From 2d51161640f6ce8407eac3b4508058b1ad23a59c Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 1 Feb 2016 10:38:21 +0100 Subject: cleaned up files. added presentation --- public/presentation/enm-workshop.html | 445 +++++++++++++++++++ public/presentation/enm-workshop.rst | 89 ++++ public/presentation/ui/small-white/blank.gif | Bin 0 -> 49 bytes public/presentation/ui/small-white/framing.css | 24 + public/presentation/ui/small-white/iepngfix.htc | 42 ++ public/presentation/ui/small-white/opera.css | 8 + public/presentation/ui/small-white/outline.css | 16 + public/presentation/ui/small-white/pretty.css | 114 +++++ public/presentation/ui/small-white/print.css | 24 + public/presentation/ui/small-white/s5-core.css | 11 + public/presentation/ui/small-white/slides.css | 10 + public/presentation/ui/small-white/slides.js | 558 ++++++++++++++++++++++++ 12 files changed, 1341 insertions(+) create mode 100644 public/presentation/enm-workshop.html create mode 100644 public/presentation/enm-workshop.rst create mode 100644 public/presentation/ui/small-white/blank.gif create mode 100644 public/presentation/ui/small-white/framing.css create mode 100644 public/presentation/ui/small-white/iepngfix.htc create mode 100644 public/presentation/ui/small-white/opera.css create mode 100644 public/presentation/ui/small-white/outline.css create mode 100644 public/presentation/ui/small-white/pretty.css create mode 100644 public/presentation/ui/small-white/print.css create mode 100644 public/presentation/ui/small-white/s5-core.css create mode 100644 public/presentation/ui/small-white/slides.css create mode 100644 public/presentation/ui/small-white/slides.js (limited to 'public') diff --git a/public/presentation/enm-workshop.html b/public/presentation/enm-workshop.html new file mode 100644 index 0000000..f0c6781 --- /dev/null +++ b/public/presentation/enm-workshop.html @@ -0,0 +1,445 @@ + + + + + + + +Read across toxicity predictions with nano-lazar + + + + + + + + + + + + + + +

+

+

+ + +

+

+

+

Read across toxicity predictions with nano-lazar

+ +

Christoph Helma

+

in silico toxicology gmbh

+

+ +

+

+

Requirements

+

Nanoparticle characterisation
Toxicity measurements

+

+

+

eNanoMapper data import

+

Nanoparticles imported: 464
Nanoparticles with particle characterisation: 394
Nanoparticles with toxicity data: 167
Nanoparticles with toxicity data and particle characterisation: 160

+

+

+

eNanoMapper toxicity endpoints

+

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

+

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/public/presentation/enm-workshop.rst b/public/presentation/enm-workshop.rst new file mode 100644 index 0000000..26a3524 --- /dev/null +++ b/public/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/public/presentation/ui/small-white/blank.gif b/public/presentation/ui/small-white/blank.gif new file mode 100644 index 0000000..75b945d Binary files /dev/null and b/public/presentation/ui/small-white/blank.gif differ diff --git a/public/presentation/ui/small-white/framing.css b/public/presentation/ui/small-white/framing.css new file mode 100644 index 0000000..70287dd --- /dev/null +++ b/public/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%; 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+ +/* 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/public/presentation/ui/small-white/slides.js b/public/presentation/ui/small-white/slides.js new file mode 100644 index 0000000..87c30c6 --- /dev/null +++ b/public/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 = '' + snum + '<\/span> ' + + '\/<\/span> ' + + '' + (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' + + '

' + + 'Ø<\/a>' + + '«<\/a>' + + '»<\/a>' + + '