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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> </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> </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 "software as a service" (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@in-silico.ch">helma@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 deleted file mode 100644 index 33f5884..0000000 --- a/public/presentations/in-silico-methods12/in-silico-methods.rst +++ /dev/null @@ -1,221 +0,0 @@ -========================================= -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 deleted file mode 100644 index 189761c..0000000 --- a/public/presentations/in-silico-methods12/index.html +++ /dev/null @@ -1,569 +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 0.9.1: 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"> - 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-</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> </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> </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 "software as a service" (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 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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>
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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 deleted file mode 100644 index 2e762bc..0000000 --- a/public/presentations/in-silico-methods12/ui/small-white/pretty.css +++ /dev/null @@ -1,115 +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 {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 deleted file mode 100644 index 9d057cc..0000000 --- a/public/presentations/in-silico-methods12/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/public/presentations/in-silico-methods12/ui/small-white/s5-core.css b/public/presentations/in-silico-methods12/ui/small-white/s5-core.css deleted file mode 100644 index 6965f5e..0000000 --- a/public/presentations/in-silico-methods12/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/public/presentations/in-silico-methods12/ui/small-white/slides.css b/public/presentations/in-silico-methods12/ui/small-white/slides.css deleted file mode 100644 index 82bdc0e..0000000 --- a/public/presentations/in-silico-methods12/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/public/presentations/in-silico-methods12/ui/small-white/slides.js b/public/presentations/in-silico-methods12/ui/small-white/slides.js deleted file mode 100644 index 87c30c6..0000000 --- a/public/presentations/in-silico-methods12/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);} |