summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorMicha Rautenberg <rautenberg@in-silico.ch>2016-07-12 10:23:12 +0200
committerMicha Rautenberg <rautenberg@in-silico.ch>2016-07-12 10:23:12 +0200
commit0e706214e89a66439228ebabb7fe116ecd081f59 (patch)
tree029b250337d5c48ea6c88a1c0b679d5fe7efabb8
parentca350a4652d35911d695d1ad21624245dac83d00 (diff)
Add in-silico-methods 2012 presentation
Diffstat
-rw-r--r--public/presentations/in-silico-methods12/in-silico-methods.html569
-rw-r--r--public/presentations/in-silico-methods12/in-silico-methods.rst221
-rw-r--r--public/presentations/in-silico-methods12/index.html569
-rw-r--r--public/presentations/in-silico-methods12/lazar-input.pngbin0 -> 54827 bytes
-rw-r--r--public/presentations/in-silico-methods12/lazar-output1.pngbin0 -> 39072 bytes
-rw-r--r--public/presentations/in-silico-methods12/lazar-output2.pngbin0 -> 60856 bytes
-rw-r--r--public/presentations/in-silico-methods12/lazar-output3.pngbin0 -> 54945 bytes
-rw-r--r--public/presentations/in-silico-methods12/ui/.DS_Storebin0 -> 6148 bytes
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/blank.gifbin0 -> 49 bytes
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/framing.css24
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/iepngfix.htc42
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/opera.css8
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/outline.css16
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/pretty.css115
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/print.css24
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/s5-core.css11
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/slides.css10
-rw-r--r--public/presentations/in-silico-methods12/ui/small-white/slides.js558
-rw-r--r--views/presentations.haml3
19 files changed, 2170 insertions, 0 deletions
diff --git a/public/presentations/in-silico-methods12/in-silico-methods.html b/public/presentations/in-silico-methods12/in-silico-methods.html
new file mode 100644
index 0000000..189761c
--- /dev/null
+++ b/public/presentations/in-silico-methods12/in-silico-methods.html
@@ -0,0 +1,569 @@
+<?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 0.9.1: http://docutils.sourceforge.net/" />
+<meta name="version" content="S5 1.1" />
+<title>In silico methods for toxicity prediction</title>
+<meta name="author" content="Christoph Helma" />
+<meta name="date" content="2012-10-04" />
+<style type="text/css">
+
+/*
+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 7434 2012-05-11 21:06:27Z 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 }
+
+div.admonition p.admonition-title, div.hint p.admonition-title,
+div.important p.admonition-title, div.note p.admonition-title,
+div.tip p.admonition-title {
+ 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 {
+ 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 }
+*/
+
+div.dedication {
+ margin: 2em 5em ;
+ text-align: center ;
+ font-style: italic }
+
+div.dedication p.topic-title {
+ font-weight: bold ;
+ font-style: normal }
+
+div.figure {
+ margin-left: 2em ;
+ margin-right: 2em }
+
+div.footer, div.header {
+ clear: both;
+ font-size: smaller }
+
+div.line-block {
+ display: block ;
+ margin-top: 1em ;
+ margin-bottom: 1em }
+
+div.line-block div.line-block {
+ margin-top: 0 ;
+ margin-bottom: 0 ;
+ margin-left: 1.5em }
+
+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 */
+div.align-right {
+ text-align: inherit }
+
+/* div.align-center * { */
+/* text-align: left } */
+
+ol.simple, ul.simple {
+ margin-bottom: 1em }
+
+ol.arabic {
+ list-style: decimal }
+
+ol.loweralpha {
+ list-style: lower-alpha }
+
+ol.upperalpha {
+ list-style: upper-alpha }
+
+ol.lowerroman {
+ list-style: lower-roman }
+
+ol.upperroman {
+ list-style: upper-roman }
+
+p.attribution {
+ text-align: right ;
+ margin-left: 50% }
+
+p.caption {
+ font-style: italic }
+
+p.credits {
+ font-style: italic ;
+ font-size: smaller }
+
+p.label {
+ white-space: nowrap }
+
+p.rubric {
+ font-weight: bold ;
+ font-size: larger ;
+ color: maroon ;
+ text-align: center }
+
+p.sidebar-title {
+ font-family: sans-serif ;
+ font-weight: bold ;
+ font-size: larger }
+
+p.sidebar-subtitle {
+ font-family: sans-serif ;
+ font-weight: bold }
+
+p.topic-title {
+ font-weight: bold }
+
+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 { /* line numbers */
+ color: grey;
+}
+
+.code {
+ background-color: #eeeeee
+}
+
+span.classifier {
+ font-family: sans-serif ;
+ font-style: oblique }
+
+span.classifier-delimiter {
+ font-family: sans-serif ;
+ font-weight: bold }
+
+span.interpreted {
+ font-family: sans-serif }
+
+span.option {
+ white-space: nowrap }
+
+span.pre {
+ white-space: pre }
+
+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 }
+
+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>In silico methods for toxicity prediction</h1>
+<h2>2012-10-04 <em>in silico</em> toxicology gmbh</h2>
+</div>
+</div>
+<div class="presentation">
+<div class="slide" id="slide0">
+<h1 class="title">In silico methods for toxicity prediction</h1>
+<table class="docinfo" frame="void" rules="none">
+<col class="docinfo-name" />
+<col class="docinfo-content" />
+<tbody valign="top">
+<tr><th class="docinfo-name">Author:</th>
+<td>Christoph Helma</td></tr>
+<tr class="field"><th class="docinfo-name">Affiliation:</th><td class="field-body">in silico toxicology gmbh</td>
+</tr>
+<tr><th class="docinfo-name">Date:</th>
+<td>2012-10-04</td></tr>
+</tbody>
+</table>
+
+</div>
+<div class="slide" id="outline">
+<h1>Outline</h1>
+<ul class="incremental simple">
+<li>In silico toxicology methods</li>
+<li>Lazar framework</li>
+<li>Products and services</li>
+</ul>
+</div>
+<div class="slide" id="in-silico-methods">
+<h1>In silico methods</h1>
+<ul class="incremental simple">
+<li>Systems biology/molecular modeling</li>
+<li>Expert systems</li>
+<li>Data driven techniques</li>
+</ul>
+</div>
+<div class="slide" id="systems-biology-molecular-modeling">
+<h1>Systems biology/molecular modeling</h1>
+<p>Model individual events (e.g. receptor interactions, (de)toxification) of the <em>adverse outcome pathway</em></p>
+<ul class="incremental small green simple">
+<li>Mechanistic interpretation</li>
+</ul>
+<ul class="incremental small red simple">
+<li>Calculations/simulations may be very time consuming</li>
+<li>May require a lot of experimental data for parameterization</li>
+<li>Impossible to model mechanisms of complex toxicological endpoints</li>
+</ul>
+<p>Examples: VirtualToxLab/Biograf</p>
+</div>
+<div class="slide" id="expert-systems">
+<h1>Expert systems</h1>
+<p>Formalize expert knowledge about chemicals and toxicity mechanisms and create a software program</p>
+<ul class="incremental small green simple">
+<li>Mechanistic interpretation</li>
+</ul>
+<ul class="incremental small red simple">
+<li>Model creation very time consuming</li>
+<li>Many toxicity mechanisms are poorly understood or even unknown</li>
+<li>Error prone and hard to validate (strong tendency towards overfitting)</li>
+</ul>
+<p>Examples: Derek/Lhasa</p>
+</div>
+<div class="slide" id="data-driven">
+<h1>Data driven</h1>
+<p>Use all existing data for a particular endpoint and apply machine learning/QSAR algorithms in order to create a prediction model</p>
+<ul class="incremental small green simple">
+<li>Comparably fast</li>
+<li>Applicable for every endpoint with sufficient experimental data</li>
+<li>Sound validation possible</li>
+</ul>
+<ul class="incremental small red simple">
+<li>Applicability domain/model quality depends on experimental data</li>
+<li>Mechanistic relevance has to be extracted from models/descriptors/predictions</li>
+</ul>
+<p>Examples: Classical QSARs, Topkat, Multicase, lazar</p>
+</div>
+<div class="slide" id="lazy-structure-activity-relationships-lazar">
+<h1>Lazy-Structure-Activity Relationships (lazar)</h1>
+<p>Automated read across predictions</p>
+<ul class="incremental small simple">
+<li>Find <em>similar</em> compounds (=neighbors) with measured activities</li>
+<li>Create a local (Q)SAR model with neighbors as training compounds</li>
+<li>Make a prediction with this model</li>
+</ul>
+<p class="incremental">Lazar estimates the confidence (<em>applicability domain</em>) for each prediction</p>
+</div>
+<div class="slide" id="chemical-similarity">
+<h1>Chemical Similarity</h1>
+<p>Can be based on</p>
+<ul class="incremental simple">
+<li>Chemical structures</li>
+<li>Chemical properties</li>
+<li>Biological properties</li>
+<li>...</li>
+</ul>
+<p class="incremental">Lazar uses <em>activity specific similarities</em></p>
+</div>
+<div class="slide" id="activity-specific-similarities">
+<h1>Activity specific similarities</h1>
+<p>Consider only <em>relevant</em> (i.e. statistically significant) substructures, properties, ... for similarity calculations</p>
+<p>Algorithms for finding relevant substructures (by A. Maunz):</p>
+<ul class="simple">
+<li>Backbone refinement classes (BBRC)</li>
+<li>Latent structure mining (LAST)</li>
+</ul>
+</div>
+<div class="slide" id="http-lazar-in-silico-ch">
+<h1><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></h1>
+<img alt="lazar-input.png" class="align-center" src="lazar-input.png" style="height: 13em;" />
+</div>
+<div class="slide" id="id1">
+<h1><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></h1>
+<img alt="lazar-output1.png" class="align-center" src="lazar-output1.png" style="height: 13em;" />
+</div>
+<div class="slide" id="id2">
+<h1><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></h1>
+<img alt="lazar-output2.png" class="align-center" src="lazar-output2.png" style="height: 13em;" />
+</div>
+<div class="slide" id="id3">
+<h1><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></h1>
+<img alt="lazar-output3.png" class="align-center" src="lazar-output3.png" style="height: 13em;" />
+</div>
+<div class="slide" id="lazar-limitations">
+<h1>Lazar limitations</h1>
+<ul class="incremental simple">
+<li>Model quality depends on data quality</li>
+<li>Applicability domain depends on learning instances</li>
+</ul>
+</div>
+<div class="slide" id="in-silico-toxicology-gmbh">
+<h1>in silico toxicology gmbh</h1>
+<p>Open source software and algorithm development</p>
+<ul class="incremental simple">
+<li>Predictive toxicology and QSAR models</li>
+<li>Toxicological data mining</li>
+<li>Life science webservices and data warehouses</li>
+</ul>
+</div>
+<div class="slide" id="why-open-source">
+<h1>Why open source?</h1>
+<ul class="incremental simple">
+<li>Clear and unambiguous documentation of implemented algorithms essential for scientific software (also required by many regulatory guidelines)</li>
+<li>Collaboration with partners, projects and external contributors</li>
+<li>Establishment of international standards</li>
+<li>Security of investment</li>
+</ul>
+</div>
+<div class="slide" id="eu-research-projects-fp6-7">
+<h1>EU Research projects (FP6/7)</h1>
+<table class="small docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Sens-it-iv:</th><td class="field-body">Novel testing strategies for in vitro assessment of allergens</td>
+</tr>
+<tr class="field"><th class="field-name">Scarlet:</th><td class="field-body">Network on in silico methods for carcinogenicity and mutagenicity</td>
+</tr>
+<tr class="field"><th class="field-name">OpenTox:</th><td class="field-body">Open source framework for predictive toxicology</td>
+</tr>
+<tr class="field"><th class="field-name">ToxBank:</th><td class="field-body">Integrated data analysis and servicing of alternative testing methods in toxicology</td>
+</tr>
+<tr class="field"><th class="field-name">ModNanoTox:</th><td class="field-body">Modelling toxicity behaviour of engineered nanoparticles</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="slide" id="free-products-and-services">
+<h1>Free products and services</h1>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name" colspan="2">Lazar application:</th></tr>
+<tr class="field"><td>&nbsp;</td><td class="field-body"><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></td>
+</tr>
+<tr class="field"><th class="field-name" colspan="2">OpenTox Webservices:</th></tr>
+<tr class="field"><td>&nbsp;</td><td class="field-body"><a class="reference external" href="http://webservices.in-silico.ch">http://webservices.in-silico.ch</a></td>
+</tr>
+<tr class="field"><th class="field-name">Source code:</th><td class="field-body"><a class="reference external" href="https://github.com/opentox">https://github.com/opentox</a></td>
+</tr>
+</tbody>
+</table>
+<p>Issue tracker, documentation, ...</p>
+</div>
+<div class="slide" id="commercial-products-and-services">
+<h1>Commercial products and services</h1>
+<ul class="incremental simple">
+<li>Lazar &quot;software as a service&quot; (SaaS): secure access for confidential predictions, batch predictions, ...</li>
+<li>Virtual appliances with lazar software for in-house/desktop installation</li>
+<li>Installation services</li>
+<li>Phone and email support</li>
+</ul>
+</div>
+<div class="slide" id="id4">
+<h1>Commercial products and services</h1>
+<ul class="incremental simple">
+<li>Virtual toxicity screening of compounds and libraries</li>
+<li>Development of prediction models for new endpoints</li>
+<li>Scientific programming, contract research and consulting</li>
+</ul>
+</div>
+<div class="slide" id="contact">
+<h1>Contact</h1>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Web:</th><td class="field-body"><a class="reference external" href="http://www.in-silico.ch">http://www.in-silico.ch</a></td>
+</tr>
+<tr class="field"><th class="field-name">Email:</th><td class="field-body"><a class="reference external" href="mailto:helma&#64;in-silico.ch">helma&#64;in-silico.ch</a></td>
+</tr>
+</tbody>
+</table>
+</div>
+</div>
+</body>
+</html>
diff --git a/public/presentations/in-silico-methods12/in-silico-methods.rst b/public/presentations/in-silico-methods12/in-silico-methods.rst
new file mode 100644
index 0000000..33f5884
--- /dev/null
+++ b/public/presentations/in-silico-methods12/in-silico-methods.rst
@@ -0,0 +1,221 @@
+=========================================
+In silico methods for toxicity prediction
+=========================================
+
+:Author: Christoph Helma
+:Affiliation: in silico toxicology gmbh
+:Date: 2012-10-04
+
+.. footer:: 2012-10-04 *in silico* toxicology gmbh
+
+Outline
+=======
+
+.. class:: incremental
+
+- In silico toxicology methods
+- Lazar framework
+- Products and services
+
+In silico methods
+=================
+.. class:: incremental
+
+- Systems biology/molecular modeling
+- Expert systems
+- Data driven techniques
+
+Systems biology/molecular modeling
+====================================
+
+Model individual events (e.g. receptor interactions, (de)toxification) of the *adverse outcome pathway*
+
+.. class:: incremental small green
+
+- Mechanistic interpretation
+
+.. class:: incremental small red
+
+- Calculations/simulations may be very time consuming
+- May require a lot of experimental data for parameterization
+- Impossible to model mechanisms of complex toxicological endpoints
+
+Examples: VirtualToxLab/Biograf
+
+Expert systems
+==============
+
+Formalize expert knowledge about chemicals and toxicity mechanisms and create a software program
+
+.. class:: incremental small green
+
+- Mechanistic interpretation
+
+.. class:: incremental small red
+
+- Model creation very time consuming
+- Many toxicity mechanisms are poorly understood or even unknown
+- Error prone and hard to validate (strong tendency towards overfitting)
+
+Examples: Derek/Lhasa
+
+Data driven
+===========
+
+Use all existing data for a particular endpoint and apply machine learning/QSAR algorithms in order to create a prediction model
+
+.. class:: incremental small green
+
+- Comparably fast
+- Applicable for every endpoint with sufficient experimental data
+- Sound validation possible
+
+.. class:: incremental small red
+
+- Applicability domain/model quality depends on experimental data
+- Mechanistic relevance has to be extracted from models/descriptors/predictions
+
+Examples: Classical QSARs, Topkat, Multicase, lazar
+
+Lazy-Structure-Activity Relationships (lazar)
+=============================================
+
+Automated read across predictions
+
+.. class:: incremental small
+
+- Find *similar* compounds (=neighbors) with measured activities
+- Create a local (Q)SAR model with neighbors as training compounds
+- Make a prediction with this model
+
+.. class:: incremental
+
+Lazar estimates the confidence (*applicability domain*) for each prediction
+
+Chemical Similarity
+===================
+
+Can be based on
+
+.. class:: incremental
+
+- Chemical structures
+- Chemical properties
+- Biological properties
+- ...
+
+.. class:: incremental
+
+Lazar uses *activity specific similarities*
+
+Activity specific similarities
+==============================
+
+Consider only *relevant* (i.e. statistically significant) substructures, properties, ... for similarity calculations
+
+Algorithms for finding relevant substructures (by A. Maunz):
+
+- Backbone refinement classes (BBRC)
+- Latent structure mining (LAST)
+
+http://lazar.in-silico.ch
+=========================
+
+.. image:: lazar-input.png
+ :height: 13em
+ :align: center
+
+http://lazar.in-silico.ch
+=========================
+
+.. image:: lazar-output1.png
+ :height: 13em
+ :align: center
+
+http://lazar.in-silico.ch
+=========================
+
+.. image:: lazar-output2.png
+ :height: 13em
+ :align: center
+
+http://lazar.in-silico.ch
+=========================
+
+.. image:: lazar-output3.png
+ :height: 13em
+ :align: center
+
+Lazar limitations
+=================
+
+.. class:: incremental
+
+- Model quality depends on data quality
+- Applicability domain depends on learning instances
+
+in silico toxicology gmbh
+=========================
+
+Open source software and algorithm development
+
+.. class:: incremental
+
+- Predictive toxicology and QSAR models
+- Toxicological data mining
+- Life science webservices and data warehouses
+
+Why open source?
+================
+
+.. class:: incremental
+
+- Clear and unambiguous documentation of implemented algorithms essential for scientific software (also required by many regulatory guidelines)
+- Collaboration with partners, projects and external contributors
+- Establishment of international standards
+- Security of investment
+
+EU Research projects (FP6/7)
+============================
+
+.. class:: small
+
+:Sens-it-iv: Novel testing strategies for in vitro assessment of allergens
+:Scarlet: Network on in silico methods for carcinogenicity and mutagenicity
+:OpenTox: Open source framework for predictive toxicology
+:ToxBank: Integrated data analysis and servicing of alternative testing methods in toxicology
+:ModNanoTox: Modelling toxicity behaviour of engineered nanoparticles
+
+Free products and services
+==========================
+
+:Lazar application: http://lazar.in-silico.ch
+:OpenTox Webservices: http://webservices.in-silico.ch
+:Source code: https://github.com/opentox
+
+Issue tracker, documentation, ...
+
+Commercial products and services
+================================
+
+.. class:: incremental
+
+- Lazar "software as a service" (SaaS): secure access for confidential predictions, batch predictions, ...
+- Virtual appliances with lazar software for in-house/desktop installation
+- Installation services
+- Phone and email support
+
+Commercial products and services
+================================
+
+.. class:: incremental
+
+- Virtual toxicity screening of compounds and libraries
+- Development of prediction models for new endpoints
+- Scientific programming, contract research and consulting
+
+Contact
+=======
+
+:Web: http://www.in-silico.ch
+:Email: helma@in-silico.ch
diff --git a/public/presentations/in-silico-methods12/index.html b/public/presentations/in-silico-methods12/index.html
new file mode 100644
index 0000000..189761c
--- /dev/null
+++ b/public/presentations/in-silico-methods12/index.html
@@ -0,0 +1,569 @@
+<?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 0.9.1: http://docutils.sourceforge.net/" />
+<meta name="version" content="S5 1.1" />
+<title>In silico methods for toxicity prediction</title>
+<meta name="author" content="Christoph Helma" />
+<meta name="date" content="2012-10-04" />
+<style type="text/css">
+
+/*
+:Author: David Goodger (goodger@python.org)
+:Id: $Id: html4css1.css 7434 2012-05-11 21:06:27Z 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 }
+
+div.admonition p.admonition-title, div.hint p.admonition-title,
+div.important p.admonition-title, div.note p.admonition-title,
+div.tip p.admonition-title {
+ 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 {
+ 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 }
+*/
+
+div.dedication {
+ margin: 2em 5em ;
+ text-align: center ;
+ font-style: italic }
+
+div.dedication p.topic-title {
+ font-weight: bold ;
+ font-style: normal }
+
+div.figure {
+ margin-left: 2em ;
+ margin-right: 2em }
+
+div.footer, div.header {
+ clear: both;
+ font-size: smaller }
+
+div.line-block {
+ display: block ;
+ margin-top: 1em ;
+ margin-bottom: 1em }
+
+div.line-block div.line-block {
+ margin-top: 0 ;
+ margin-bottom: 0 ;
+ margin-left: 1.5em }
+
+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 */
+div.align-right {
+ text-align: inherit }
+
+/* div.align-center * { */
+/* text-align: left } */
+
+ol.simple, ul.simple {
+ margin-bottom: 1em }
+
+ol.arabic {
+ list-style: decimal }
+
+ol.loweralpha {
+ list-style: lower-alpha }
+
+ol.upperalpha {
+ list-style: upper-alpha }
+
+ol.lowerroman {
+ list-style: lower-roman }
+
+ol.upperroman {
+ list-style: upper-roman }
+
+p.attribution {
+ text-align: right ;
+ margin-left: 50% }
+
+p.caption {
+ font-style: italic }
+
+p.credits {
+ font-style: italic ;
+ font-size: smaller }
+
+p.label {
+ white-space: nowrap }
+
+p.rubric {
+ font-weight: bold ;
+ font-size: larger ;
+ color: maroon ;
+ text-align: center }
+
+p.sidebar-title {
+ font-family: sans-serif ;
+ font-weight: bold ;
+ font-size: larger }
+
+p.sidebar-subtitle {
+ font-family: sans-serif ;
+ font-weight: bold }
+
+p.topic-title {
+ font-weight: bold }
+
+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 { /* line numbers */
+ color: grey;
+}
+
+.code {
+ background-color: #eeeeee
+}
+
+span.classifier {
+ font-family: sans-serif ;
+ font-style: oblique }
+
+span.classifier-delimiter {
+ font-family: sans-serif ;
+ font-weight: bold }
+
+span.interpreted {
+ font-family: sans-serif }
+
+span.option {
+ white-space: nowrap }
+
+span.pre {
+ white-space: pre }
+
+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 }
+
+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>In silico methods for toxicity prediction</h1>
+<h2>2012-10-04 <em>in silico</em> toxicology gmbh</h2>
+</div>
+</div>
+<div class="presentation">
+<div class="slide" id="slide0">
+<h1 class="title">In silico methods for toxicity prediction</h1>
+<table class="docinfo" frame="void" rules="none">
+<col class="docinfo-name" />
+<col class="docinfo-content" />
+<tbody valign="top">
+<tr><th class="docinfo-name">Author:</th>
+<td>Christoph Helma</td></tr>
+<tr class="field"><th class="docinfo-name">Affiliation:</th><td class="field-body">in silico toxicology gmbh</td>
+</tr>
+<tr><th class="docinfo-name">Date:</th>
+<td>2012-10-04</td></tr>
+</tbody>
+</table>
+
+</div>
+<div class="slide" id="outline">
+<h1>Outline</h1>
+<ul class="incremental simple">
+<li>In silico toxicology methods</li>
+<li>Lazar framework</li>
+<li>Products and services</li>
+</ul>
+</div>
+<div class="slide" id="in-silico-methods">
+<h1>In silico methods</h1>
+<ul class="incremental simple">
+<li>Systems biology/molecular modeling</li>
+<li>Expert systems</li>
+<li>Data driven techniques</li>
+</ul>
+</div>
+<div class="slide" id="systems-biology-molecular-modeling">
+<h1>Systems biology/molecular modeling</h1>
+<p>Model individual events (e.g. receptor interactions, (de)toxification) of the <em>adverse outcome pathway</em></p>
+<ul class="incremental small green simple">
+<li>Mechanistic interpretation</li>
+</ul>
+<ul class="incremental small red simple">
+<li>Calculations/simulations may be very time consuming</li>
+<li>May require a lot of experimental data for parameterization</li>
+<li>Impossible to model mechanisms of complex toxicological endpoints</li>
+</ul>
+<p>Examples: VirtualToxLab/Biograf</p>
+</div>
+<div class="slide" id="expert-systems">
+<h1>Expert systems</h1>
+<p>Formalize expert knowledge about chemicals and toxicity mechanisms and create a software program</p>
+<ul class="incremental small green simple">
+<li>Mechanistic interpretation</li>
+</ul>
+<ul class="incremental small red simple">
+<li>Model creation very time consuming</li>
+<li>Many toxicity mechanisms are poorly understood or even unknown</li>
+<li>Error prone and hard to validate (strong tendency towards overfitting)</li>
+</ul>
+<p>Examples: Derek/Lhasa</p>
+</div>
+<div class="slide" id="data-driven">
+<h1>Data driven</h1>
+<p>Use all existing data for a particular endpoint and apply machine learning/QSAR algorithms in order to create a prediction model</p>
+<ul class="incremental small green simple">
+<li>Comparably fast</li>
+<li>Applicable for every endpoint with sufficient experimental data</li>
+<li>Sound validation possible</li>
+</ul>
+<ul class="incremental small red simple">
+<li>Applicability domain/model quality depends on experimental data</li>
+<li>Mechanistic relevance has to be extracted from models/descriptors/predictions</li>
+</ul>
+<p>Examples: Classical QSARs, Topkat, Multicase, lazar</p>
+</div>
+<div class="slide" id="lazy-structure-activity-relationships-lazar">
+<h1>Lazy-Structure-Activity Relationships (lazar)</h1>
+<p>Automated read across predictions</p>
+<ul class="incremental small simple">
+<li>Find <em>similar</em> compounds (=neighbors) with measured activities</li>
+<li>Create a local (Q)SAR model with neighbors as training compounds</li>
+<li>Make a prediction with this model</li>
+</ul>
+<p class="incremental">Lazar estimates the confidence (<em>applicability domain</em>) for each prediction</p>
+</div>
+<div class="slide" id="chemical-similarity">
+<h1>Chemical Similarity</h1>
+<p>Can be based on</p>
+<ul class="incremental simple">
+<li>Chemical structures</li>
+<li>Chemical properties</li>
+<li>Biological properties</li>
+<li>...</li>
+</ul>
+<p class="incremental">Lazar uses <em>activity specific similarities</em></p>
+</div>
+<div class="slide" id="activity-specific-similarities">
+<h1>Activity specific similarities</h1>
+<p>Consider only <em>relevant</em> (i.e. statistically significant) substructures, properties, ... for similarity calculations</p>
+<p>Algorithms for finding relevant substructures (by A. Maunz):</p>
+<ul class="simple">
+<li>Backbone refinement classes (BBRC)</li>
+<li>Latent structure mining (LAST)</li>
+</ul>
+</div>
+<div class="slide" id="http-lazar-in-silico-ch">
+<h1><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></h1>
+<img alt="lazar-input.png" class="align-center" src="lazar-input.png" style="height: 13em;" />
+</div>
+<div class="slide" id="id1">
+<h1><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></h1>
+<img alt="lazar-output1.png" class="align-center" src="lazar-output1.png" style="height: 13em;" />
+</div>
+<div class="slide" id="id2">
+<h1><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></h1>
+<img alt="lazar-output2.png" class="align-center" src="lazar-output2.png" style="height: 13em;" />
+</div>
+<div class="slide" id="id3">
+<h1><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></h1>
+<img alt="lazar-output3.png" class="align-center" src="lazar-output3.png" style="height: 13em;" />
+</div>
+<div class="slide" id="lazar-limitations">
+<h1>Lazar limitations</h1>
+<ul class="incremental simple">
+<li>Model quality depends on data quality</li>
+<li>Applicability domain depends on learning instances</li>
+</ul>
+</div>
+<div class="slide" id="in-silico-toxicology-gmbh">
+<h1>in silico toxicology gmbh</h1>
+<p>Open source software and algorithm development</p>
+<ul class="incremental simple">
+<li>Predictive toxicology and QSAR models</li>
+<li>Toxicological data mining</li>
+<li>Life science webservices and data warehouses</li>
+</ul>
+</div>
+<div class="slide" id="why-open-source">
+<h1>Why open source?</h1>
+<ul class="incremental simple">
+<li>Clear and unambiguous documentation of implemented algorithms essential for scientific software (also required by many regulatory guidelines)</li>
+<li>Collaboration with partners, projects and external contributors</li>
+<li>Establishment of international standards</li>
+<li>Security of investment</li>
+</ul>
+</div>
+<div class="slide" id="eu-research-projects-fp6-7">
+<h1>EU Research projects (FP6/7)</h1>
+<table class="small docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Sens-it-iv:</th><td class="field-body">Novel testing strategies for in vitro assessment of allergens</td>
+</tr>
+<tr class="field"><th class="field-name">Scarlet:</th><td class="field-body">Network on in silico methods for carcinogenicity and mutagenicity</td>
+</tr>
+<tr class="field"><th class="field-name">OpenTox:</th><td class="field-body">Open source framework for predictive toxicology</td>
+</tr>
+<tr class="field"><th class="field-name">ToxBank:</th><td class="field-body">Integrated data analysis and servicing of alternative testing methods in toxicology</td>
+</tr>
+<tr class="field"><th class="field-name">ModNanoTox:</th><td class="field-body">Modelling toxicity behaviour of engineered nanoparticles</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="slide" id="free-products-and-services">
+<h1>Free products and services</h1>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name" colspan="2">Lazar application:</th></tr>
+<tr class="field"><td>&nbsp;</td><td class="field-body"><a class="reference external" href="http://lazar.in-silico.ch">http://lazar.in-silico.ch</a></td>
+</tr>
+<tr class="field"><th class="field-name" colspan="2">OpenTox Webservices:</th></tr>
+<tr class="field"><td>&nbsp;</td><td class="field-body"><a class="reference external" href="http://webservices.in-silico.ch">http://webservices.in-silico.ch</a></td>
+</tr>
+<tr class="field"><th class="field-name">Source code:</th><td class="field-body"><a class="reference external" href="https://github.com/opentox">https://github.com/opentox</a></td>
+</tr>
+</tbody>
+</table>
+<p>Issue tracker, documentation, ...</p>
+</div>
+<div class="slide" id="commercial-products-and-services">
+<h1>Commercial products and services</h1>
+<ul class="incremental simple">
+<li>Lazar &quot;software as a service&quot; (SaaS): secure access for confidential predictions, batch predictions, ...</li>
+<li>Virtual appliances with lazar software for in-house/desktop installation</li>
+<li>Installation services</li>
+<li>Phone and email support</li>
+</ul>
+</div>
+<div class="slide" id="id4">
+<h1>Commercial products and services</h1>
+<ul class="incremental simple">
+<li>Virtual toxicity screening of compounds and libraries</li>
+<li>Development of prediction models for new endpoints</li>
+<li>Scientific programming, contract research and consulting</li>
+</ul>
+</div>
+<div class="slide" id="contact">
+<h1>Contact</h1>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Web:</th><td class="field-body"><a class="reference external" href="http://www.in-silico.ch">http://www.in-silico.ch</a></td>
+</tr>
+<tr class="field"><th class="field-name">Email:</th><td class="field-body"><a class="reference external" href="mailto:helma&#64;in-silico.ch">helma&#64;in-silico.ch</a></td>
+</tr>
+</tbody>
+</table>
+</div>
+</div>
+</body>
+</html>
diff --git a/public/presentations/in-silico-methods12/lazar-input.png b/public/presentations/in-silico-methods12/lazar-input.png
new file mode 100644
index 0000000..196e71b
--- /dev/null
+++ b/public/presentations/in-silico-methods12/lazar-input.png
Binary files differ
diff --git a/public/presentations/in-silico-methods12/lazar-output1.png b/public/presentations/in-silico-methods12/lazar-output1.png
new file mode 100644
index 0000000..18fa0d1
--- /dev/null
+++ b/public/presentations/in-silico-methods12/lazar-output1.png
Binary files differ
diff --git a/public/presentations/in-silico-methods12/lazar-output2.png b/public/presentations/in-silico-methods12/lazar-output2.png
new file mode 100644
index 0000000..faf0839
--- /dev/null
+++ b/public/presentations/in-silico-methods12/lazar-output2.png
Binary files differ
diff --git a/public/presentations/in-silico-methods12/lazar-output3.png b/public/presentations/in-silico-methods12/lazar-output3.png
new file mode 100644
index 0000000..17480d7
--- /dev/null
+++ b/public/presentations/in-silico-methods12/lazar-output3.png
Binary files differ
diff --git a/public/presentations/in-silico-methods12/ui/.DS_Store b/public/presentations/in-silico-methods12/ui/.DS_Store
new file mode 100644
index 0000000..7738c28
--- /dev/null
+++ b/public/presentations/in-silico-methods12/ui/.DS_Store
Binary files differ
diff --git a/public/presentations/in-silico-methods12/ui/small-white/blank.gif b/public/presentations/in-silico-methods12/ui/small-white/blank.gif
new file mode 100644
index 0000000..75b945d
--- /dev/null
+++ b/public/presentations/in-silico-methods12/ui/small-white/blank.gif
Binary files differ
diff --git a/public/presentations/in-silico-methods12/ui/small-white/framing.css b/public/presentations/in-silico-methods12/ui/small-white/framing.css
new file mode 100644
index 0000000..70287dd
--- /dev/null
+++ b/public/presentations/in-silico-methods12/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;}
+.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/public/presentations/in-silico-methods12/ui/small-white/iepngfix.htc b/public/presentations/in-silico-methods12/ui/small-white/iepngfix.htc
new file mode 100644
index 0000000..2a44681
--- /dev/null
+++ b/public/presentations/in-silico-methods12/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/public/presentations/in-silico-methods12/ui/small-white/opera.css b/public/presentations/in-silico-methods12/ui/small-white/opera.css
new file mode 100644
index 0000000..c9d1148
--- /dev/null
+++ b/public/presentations/in-silico-methods12/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/public/presentations/in-silico-methods12/ui/small-white/outline.css b/public/presentations/in-silico-methods12/ui/small-white/outline.css
new file mode 100644
index 0000000..fa767e2
--- /dev/null
+++ b/public/presentations/in-silico-methods12/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/public/presentations/in-silico-methods12/ui/small-white/pretty.css b/public/presentations/in-silico-methods12/ui/small-white/pretty.css
new file mode 100644
index 0000000..2e762bc
--- /dev/null
+++ b/public/presentations/in-silico-methods12/ui/small-white/pretty.css
@@ -0,0 +1,115 @@
+/* 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 {margin-top: 0.5em}
+.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/public/presentations/in-silico-methods12/ui/small-white/print.css b/public/presentations/in-silico-methods12/ui/small-white/print.css
new file mode 100644
index 0000000..9d057cc
--- /dev/null
+++ b/public/presentations/in-silico-methods12/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/public/presentations/in-silico-methods12/ui/small-white/s5-core.css b/public/presentations/in-silico-methods12/ui/small-white/s5-core.css
new file mode 100644
index 0000000..6965f5e
--- /dev/null
+++ b/public/presentations/in-silico-methods12/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/public/presentations/in-silico-methods12/ui/small-white/slides.css b/public/presentations/in-silico-methods12/ui/small-white/slides.css
new file mode 100644
index 0000000..82bdc0e
--- /dev/null
+++ b/public/presentations/in-silico-methods12/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/public/presentations/in-silico-methods12/ui/small-white/slides.js b/public/presentations/in-silico-methods12/ui/small-white/slides.js
new file mode 100644
index 0000000..87c30c6
--- /dev/null
+++ b/public/presentations/in-silico-methods12/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/views/presentations.haml b/views/presentations.haml
index bce67ef..93384dc 100644
--- a/views/presentations.haml
+++ b/views/presentations.haml
@@ -9,4 +9,7 @@ View recent presentations and slides :
%li
%a{:href => "/presentations/opentox-dublin/index.html", :rel => "external"} Extending OpenTox to Nano Safety with eNanoMapper
(OpenTox Euro Dublin 2015)
+ %li
+ %a{:href => "/presentations/in-silico-methods12/index.html", :rel => "external"} In silico methods for toxicity prediction
+ (2012)
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-03 01:58:38 +0000