+ page-break-before: always;
+}
+#slide0 {page-break-before: avoid;}
diff --git a/presentation/ui/small-white/outline.css b/presentation/ui/small-white/outline.css
new file mode 100644
index 0000000..fa767e2
--- /dev/null
+++ b/presentation/ui/small-white/outline.css
@@ -0,0 +1,16 @@
+/* This file has been placed in the public domain. */
+/* Don't change this unless you want the layout stuff to show up in the
+ outline view! */
+
+.layout div, #footer *, #controlForm * {display: none;}
+#footer, #controls, #controlForm, #navLinks, #toggle {
+ display: block; visibility: visible; margin: 0; padding: 0;}
+#toggle {float: right; padding: 0.5em;}
+html>body #toggle {position: fixed; top: 0; right: 0;}
+
+/* making the outline look pretty-ish */
+
+#slide0 h1, #slide0 h2, #slide0 h3, #slide0 h4 {border: none; margin: 0;}
+#toggle {border: 1px solid; border-width: 0 0 1px 1px; background: #FFF;}
+
+.outline {display: inline ! important;}
diff --git a/presentation/ui/small-white/pretty.css b/presentation/ui/small-white/pretty.css
new file mode 100644
index 0000000..ba988e1
--- /dev/null
+++ b/presentation/ui/small-white/pretty.css
@@ -0,0 +1,114 @@
+/* This file has been placed in the public domain. */
+/* Following are the presentation styles -- edit away! */
+
+html, body {margin: 0; padding: 0;}
+body {background: white; color: black;}
+:link, :visited {text-decoration: none; color: #00C;}
+#controls :active {color: #888 !important;}
+#controls :focus {outline: 1px dotted #222;}
+h1, h2, h3, h4 {font-size: 100%; margin: 0; padding: 0; font-weight: inherit;}
+
+blockquote {padding: 0 2em 0.5em; margin: 0 1.5em 0.5em;}
+blockquote p {margin: 0;}
+
+kbd {font-weight: bold; font-size: 1em;}
+sup {font-size: smaller; line-height: 1px;}
+
+.slide pre {padding: 0; margin-left: 0; margin-right: 0; font-size: 90%;}
+.slide ul ul li {list-style: square;}
+.slide img.leader {display: block; margin: 0 auto;}
+.slide tt {font-size: 90%;}
+
+div#footer {font-family: sans-serif; color: #444;
+ font-size: 0.5em; font-weight: bold; padding: 1em 0;}
+#footer h1 {display: block; padding: 0 1em;}
+#footer h2 {display: block; padding: 0.8em 1em 0;}
+
+.slide {font-size: 1.2em;}
+.slide h1 {padding-top: 0; z-index: 1; margin: 0; font: bold 150% sans-serif;}
+.slide h2 {font: bold 120% sans-serif; padding-top: 0.5em;}
+.slide h3 {font: bold 100% sans-serif; padding-top: 0.5em;}
+h1 abbr {font-variant: small-caps;}
+
+div#controls {position: absolute; left: 50%; bottom: 0;
+ width: 50%; text-align: right; font: bold 0.9em sans-serif;}
+html>body div#controls {position: fixed; padding: 0 0 1em 0; top: auto;}
+div#controls form {position: absolute; bottom: 0; right: 0; width: 100%;
+ margin: 0; padding: 0;}
+#controls #navLinks a {padding: 0; margin: 0 0.5em;
+ border: none; color: #888; cursor: pointer;}
+#controls #navList {height: 1em;}
+#controls #navList #jumplist {position: absolute; bottom: 0; right: 0;
+ background: #DDD; color: #222;}
+
+#currentSlide {text-align: center; font-size: 0.5em; color: #444;
+ font-family: sans-serif; font-weight: bold;}
+
+#slide0 {padding-top: 0em}
+#slide0 h1 {position: static; margin: 1em 0 0; padding: 0;
+ font: bold 2em sans-serif; white-space: normal; background: transparent;}
+#slide0 h2 {font: bold italic 1em sans-serif; margin: 0.25em;}
+#slide0 h3 {margin-top: 1.5em; font-size: 1.5em;}
+#slide0 h4 {margin-top: 0; font-size: 1em;}
+
+ul.urls {list-style: none; display: inline; margin: 0;}
+.urls li {display: inline; margin: 0;}
+.external {border-bottom: 1px dotted gray;}
+html>body .external {border-bottom: none;}
+.external:after {content: " \274F"; font-size: smaller; color: #77B;}
+
+.incremental, .incremental *, .incremental *:after {
+ color: white; visibility: visible; border: 0; border: 0;}
+img.incremental {visibility: hidden;}
+.slide .current {color: green;}
+
+.slide-display {display: inline ! important;}
+
+.huge {font-family: sans-serif; font-weight: bold; font-size: 150%;}
+.big {font-family: sans-serif; font-weight: bold; font-size: 120%;}
+.small {font-size: 75%;}
+.tiny {font-size: 50%;}
+.huge tt, .big tt, .small tt, .tiny tt {font-size: 115%;}
+.huge pre, .big pre, .small pre, .tiny pre {font-size: 115%;}
+
+.maroon {color: maroon;}
+.red {color: red;}
+.magenta {color: magenta;}
+.fuchsia {color: fuchsia;}
+.pink {color: #FAA;}
+.orange {color: orange;}
+.yellow {color: yellow;}
+.lime {color: lime;}
+.green {color: green;}
+.olive {color: olive;}
+.teal {color: teal;}
+.cyan {color: cyan;}
+.aqua {color: aqua;}
+.blue {color: blue;}
+.navy {color: navy;}
+.purple {color: purple;}
+.black {color: black;}
+.gray {color: gray;}
+.silver {color: silver;}
+.white {color: white;}
+
+.left {text-align: left ! important;}
+.center {text-align: center ! important;}
+.right {text-align: right ! important;}
+
+.animation {position: relative; margin: 1em 0; padding: 0;}
+.animation img {position: absolute;}
+
+/* Docutils-specific overrides */
+
+.slide table.docinfo {margin: 1em 0 0.5em 2em;}
+
+pre.literal-block, pre.doctest-block {background-color: white;}
+
+tt.docutils {background-color: white;}
+
+/* diagnostics */
+/*
+li:after {content: " [" attr(class) "]"; color: #F88;}
+div:before {content: "[" attr(class) "]"; color: #F88;}
+*/
diff --git a/presentation/ui/small-white/print.css b/presentation/ui/small-white/print.css
new file mode 100644
index 0000000..9d057cc
--- /dev/null
+++ b/presentation/ui/small-white/print.css
@@ -0,0 +1,24 @@
+/* This file has been placed in the public domain. */
+/* The following rule is necessary to have all slides appear in print!
+ DO NOT REMOVE IT! */
+.slide, ul {page-break-inside: avoid; visibility: visible !important;}
+h1 {page-break-after: avoid;}
+
+body {font-size: 12pt; background: white;}
+* {color: black;}
+
+#slide0 h1 {font-size: 200%; border: none; margin: 0.5em 0 0.25em;}
+#slide0 h3 {margin: 0; padding: 0;}
+#slide0 h4 {margin: 0 0 0.5em; padding: 0;}
+#slide0 {margin-bottom: 3em;}
+
+#header {display: none;}
+#footer h1 {margin: 0; border-bottom: 1px solid; color: gray;
+ font-style: italic;}
+#footer h2, #controls {display: none;}
+
+.print {display: inline ! important;}
+
+/* The following rule keeps the layout stuff out of print.
+ Remove at your own risk! */
+.layout, .layout * {display: none !important;}
diff --git a/presentation/ui/small-white/s5-core.css b/presentation/ui/small-white/s5-core.css
new file mode 100644
index 0000000..6965f5e
--- /dev/null
+++ b/presentation/ui/small-white/s5-core.css
@@ -0,0 +1,11 @@
+/* This file has been placed in the public domain. */
+/* Do not edit or override these styles!
+ The system will likely break if you do. */
+
+div#header, div#footer, div#controls, .slide {position: absolute;}
+html>body div#header, html>body div#footer,
+ html>body div#controls, html>body .slide {position: fixed;}
+.handout {display: none;}
+.layout {display: block;}
+.slide, .hideme, .incremental {visibility: hidden;}
+#slide0 {visibility: visible;}
diff --git a/presentation/ui/small-white/slides.css b/presentation/ui/small-white/slides.css
new file mode 100644
index 0000000..82bdc0e
--- /dev/null
+++ b/presentation/ui/small-white/slides.css
@@ -0,0 +1,10 @@
+/* This file has been placed in the public domain. */
+
+/* required to make the slide show run at all */
+@import url(s5-core.css);
+
+/* sets basic placement and size of slide components */
+@import url(framing.css);
+
+/* styles that make the slides look good */
+@import url(pretty.css);
diff --git a/presentation/ui/small-white/slides.js b/presentation/ui/small-white/slides.js
new file mode 100644
index 0000000..87c30c6
--- /dev/null
+++ b/presentation/ui/small-white/slides.js
@@ -0,0 +1,558 @@
+// S5 v1.1 slides.js -- released into the Public Domain
+// Modified for Docutils (http://docutils.sf.net) by David Goodger
+//
+// Please see http://www.meyerweb.com/eric/tools/s5/credits.html for
+// information about all the wonderful and talented contributors to this code!
+
+var undef;
+var slideCSS = '';
+var snum = 0;
+var smax = 1;
+var slideIDs = new Array();
+var incpos = 0;
+var number = undef;
+var s5mode = true;
+var defaultView = 'slideshow';
+var controlVis = 'visible';
+
+var isIE = navigator.appName == 'Microsoft Internet Explorer' ? 1 : 0;
+var isOp = navigator.userAgent.indexOf('Opera') > -1 ? 1 : 0;
+var isGe = navigator.userAgent.indexOf('Gecko') > -1 && navigator.userAgent.indexOf('Safari') < 1 ? 1 : 0;
+
+function hasClass(object, className) {
+ if (!object.className) return false;
+ return (object.className.search('(^|\\s)' + className + '(\\s|$)') != -1);
+}
+
+function hasValue(object, value) {
+ if (!object) return false;
+ return (object.search('(^|\\s)' + value + '(\\s|$)') != -1);
+}
+
+function removeClass(object,className) {
+ if (!object) return;
+ object.className = object.className.replace(new RegExp('(^|\\s)'+className+'(\\s|$)'), RegExp.$1+RegExp.$2);
+}
+
+function addClass(object,className) {
+ if (!object || hasClass(object, className)) return;
+ if (object.className) {
+ object.className += ' '+className;
+ } else {
+ object.className = className;
+ }
+}
+
+function GetElementsWithClassName(elementName,className) {
+ var allElements = document.getElementsByTagName(elementName);
+ var elemColl = new Array();
+ for (var i = 0; i< allElements.length; i++) {
+ if (hasClass(allElements[i], className)) {
+ elemColl[elemColl.length] = allElements[i];
+ }
+ }
+ return elemColl;
+}
+
+function isParentOrSelf(element, id) {
+ if (element == null || element.nodeName=='BODY') return false;
+ else if (element.id == id) return true;
+ else return isParentOrSelf(element.parentNode, id);
+}
+
+function nodeValue(node) {
+ var result = "";
+ if (node.nodeType == 1) {
+ var children = node.childNodes;
+ for (var i = 0; i < children.length; ++i) {
+ result += nodeValue(children[i]);
+ }
+ }
+ else if (node.nodeType == 3) {
+ result = node.nodeValue;
+ }
+ return(result);
+}
+
+function slideLabel() {
+ var slideColl = GetElementsWithClassName('*','slide');
+ var list = document.getElementById('jumplist');
+ smax = slideColl.length;
+ for (var n = 0; n < smax; n++) {
+ var obj = slideColl[n];
+
+ var did = 'slide' + n.toString();
+ if (obj.getAttribute('id')) {
+ slideIDs[n] = obj.getAttribute('id');
+ }
+ else {
+ obj.setAttribute('id',did);
+ slideIDs[n] = did;
+ }
+ if (isOp) continue;
+
+ var otext = '';
+ var menu = obj.firstChild;
+ if (!menu) continue; // to cope with empty slides
+ while (menu && menu.nodeType == 3) {
+ menu = menu.nextSibling;
+ }
+ if (!menu) continue; // to cope with slides with only text nodes
+
+ var menunodes = menu.childNodes;
+ for (var o = 0; o < menunodes.length; o++) {
+ otext += nodeValue(menunodes[o]);
+ }
+ list.options[list.length] = new Option(n + ' : ' + otext, n);
+ }
+}
+
+function currentSlide() {
+ var cs;
+ var footer_nodes;
+ var vis = 'visible';
+ if (document.getElementById) {
+ cs = document.getElementById('currentSlide');
+ footer_nodes = document.getElementById('footer').childNodes;
+ } else {
+ cs = document.currentSlide;
+ footer = document.footer.childNodes;
+ }
+ cs.innerHTML = '<span id="csHere">' + snum + '<\/span> ' +
+ '<span id="csSep">\/<\/span> ' +
+ '<span id="csTotal">' + (smax-1) + '<\/span>';
+ if (snum == 0) {
+ vis = 'hidden';
+ }
+ cs.style.visibility = vis;
+ for (var i = 0; i < footer_nodes.length; i++) {
+ if (footer_nodes[i].nodeType == 1) {
+ footer_nodes[i].style.visibility = vis;
+ }
+ }
+}
+
+function go(step) {
+ if (document.getElementById('slideProj').disabled || step == 0) return;
+ var jl = document.getElementById('jumplist');
+ var cid = slideIDs[snum];
+ var ce = document.getElementById(cid);
+ if (incrementals[snum].length > 0) {
+ for (var i = 0; i < incrementals[snum].length; i++) {
+ removeClass(incrementals[snum][i], 'current');
+ removeClass(incrementals[snum][i], 'incremental');
+ }
+ }
+ if (step != 'j') {
+ snum += step;
+ lmax = smax - 1;
+ if (snum > lmax) snum = lmax;
+ if (snum < 0) snum = 0;
+ } else
+ snum = parseInt(jl.value);
+ var nid = slideIDs[snum];
+ var ne = document.getElementById(nid);
+ if (!ne) {
+ ne = document.getElementById(slideIDs[0]);
+ snum = 0;
+ }
+ if (step < 0) {incpos = incrementals[snum].length} else {incpos = 0;}
+ if (incrementals[snum].length > 0 && incpos == 0) {
+ for (var i = 0; i < incrementals[snum].length; i++) {
+ if (hasClass(incrementals[snum][i], 'current'))
+ incpos = i + 1;
+ else
+ addClass(incrementals[snum][i], 'incremental');
+ }
+ }
+ if (incrementals[snum].length > 0 && incpos > 0)
+ addClass(incrementals[snum][incpos - 1], 'current');
+ ce.style.visibility = 'hidden';
+ ne.style.visibility = 'visible';
+ jl.selectedIndex = snum;
+ currentSlide();
+ number = 0;
+}
+
+function goTo(target) {
+ if (target >= smax || target == snum) return;
+ go(target - snum);
+}
+
+function subgo(step) {
+ if (step > 0) {
+ removeClass(incrementals[snum][incpos - 1],'current');
+ removeClass(incrementals[snum][incpos], 'incremental');
+ addClass(incrementals[snum][incpos],'current');
+ incpos++;
+ } else {
+ incpos--;
+ removeClass(incrementals[snum][incpos],'current');
+ addClass(incrementals[snum][incpos], 'incremental');
+ addClass(incrementals[snum][incpos - 1],'current');
+ }
+}
+
+function toggle() {
+ var slideColl = GetElementsWithClassName('*','slide');
+ var slides = document.getElementById('slideProj');
+ var outline = document.getElementById('outlineStyle');
+ if (!slides.disabled) {
+ slides.disabled = true;
+ outline.disabled = false;
+ s5mode = false;
+ fontSize('1em');
+ for (var n = 0; n < smax; n++) {
+ var slide = slideColl[n];
+ slide.style.visibility = 'visible';
+ }
+ } else {
+ slides.disabled = false;
+ outline.disabled = true;
+ s5mode = true;
+ fontScale();
+ for (var n = 0; n < smax; n++) {
+ var slide = slideColl[n];
+ slide.style.visibility = 'hidden';
+ }
+ slideColl[snum].style.visibility = 'visible';
+ }
+}
+
+function showHide(action) {
+ var obj = GetElementsWithClassName('*','hideme')[0];
+ switch (action) {
+ case 's': obj.style.visibility = 'visible'; break;
+ case 'h': obj.style.visibility = 'hidden'; break;
+ case 'k':
+ if (obj.style.visibility != 'visible') {
+ obj.style.visibility = 'visible';
+ } else {
+ obj.style.visibility = 'hidden';
+ }
+ break;
+ }
+}
+
+// 'keys' code adapted from MozPoint (http://mozpoint.mozdev.org/)
+function keys(key) {
+ if (!key) {
+ key = event;
+ key.which = key.keyCode;
+ }
+ if (key.which == 84) {
+ toggle();
+ return;
+ }
+ if (s5mode) {
+ switch (key.which) {
+ case 10: // return
+ case 13: // enter
+ if (window.event && isParentOrSelf(window.event.srcElement, 'controls')) return;
+ if (key.target && isParentOrSelf(key.target, 'controls')) return;
+ if(number != undef) {
+ goTo(number);
+ break;
+ }
+ case 32: // spacebar
+ case 34: // page down
+ case 39: // rightkey
+ case 40: // downkey
+ if(number != undef) {
+ go(number);
+ } else if (!incrementals[snum] || incpos >= incrementals[snum].length) {
+ go(1);
+ } else {
+ subgo(1);
+ }
+ break;
+ case 33: // page up
+ case 37: // leftkey
+ case 38: // upkey
+ if(number != undef) {
+ go(-1 * number);
+ } else if (!incrementals[snum] || incpos <= 0) {
+ go(-1);
+ } else {
+ subgo(-1);
+ }
+ break;
+ case 36: // home
+ goTo(0);
+ break;
+ case 35: // end
+ goTo(smax-1);
+ break;
+ case 67: // c
+ showHide('k');
+ break;
+ }
+ if (key.which < 48 || key.which > 57) {
+ number = undef;
+ } else {
+ if (window.event && isParentOrSelf(window.event.srcElement, 'controls')) return;
+ if (key.target && isParentOrSelf(key.target, 'controls')) return;
+ number = (((number != undef) ? number : 0) * 10) + (key.which - 48);
+ }
+ }
+ return false;
+}
+
+function clicker(e) {
+ number = undef;
+ var target;
+ if (window.event) {
+ target = window.event.srcElement;
+ e = window.event;
+ } else target = e.target;
+ if (target.href != null || hasValue(target.rel, 'external') || isParentOrSelf(target, 'controls') || isParentOrSelf(target,'embed') || isParentOrSelf(target, 'object')) return true;
+ if (!e.which || e.which == 1) {
+ if (!incrementals[snum] || incpos >= incrementals[snum].length) {
+ go(1);
+ } else {
+ subgo(1);
+ }
+ }
+}
+
+function findSlide(hash) {
+ var target = document.getElementById(hash);
+ if (target) {
+ for (var i = 0; i < slideIDs.length; i++) {
+ if (target.id == slideIDs[i]) return i;
+ }
+ }
+ return null;
+}
+
+function slideJump() {
+ if (window.location.hash == null || window.location.hash == '') {
+ currentSlide();
+ return;
+ }
+ if (window.location.hash == null) return;
+ var dest = null;
+ dest = findSlide(window.location.hash.slice(1));
+ if (dest == null) {
+ dest = 0;
+ }
+ go(dest - snum);
+}
+
+function fixLinks() {
+ var thisUri = window.location.href;
+ thisUri = thisUri.slice(0, thisUri.length - window.location.hash.length);
+ var aelements = document.getElementsByTagName('A');
+ for (var i = 0; i < aelements.length; i++) {
+ var a = aelements[i].href;
+ var slideID = a.match('\#.+');
+ if ((slideID) && (slideID[0].slice(0,1) == '#')) {
+ var dest = findSlide(slideID[0].slice(1));
+ if (dest != null) {
+ if (aelements[i].addEventListener) {
+ aelements[i].addEventListener("click", new Function("e",
+ "if (document.getElementById('slideProj').disabled) return;" +
+ "go("+dest+" - snum); " +
+ "if (e.preventDefault) e.preventDefault();"), true);
+ } else if (aelements[i].attachEvent) {
+ aelements[i].attachEvent("onclick", new Function("",
+ "if (document.getElementById('slideProj').disabled) return;" +
+ "go("+dest+" - snum); " +
+ "event.returnValue = false;"));
+ }
+ }
+ }
+ }
+}
+
+function externalLinks() {
+ if (!document.getElementsByTagName) return;
+ var anchors = document.getElementsByTagName('a');
+ for (var i=0; i<anchors.length; i++) {
+ var anchor = anchors[i];
+ if (anchor.getAttribute('href') && hasValue(anchor.rel, 'external')) {
+ anchor.target = '_blank';
+ addClass(anchor,'external');
+ }
+ }
+}
+
+function createControls() {
+ var controlsDiv = document.getElementById("controls");
+ if (!controlsDiv) return;
+ var hider = ' onmouseover="showHide(\'s\');" onmouseout="showHide(\'h\');"';
+ var hideDiv, hideList = '';
+ if (controlVis == 'hidden') {
+ hideDiv = hider;
+ } else {
+ hideList = hider;
+ }
+ controlsDiv.innerHTML = '<form action="#" id="controlForm"' + hideDiv + '>' +
+ '<div id="navLinks">' +
+ '<a accesskey="t" id="toggle" href="javascript:toggle();">&#216;<\/a>' +
+ '<a accesskey="z" id="prev" href="javascript:go(-1);">&laquo;<\/a>' +
+ '<a accesskey="x" id="next" href="javascript:go(1);">&raquo;<\/a>' +
+ '<div id="navList"' + hideList + '><select id="jumplist" onchange="go(\'j\');"><\/select><\/div>' +
+ '<\/div><\/form>';
+ if (controlVis == 'hidden') {
+ var hidden = document.getElementById('navLinks');
+ } else {
+ var hidden = document.getElementById('jumplist');
+ }
+ addClass(hidden,'hideme');
+}
+
+function fontScale() { // causes layout problems in FireFox that get fixed if browser's Reload is used; same may be true of other Gecko-based browsers
+ if (!s5mode) return false;
+ var vScale = 22; // both yield 32 (after rounding) at 1024x768
+ var hScale = 32; // perhaps should auto-calculate based on theme's declared value?
+ if (window.innerHeight) {
+ var vSize = window.innerHeight;
+ var hSize = window.innerWidth;
+ } else if (document.documentElement.clientHeight) {
+ var vSize = document.documentElement.clientHeight;
+ var hSize = document.documentElement.clientWidth;
+ } else if (document.body.clientHeight) {
+ var vSize = document.body.clientHeight;
+ var hSize = document.body.clientWidth;
+ } else {
+ var vSize = 700; // assuming 1024x768, minus chrome and such
+ var hSize = 1024; // these do not account for kiosk mode or Opera Show
+ }
+ var newSize = Math.min(Math.round(vSize/vScale),Math.round(hSize/hScale));
+ fontSize(newSize + 'px');
+ if (isGe) { // hack to counter incremental reflow bugs
+ var obj = document.getElementsByTagName('body')[0];
+ obj.style.display = 'none';
+ obj.style.display = 'block';
+ }
+}
+
+function fontSize(value) {
+ if (!(s5ss = document.getElementById('s5ss'))) {
+ if (!isIE) {
+ document.getElementsByTagName('head')[0].appendChild(s5ss = document.createElement('style'));
+ s5ss.setAttribute('media','screen, projection');
+ s5ss.setAttribute('id','s5ss');
+ } else {
+ document.createStyleSheet();
+ document.s5ss = document.styleSheets[document.styleSheets.length - 1];
+ }
+ }
+ if (!isIE) {
+ while (s5ss.lastChild) s5ss.removeChild(s5ss.lastChild);
+ s5ss.appendChild(document.createTextNode('body {font-size: ' + value + ' !important;}'));
+ } else {
+ document.s5ss.addRule('body','font-size: ' + value + ' !important;');
+ }
+}
+
+function notOperaFix() {
+ slideCSS = document.getElementById('slideProj').href;
+ var slides = document.getElementById('slideProj');
+ var outline = document.getElementById('outlineStyle');
+ slides.setAttribute('media','screen');
+ outline.disabled = true;
+ if (isGe) {
+ slides.setAttribute('href','null'); // Gecko fix
+ slides.setAttribute('href',slideCSS); // Gecko fix
+ }
+ if (isIE && document.styleSheets && document.styleSheets[0]) {
+ document.styleSheets[0].addRule('img', 'behavior: url(ui/small-white/iepngfix.htc)');
+ document.styleSheets[0].addRule('div', 'behavior: url(ui/small-white/iepngfix.htc)');
+ document.styleSheets[0].addRule('.slide', 'behavior: url(ui/small-white/iepngfix.htc)');
+ }
+}
+
+function getIncrementals(obj) {
+ var incrementals = new Array();
+ if (!obj)
+ return incrementals;
+ var children = obj.childNodes;
+ for (var i = 0; i < children.length; i++) {
+ var child = children[i];
+ if (hasClass(child, 'incremental')) {
+ if (child.nodeName == 'OL' || child.nodeName == 'UL') {
+ removeClass(child, 'incremental');
+ for (var j = 0; j < child.childNodes.length; j++) {
+ if (child.childNodes[j].nodeType == 1) {
+ addClass(child.childNodes[j], 'incremental');
+ }
+ }
+ } else {
+ incrementals[incrementals.length] = child;
+ removeClass(child,'incremental');
+ }
+ }
+ if (hasClass(child, 'show-first')) {
+ if (child.nodeName == 'OL' || child.nodeName == 'UL') {
+ removeClass(child, 'show-first');
+ if (child.childNodes[isGe].nodeType == 1) {
+ removeClass(child.childNodes[isGe], 'incremental');
+ }
+ } else {
+ incrementals[incrementals.length] = child;
+ }
+ }
+ incrementals = incrementals.concat(getIncrementals(child));
+ }
+ return incrementals;
+}
+
+function createIncrementals() {
+ var incrementals = new Array();
+ for (var i = 0; i < smax; i++) {
+ incrementals[i] = getIncrementals(document.getElementById(slideIDs[i]));
+ }
+ return incrementals;
+}
+
+function defaultCheck() {
+ var allMetas = document.getElementsByTagName('meta');
+ for (var i = 0; i< allMetas.length; i++) {
+ if (allMetas[i].name == 'defaultView') {
+ defaultView = allMetas[i].content;
+ }
+ if (allMetas[i].name == 'controlVis') {
+ controlVis = allMetas[i].content;
+ }
+ }
+}
+
+// Key trap fix, new function body for trap()
+function trap(e) {
+ if (!e) {
+ e = event;
+ e.which = e.keyCode;
+ }
+ try {
+ modifierKey = e.ctrlKey || e.altKey || e.metaKey;
+ }
+ catch(e) {
+ modifierKey = false;
+ }
+ return modifierKey || e.which == 0;
+}
+
+function startup() {
+ defaultCheck();
+ if (!isOp) createControls();
+ slideLabel();
+ fixLinks();
+ externalLinks();
+ fontScale();
+ if (!isOp) {
+ notOperaFix();
+ incrementals = createIncrementals();
+ slideJump();
+ if (defaultView == 'outline') {
+ toggle();
+ }
+ document.onkeyup = keys;
+ document.onkeypress = trap;
+ document.onclick = clicker;
+ }
+}
+
+window.onload = startup;
+window.onresize = function(){setTimeout('fontScale()', 50);}
diff --git a/query-features.json b/query-features.json
new file mode 100644
index 0000000..81c5e1d
--- /dev/null
+++ b/query-features.json
@@ -0,0 +1,15 @@
+[
+ "Localized Surface Plasmon Resonance (LSPR) index",
+ "Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)",
+ "ZETA POTENTIAL [mV]",
+ "ZETA POTENTIAL Human serum (Sigma #H4522) [mV]",
+ "Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]",
+ "Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]",
+ "Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]",
+ "Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]",
+ "Polydispersity index [nm]",
+ "Polydispersity index Human serum (Sigma #H4522) [nm]",
+ "Volume Mean Hydrodynamic Diameter [nm]",
+ "Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]",
+ "Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]"
+]
diff --git a/relevant-features.json b/relevant-features.json
new file mode 100644
index 0000000..8da5f0a
--- /dev/null
+++ b/relevant-features.json
@@ -0,0 +1 @@
+{"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":{"pvalue":2.7781332789800217e-10,"r":0.5673665177300351},"ZETA POTENTIAL Change":{"pvalue":2.071052722262855e-09,"r":-0.5435850485069125},"ZETA POTENTIAL [mV]":{"pvalue":2.025461243171378e-08,"r":0.5141366184476799},"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":{"pvalue":7.296459421546331e-06,"r":0.4220954992507819},"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":{"pvalue":0.00014304093718453537,"r":0.3627394229575142},"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":{"pvalue":0.0013415551974216289,"r":0.3089691292079323},"Localized Surface Plasmon Resonance (LSPR) index Change":{"pvalue":0.0020134808685383643,"r":0.2980672974262308},"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":{"pvalue":0.009242146870015556,"r":-0.2529069909205578},"Localized Surface Plasmon Resonance (LSPR) index":{"pvalue":0.010019903744117542,"r":0.2502907155942361},"Volume Mean Hydrodynamic Diameter Change":{"pvalue":0.013109585368169974,"r":0.24139711318406543},"Polydispersity index Change":{"pvalue":0.020454612521909568,"r":-0.22597482832068308},"Volume Mean Hydrodynamic Diameter [nm]":{"pvalue":0.033722917694600785,"r":0.20744306643756433},"Polydispersity index [nm]":{"pvalue":0.04433575298419301,"r":0.19667713971723438},"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":{"pvalue":0.04474107346052025,"r":0.19631065152636545}}
diff --git a/test/predict.rb b/test/predict.rb
new file mode 100644
index 0000000..c72de02
--- /dev/null
+++ b/test/predict.rb
@@ -0,0 +1,11 @@
+require_relative "../nanoparticles.rb"
+data = JSON.parse(File.read("./data.json"))
+query_features = JSON.parse(File.read("./query-features.json"))
+key = data.keys.sample
+p key
+example = data[key]["physchem"].select{|f,v| query_features.include? f}
+prediction = predict(example)
+puts prediction[:match].collect{|id,v| v["tox"]}.first
+puts prediction[:prediction]
+puts prediction[:neighbors].size
+