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diff --git a/data.json b/data.json deleted file mode 100644 index 5d38cc4..0000000 --- a/data.json +++ /dev/null @@ -1 +0,0 @@ -{"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 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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 deleted file mode 100644 index d3399e9..0000000 --- a/nanoparticles.rb +++ /dev/null @@ -1,182 +0,0 @@ -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 deleted file mode 100644 index f0c6781..0000000 --- a/presentation/enm-workshop.html +++ /dev/null @@ -1,445 +0,0 @@ -<?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"> - -/* 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-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 deleted file mode 100644 index 26a3524..0000000 --- a/presentation/enm-workshop.rst +++ /dev/null @@ -1,89 +0,0 @@ -.. |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 Binary files differdeleted file mode 100644 index 75b945d..0000000 --- a/presentation/ui/small-white/blank.gif +++ /dev/null diff --git a/presentation/ui/small-white/framing.css b/presentation/ui/small-white/framing.css deleted file mode 100644 index 70287dd..0000000 --- a/presentation/ui/small-white/framing.css +++ /dev/null @@ -1,24 +0,0 @@ -/* 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;} -.slide {top: 0; width: 92%; padding: 1em 4% 0 4%; z-index: 2;} -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;} -div#currentSlide {background: #FFC;} -*/ diff --git a/presentation/ui/small-white/iepngfix.htc b/presentation/ui/small-white/iepngfix.htc deleted file mode 100644 index 2a44681..0000000 --- a/presentation/ui/small-white/iepngfix.htc +++ /dev/null @@ -1,42 +0,0 @@ -<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 deleted file mode 100644 index c9d1148..0000000 --- a/presentation/ui/small-white/opera.css +++ /dev/null @@ -1,8 +0,0 @@ -/* 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 deleted file mode 100644 index fa767e2..0000000 --- a/presentation/ui/small-white/outline.css +++ /dev/null @@ -1,16 +0,0 @@ -/* 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 deleted file mode 100644 index ba988e1..0000000 --- a/presentation/ui/small-white/pretty.css +++ /dev/null @@ -1,114 +0,0 @@ -/* 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 deleted file mode 100644 index 9d057cc..0000000 --- a/presentation/ui/small-white/print.css +++ /dev/null @@ -1,24 +0,0 @@ -/* 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 deleted file mode 100644 index 6965f5e..0000000 --- a/presentation/ui/small-white/s5-core.css +++ /dev/null @@ -1,11 +0,0 @@ -/* 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 deleted file mode 100644 index 82bdc0e..0000000 --- a/presentation/ui/small-white/slides.css +++ /dev/null @@ -1,10 +0,0 @@ -/* 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 deleted file mode 100644 index 87c30c6..0000000 --- a/presentation/ui/small-white/slides.js +++ /dev/null @@ -1,558 +0,0 @@ -// 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();">Ø<\/a>' + - '<a accesskey="z" id="prev" href="javascript:go(-1);">«<\/a>' + - '<a accesskey="x" id="next" href="javascript:go(1);">»<\/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 deleted file mode 100644 index 81c5e1d..0000000 --- a/query-features.json +++ /dev/null @@ -1,15 +0,0 @@ -[ - "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 deleted file mode 100644 index 8da5f0a..0000000 --- a/relevant-features.json +++ /dev/null @@ -1 +0,0 @@ -{"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 deleted file mode 100644 index c72de02..0000000 --- a/test/predict.rb +++ /dev/null @@ -1,11 +0,0 @@ -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 - |
